From a62a9f02a356e17e07488aa24905bc55725cb6ef Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 6 May 2024 14:24:46 +0000 Subject: [PATCH 001/158] added development Jenkninsfile for dispatching from GitHub Actions --- ci/Jenkinsfile_dispatch | 294 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 294 insertions(+) create mode 100644 ci/Jenkinsfile_dispatch diff --git a/ci/Jenkinsfile_dispatch b/ci/Jenkinsfile_dispatch new file mode 100644 index 0000000000..ec3c41d67c --- /dev/null +++ b/ci/Jenkinsfile_dispatch @@ -0,0 +1,294 @@ +def Machine = 'none' +def machine = 'none' +def HOME = 'none' +def caseList = '' +// Location of the custom workspaces for each machine in the CI system. They are persitent for each iteration of the PR. +def custom_workspace = [hera: '/scratch1/NCEPDEV/global/CI', orion: '/work2/noaa/stmp/CI/ORION', hercules: '/work2/noaa/stmp/CI/HERCULES'] +def repo_url = 'git@github.com:TerrenceMcGUinness-NOAA/global-workflow.git' +def STATUS = 'Passed' + + +pipeline { + + agent { label 'built-in' } + + options { + skipDefaultCheckout() + //parallelsAlwaysFailFast() + } + + stages { // This initial stage is used to get the Machine name from the GitHub labels on the PR + // which is used to designate the Nodes in the Jenkins Controler by the agent label + // Each Jenknis Node is connected to said machine via an JAVA agent via an ssh tunnel + // no op 2 + + stage('1. Get Machine') { + agent { label 'built-in' } + steps { + script { + + def causes = currentBuild.rawBuild.getCauses() + def isSpawnedFromAnotherJob = causes.any { cause -> + cause instanceof hudson.model.Cause.UpstreamCause + } + + def run_nodes = [] + if (isSpawnedFromAnotherJob) { + echo "machine being set to value passed to this spawned job" + echo "passed machine: ${params.machine}" + machine = params.machine + } else { + echo "This is parent job so getting list of nodes from dispatched inputs" + echo "machine: ${params.machine}" + echo "Node: ${params.Node}" + run_nodes.add(params.Node) + + // for (label in pullRequest.labels) { + // if (label.matches("CI-(.*?)-Ready")) { + // def Machine_name = label.split('-')[1].toString() + // jenkins.model.Jenkins.get().computers.each { c -> + // if (c.node.selfLabel.name == "${Machine_name}-EMC") { + // run_nodes.add(c.node.selfLabel.name) + // } + // } + // } + // } + // Spawning all the jobs on the nodes matching the labels + if (run_nodes.size() > 1) { + run_nodes.init().each { node -> + def machine_name = node.split('-')[0].toLowerCase() + echo "Spawning job on node: ${node} with machine name: ${machine_name}" + build job: "/global-workflow/EMC-Global-Pipeline/PR-${env.CHANGE_ID}", parameters: [ + string(name: 'machine', value: machine_name), + string(name: 'Node', value: node) ], + wait: false + } + machine = run_nodes.last().split('-')[0].toLowerCase() + echo "Running parent job: ${machine}" + } else { + machine = run_nodes[0].split('-')[0].toLowerCase() + echo "Running only the parent job: ${machine}" + } + } + } + } + } + + stage('2. Get Common Workspace') { + agent { label "${machine}-emc" } + steps { + script { + Machine = machine[0].toUpperCase() + machine.substring(1) + echo "Getting Common Workspace for ${Machine}" + ws("${custom_workspace[machine]}/${env.CHANGE_ID}") { + properties([ + parameters([ + [$class: 'NodeParameterDefinition', + allowedSlaves: ['built-in', 'Hera-EMC', 'Orion-EMC'], + defaultSlaves: ['built-in'], name: 'Node', + nodeEligibility: [$class: 'AllNodeEligibility'], + triggerIfResult: 'allCases'], + string(name: 'machine', defaultValue: 'hera', description: 'Machine to run the job on') + ]) + ]) + HOME = "${WORKSPACE}" + sh(script: "mkdir -p ${HOME}/RUNTESTS;rm -Rf ${HOME}/RUNTESTS/error.logs") + sh(script: """${GH} pr edit ${env.CHANGE_ID} --repo ${repo_url} --add-label "CI-${Machine}-Building" --remove-label "CI-${Machine}-Ready" """) + } + echo "Building and running on ${Machine} in directory ${HOME}" + } + } + } + + stage('3. Build System') { + matrix { + agent { label "${machine}-emc" } + //options { + // throttle(['global_matrix_build']) + //} + axes { + axis { + name 'system' + values 'gfs', 'gefs' + } + } + stages { + stage('build system') { + steps { + script { + def HOMEgfs = "${HOME}/${system}" // local HOMEgfs is used to build the system on per system basis under the common workspace HOME + sh(script: "mkdir -p ${HOMEgfs}") + ws(HOMEgfs) { + if (fileExists("${HOMEgfs}/sorc/BUILT_semaphor")) { // if the system is already built, skip the build in the case of re-runs + sh(script: "cat ${HOMEgfs}/sorc/BUILT_semaphor", returnStdout: true).trim() // TODO: and user configurable control to manage build semphore + checkout scm + dir('sorc') { + sh(script: './link_workflow.sh') + } + } else { + checkout scm + def gist_url = "" + def error_logs = "" + def error_logs_message = "" + def builds_file = readYaml file: 'ci/cases/yamls/build.yaml' + def build_args_list = builds_file['builds'] + def build_args = build_args_list[system].join(' ').trim().replaceAll('null', '') + dir("${HOMEgfs}/sorc") { + try { + sh(script: "${build_args}") + } catch (Exception error_build) { + echo "Failed to build system: ${error_build.getMessage()}" + if ( fileExists("logs/error.logs") ) { + def fileContent = readFile 'logs/error.logs' + def lines = fileContent.readLines() + for (line in lines) { + echo "archiving: ${line}" + if (fileExists("${line}") && readFile("${line}").length() > 0 ){ + try { + archiveArtifacts artifacts: "${line}", fingerprint: true + error_logs = error_logs + "${HOMEgfs}/sorc/${line} " + error_logs_message = error_logs_message + "${HOMEgfs}/sorc/${line}\n" + } + catch (Exception error_arch) { echo "Failed to archive error log ${line}: ${error_arch.getMessage()}" } + } + } + try { + sh(script: "${HOMEgfs}/ci/scripts/utils/publish_logs.py --file ${error_logs} --repo PR_BUILD_${env.CHANGE_ID}") + gist_url=sh(script: "${HOMEgfs}/ci/scripts/utils/publish_logs.py --file ${error_logs} --gist PR_BUILD_${env.CHANGE_ID}", returnStdout: true).trim() + sh(script: """${GH} pr comment ${env.CHANGE_ID} --repo ${repo_url} --body "Build **FAILED** on **${Machine}** with error logs:\n\\`\\`\\`\n${error_logs_message}\\`\\`\\`\n\nFollow link here to view the contents of the above file(s): [(link)](${gist_url})" """) + } catch (Exception error_comment) { + echo "Failed to comment on PR: ${error_comment.getMessage()}" + } + error("Failed to build system on ${Machine}") + } + } + sh(script: './link_workflow.sh') + sh(script: "echo ${HOMEgfs} > BUILT_semaphor") + } + } + if (env.CHANGE_ID && system == 'gfs') { + try { + sh(script: """${GH} pr edit ${env.CHANGE_ID} --repo ${repo_url} --add-label "CI-${Machine}-Running" --remove-label "CI-${Machine}-Building" """) + } catch (Exception e) { + echo "Failed to update label from Buildng to Running: ${e.getMessage()}" + } + } + if (system == 'gfs') { + caseList = sh(script: "${HOMEgfs}/ci/scripts/utils/get_host_case_list.py ${machine}", returnStdout: true).trim().split() + } + } + } + } + } + } + } + } + + stage('4. Run Tests') { + failFast false + matrix { + agent { label "${machine}-emc" } + axes { + axis { + name 'Case' + // TODO add dynamic list of cases from env vars (needs addtional plugins) + values 'C48C48_ufs_hybatmDA', 'C48_ATM', 'C48_S2SW', 'C48_S2SWA_gefs', 'C48mx500_3DVarAOWCDA', 'C96C48_hybatmDA', 'C96_atm3DVar', 'C96_atmaerosnowDA' + } + } + stages { + + stage('Create Experiments') { + when { + expression { return caseList.contains(Case) } + } + steps { + script { + sh(script: "sed -n '/{.*}/!p' ${HOME}/gfs/ci/cases/pr/${Case}.yaml > ${HOME}/gfs/ci/cases/pr/${Case}.yaml.tmp") + def yaml_case = readYaml file: "${HOME}/gfs/ci/cases/pr/${Case}.yaml.tmp" + system = yaml_case.experiment.system + def HOMEgfs = "${HOME}/${system}" // local HOMEgfs is used to populate the XML on per system basis + env.RUNTESTS = "${HOME}/RUNTESTS" + sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh create_experiment ${HOMEgfs}/ci/cases/pr/${Case}.yaml") + } + } + } + + stage('Run Experiments') { + when { + expression { return caseList.contains(Case) } + } + failFast false + steps { + script { + HOMEgfs = "${HOME}/gfs" // common HOMEgfs is used to launch the scripts that run the experiments + def pslot = sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh get_pslot ${HOME}/RUNTESTS ${Case}", returnStdout: true).trim() + def error_file = "${HOME}/RUNTESTS/${pslot}_error.logs" + sh(script: " rm -f ${error_file}") + try { + sh(script: "${HOMEgfs}/ci/scripts/run-check_ci.sh ${HOME} ${pslot} ${system}") + } catch (Exception error_experment) { + sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh cancel_batch_jobs ${pslot}") + ws(HOME) { + def error_logs = "" + def error_logs_message = "" + if (fileExists(error_file)) { + def fileContent = readFile error_file + def lines = fileContent.readLines() + for (line in lines) { + echo "archiving: ${line}" + if (fileExists("${HOME}/${line}") && readFile("${HOME}/${line}").length() > 0) { + try { + archiveArtifacts artifacts: "${line}", fingerprint: true + error_logs = error_logs + "${HOME}/${line} " + error_logs_message = error_logs_message + "${HOME}/${line}\n" + } catch (Exception error_arch) { + echo "Failed to archive error log ${line}: ${error_arch.getMessage()}" + } + } + } + try { + gist_url = sh(script: "${HOMEgfs}/ci/scripts/utils/publish_logs.py --file ${error_logs} --gist PR_${env.CHANGE_ID}", returnStdout: true).trim() + sh(script: """${GH} pr comment ${env.CHANGE_ID} --repo ${repo_url} --body "Experiment ${Case} **FAILED** on ${Machine} with error logs:\n\\`\\`\\`\n${error_logs_message}\\`\\`\\`\n\nFollow link here to view the contents of the above file(s): [(link)](${gist_url})" """) + sh(script: "${HOMEgfs}/ci/scripts/utils/publish_logs.py --file ${error_logs} --repo PR_${env.CHANGE_ID}") + } catch (Exception error_comment) { + echo "Failed to comment on PR: ${error_comment.getMessage()}" + } + } else { + echo "No error logs found for failed cases in $HOME/RUNTESTS/${pslot}_error.logs" + } + STATUS = 'Failed' + try { + sh(script: """${GH} pr edit ${env.CHANGE_ID} --repo ${repo_url} --remove-label "CI-${Machine}-Running" --add-label "CI-${Machine}-${STATUS}" """, returnStatus: true) + sh(script: """${GH} pr comment ${env.CHANGE_ID} --repo ${repo_url} --body "Experiment ${Case} **FAILED** on ${Machine} in\n\\`${HOME}/RUNTESTS/${pslot}\\`" """) + } catch (Exception e) { + echo "Failed to update label from Running to ${STATUS}: ${e.getMessage()}" + } + error("Failed to run experiments ${Case} on ${Machine}") + } + } + } + } + } + } + } + } + stage( '5. FINALIZE' ) { + when { + expression { + STATUS == 'Passed' + } + } + agent { label "${machine}-emc" } + steps { + script { + try { + sh(script: """${GH} pr edit ${env.CHANGE_ID} --repo ${repo_url} --remove-label "CI-${Machine}-Running" --remove-label "CI-${Machine}-Building" --add-label "CI-${Machine}-${STATUS}" """, returnStatus: true) + sh(script: """${GH} pr comment ${env.CHANGE_ID} --repo ${repo_url} --body "**CI ${STATUS}** ${Machine} at
Built and ran in directory \\`${HOME}\\`" """, returnStatus: true) + } catch (Exception e) { + echo "Failed to update label from Running to ${STATUS}: ${e.getMessage()}" + } + } + } + } + } +} From 002c985a03d78399671f4088fdc9051678b1202b Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 13:55:42 +0000 Subject: [PATCH 002/158] updated method for counting status cases from rocotostat --- ci/scripts/utils/rocotostat.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 884ff82e3d..d434c4a795 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -6,6 +6,8 @@ from wxflow import Executable, which, Logger, CommandNotFoundError from argparse import ArgumentParser, FileType +from collections import Counter + logger = Logger(level=os.environ.get("LOGGING_LEVEL", "DEBUG"), colored_log=False) @@ -71,8 +73,13 @@ def rocoto_statcount(): } status_cases = ['SUCCEEDED', 'FAIL', 'DEAD', 'RUNNING', 'SUBMITTING', 'QUEUED'] + + status_counts = Counter(case for sublist in rocotostat_output_all for case in sublist) for case in status_cases: - rocoto_status[case] = sum([sublist.count(case) for sublist in rocotostat_output_all]) + rocoto_status[case] = status_counts[case] + + #for case in status_cases: + # rocoto_status[case] = sum([sublist.count(case) for sublist in rocotostat_output_all]) return rocoto_status From 024329463cb1e169606169611e938d0f70208c6f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 14:51:16 +0000 Subject: [PATCH 003/158] started a unit test for rocotostat --- ci/scripts/utils/test_rocotostat.py | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100755 ci/scripts/utils/test_rocotostat.py diff --git a/ci/scripts/utils/test_rocotostat.py b/ci/scripts/utils/test_rocotostat.py new file mode 100755 index 0000000000..500c3b2cc7 --- /dev/null +++ b/ci/scripts/utils/test_rocotostat.py @@ -0,0 +1,27 @@ +import pytest +from unittest.mock import patch, MagicMock +from rocotostat import rocoto_statcount + +@patch('rocotostat.which') +@patch('rocotostat.input_args') +def test_rocoto_statcount(mock_input_args, mock_which): + # Arrange + mock_input_args.return_value = MagicMock(w=MagicMock(name='workflow.xml'), d=MagicMock(name='database.db')) + mock_which.return_value = MagicMock(add_default_arg=MagicMock(), output='') + + # Act + rocoto_statcount() + + # Assert + mock_which.assert_called_with('rocotostat') + mock_input_args.assert_called_once() + +@patch('rocotostat.which', side_effect=CommandNotFoundError('rocotostat not found in PATH')) +@patch('rocotostat.input_args') +def test_rocoto_statcount_raises_error_when_rocotostat_not_found(mock_input_args, mock_which): + # Arrange + mock_input_args.return_value = MagicMock(w=MagicMock(name='workflow.xml'), d=MagicMock(name='database.db')) + + # Act and Assert + with pytest.raises(CommandNotFoundError): + rocoto_statcount() \ No newline at end of file From 233c6145243ebfeb7eb217f3efedfd46201bf796 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 15:25:25 +0000 Subject: [PATCH 004/158] added more moc args --- ci/scripts/utils/test_rocotostat.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/ci/scripts/utils/test_rocotostat.py b/ci/scripts/utils/test_rocotostat.py index 500c3b2cc7..ae3ec3b04e 100755 --- a/ci/scripts/utils/test_rocotostat.py +++ b/ci/scripts/utils/test_rocotostat.py @@ -1,13 +1,17 @@ import pytest from unittest.mock import patch, MagicMock -from rocotostat import rocoto_statcount +from rocotostat import rocoto_statcount, CommandNotFoundError -@patch('rocotostat.which') +class MockCommand: + def __init__(self): + self.add_default_arg = MagicMock() + +@patch('os.path.abspath', return_value='path/to/workflow.xml') +@patch('rocotostat.which', return_value=MockCommand()) @patch('rocotostat.input_args') def test_rocoto_statcount(mock_input_args, mock_which): # Arrange mock_input_args.return_value = MagicMock(w=MagicMock(name='workflow.xml'), d=MagicMock(name='database.db')) - mock_which.return_value = MagicMock(add_default_arg=MagicMock(), output='') # Act rocoto_statcount() @@ -18,7 +22,7 @@ def test_rocoto_statcount(mock_input_args, mock_which): @patch('rocotostat.which', side_effect=CommandNotFoundError('rocotostat not found in PATH')) @patch('rocotostat.input_args') -def test_rocoto_statcount_raises_error_when_rocotostat_not_found(mock_input_args, mock_which): +def test_rocoto_statcount_raises_error_when_rocotostat_not_found(mock_input_args, mock_which, mock_abspath): # Arrange mock_input_args.return_value = MagicMock(w=MagicMock(name='workflow.xml'), d=MagicMock(name='database.db')) From eb3589c549186845f1d119fdc6042a53651adbde Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 15:31:44 +0000 Subject: [PATCH 005/158] updated third arg to moc --- ci/scripts/utils/test_rocotostat.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/ci/scripts/utils/test_rocotostat.py b/ci/scripts/utils/test_rocotostat.py index ae3ec3b04e..dee7fbafb7 100755 --- a/ci/scripts/utils/test_rocotostat.py +++ b/ci/scripts/utils/test_rocotostat.py @@ -6,10 +6,10 @@ class MockCommand: def __init__(self): self.add_default_arg = MagicMock() -@patch('os.path.abspath', return_value='path/to/workflow.xml') +@patch('os.path.abspath', return_value='workflow.xml') @patch('rocotostat.which', return_value=MockCommand()) @patch('rocotostat.input_args') -def test_rocoto_statcount(mock_input_args, mock_which): +def test_rocoto_statcount(mock_input_args, mock_which, mock_abspath): # Arrange mock_input_args.return_value = MagicMock(w=MagicMock(name='workflow.xml'), d=MagicMock(name='database.db')) @@ -20,6 +20,7 @@ def test_rocoto_statcount(mock_input_args, mock_which): mock_which.assert_called_with('rocotostat') mock_input_args.assert_called_once() +@patch('os.path.abspath', return_value='workflow.xml') @patch('rocotostat.which', side_effect=CommandNotFoundError('rocotostat not found in PATH')) @patch('rocotostat.input_args') def test_rocoto_statcount_raises_error_when_rocotostat_not_found(mock_input_args, mock_which, mock_abspath): From 060f2a82c9ee6f77c232e972c2ed18e91992518e Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 15:53:29 +0000 Subject: [PATCH 006/158] removed moc stuff from test --- ci/scripts/utils/test_rocotostat.py | 36 ++++++++--------------------- 1 file changed, 10 insertions(+), 26 deletions(-) diff --git a/ci/scripts/utils/test_rocotostat.py b/ci/scripts/utils/test_rocotostat.py index dee7fbafb7..095f78329e 100755 --- a/ci/scripts/utils/test_rocotostat.py +++ b/ci/scripts/utils/test_rocotostat.py @@ -1,32 +1,16 @@ + import pytest -from unittest.mock import patch, MagicMock from rocotostat import rocoto_statcount, CommandNotFoundError -class MockCommand: - def __init__(self): - self.add_default_arg = MagicMock() - -@patch('os.path.abspath', return_value='workflow.xml') -@patch('rocotostat.which', return_value=MockCommand()) -@patch('rocotostat.input_args') -def test_rocoto_statcount(mock_input_args, mock_which, mock_abspath): - # Arrange - mock_input_args.return_value = MagicMock(w=MagicMock(name='workflow.xml'), d=MagicMock(name='database.db')) - - # Act - rocoto_statcount() +import os - # Assert - mock_which.assert_called_with('rocotostat') - mock_input_args.assert_called_once() +workflow_file = os.path.join(os.getcwd(), "workflow.xml") +database_file = os.path.join(os.getcwd(), "database.db") -@patch('os.path.abspath', return_value='workflow.xml') -@patch('rocotostat.which', side_effect=CommandNotFoundError('rocotostat not found in PATH')) -@patch('rocotostat.input_args') -def test_rocoto_statcount_raises_error_when_rocotostat_not_found(mock_input_args, mock_which, mock_abspath): - # Arrange - mock_input_args.return_value = MagicMock(w=MagicMock(name='workflow.xml'), d=MagicMock(name='database.db')) +def test_rocoto_statcount( + result = rocoto_statcount(w=workflow_file, d=database_file) - # Act and Assert - with pytest.raises(CommandNotFoundError): - rocoto_statcount() \ No newline at end of file + assert result['CYCLES_TOTAL'] == 1 + assert result['CYCLES_DONE'] == 1 + assert result['SUCCEDED'] == 20 + assert result['ROCOTO_STATE'] == 'DONE' From 2f9662d853e87b5446bad7e4409d2942b1009912 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Wed, 8 May 2024 10:57:06 -0500 Subject: [PATCH 007/158] added data for unit testing rocotostat --- ci/scripts/utils/database.db | Bin 0 -> 28672 bytes ci/scripts/utils/test_rocotostat.py | 2 +- ci/scripts/utils/workflow.xml | 284 ++++++++++++++++++++++++++++ 3 files changed, 285 insertions(+), 1 deletion(-) create mode 100644 ci/scripts/utils/database.db create mode 100644 ci/scripts/utils/workflow.xml diff --git a/ci/scripts/utils/database.db b/ci/scripts/utils/database.db new file mode 100644 index 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DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + + + + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_ctrl.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile1.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile2.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile3.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile4.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile5.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile6.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile1.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile2.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile3.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile4.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile5.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile6.nc + + + + + + + + /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/fcst.sh + + C48_ATM_0ad155f1_gfsfcst_@H + nems + batch + orion + 03:00:00 + 1:ppn=40:tpp=1 + --export=NONE + + /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsfcst.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs + EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + NETgfs + CDUMPgfs + RUNgfs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + + + + + + + + + + + + _f000-f006 _f009-f015 _f018-f024 _f027-f033 _f036-f042 _f045-f051 _f054-f060 _f063-f069 _f072-f078 _f081-f087 _f090-f096 _f099-f105 _f108-f114 _f117-f120 + f006 f015 f024 f033 f042 f051 f060 f069 f078 f087 f096 f105 f114 f120 + f000_f003_f006 f009_f012_f015 f018_f021_f024 f027_f030_f033 f036_f039_f042 f045_f048_f051 f054_f057_f060 f063_f066_f069 f072_f075_f078 f081_f084_f087 f090_f093_f096 f099_f102_f105 f108_f111_f114 f117_f120 + + + + /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/atmos_products.sh + + C48_ATM_0ad155f1_gfsatmos_prod#grp#_@H + nems + batch + orion + 00:15:00 + 1:ppn=24:tpp=1 + --export=NONE + + /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsatmos_prod#grp#.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs + EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + NETgfs + CDUMPgfs + RUNgfs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + FHRLST#lst# + COMPONENTatmos + + + &ROTDIR;/gfs.@Y@m@d/@H//model_data/atmos/master/gfs.t@Hz.master.grb2#dep# + + + + + + + + + /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/tracker.sh + + C48_ATM_0ad155f1_gfstracker_@H + nems + batch + orion + 00:10:00 + 1:ppn=1:tpp=1 + 4G + --export=NONE + + /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfstracker.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs + EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + NETgfs + CDUMPgfs + RUNgfs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + + + + + + + + + + /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/genesis.sh + + C48_ATM_0ad155f1_gfsgenesis_@H + nems + batch + orion + 00:25:00 + 1:ppn=1:tpp=1 + 10G + --export=NONE + + /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsgenesis.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs + EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + NETgfs + CDUMPgfs + RUNgfs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + + + + + + + + + + /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/arch.sh + + C48_ATM_0ad155f1_gfsarch_@H + nems + batch + service + 06:00:00 + 1:ppn=1:tpp=1 + 4096M + --export=NONE + + /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsarch.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs + EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + NETgfs + CDUMPgfs + RUNgfs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + + + + + + + + + + + + + + /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/cleanup.sh + + C48_ATM_0ad155f1_gfscleanup_@H + nems + batch + orion + 00:15:00 + 1:ppn=1:tpp=1 + 4096M + --export=NONE + + /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfscleanup.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs + EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + NETgfs + CDUMPgfs + RUNgfs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + + + + + + + + + + From b01504da723965e0aa23ba5a80d22ca925295732 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 17:48:01 +0000 Subject: [PATCH 008/158] moved tests dir for ci unit tests under scripts --- ci/scripts/{utils => tests}/database.db | Bin ci/scripts/tests/test_rocotostat.py | 34 ++++++++++++++ ci/scripts/{utils => tests}/workflow.xml | 0 ci/scripts/utils/rocotostat.py | 57 +++++++++++------------ ci/scripts/utils/test_rocotostat.py | 16 ------- 5 files changed, 62 insertions(+), 45 deletions(-) rename ci/scripts/{utils => tests}/database.db (100%) create mode 100755 ci/scripts/tests/test_rocotostat.py rename ci/scripts/{utils => tests}/workflow.xml (100%) delete mode 100755 ci/scripts/utils/test_rocotostat.py diff --git a/ci/scripts/utils/database.db b/ci/scripts/tests/database.db similarity index 100% rename from ci/scripts/utils/database.db rename to ci/scripts/tests/database.db diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py new file mode 100755 index 0000000000..781db64e9c --- /dev/null +++ b/ci/scripts/tests/test_rocotostat.py @@ -0,0 +1,34 @@ +import sys +import os + +sys.path.append(os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'utils')) + +from rocotostat import rocoto_statcount, rocotostat_summary, CommandNotFoundError +from wxflow import which + +workflow_file = os.path.join(os.getcwd(), "workflow.xml") +database_file = os.path.join(os.getcwd(), "database.db") + +try: + rocotostat = which("rocotostat") +except CommandNotFoundError: + raise CommandNotFoundError("rocotostat not found in PATH") +rocotostat.add_default_arg(['-w', workflow_file, '-d', database_file]) + +def test_rocoto_statcount(): + + result = rocoto_statcount(rocotostat) + + assert result['SUCCEEDED'] == 20 + assert result['FAIL'] == 0 + assert result['DEAD'] == 0 + assert result['RUNNING'] == 0 + assert result['SUBMITTING'] == 0 + assert result['QUEUED'] == 0 + +def test_rocoto_summary(): + + result = rocotostat_summary(rocotostat) + + assert result['CYCLES_TOTAL'] == 1 + assert result['CYCLES_DONE'] == 1 diff --git a/ci/scripts/utils/workflow.xml b/ci/scripts/tests/workflow.xml similarity index 100% rename from ci/scripts/utils/workflow.xml rename to ci/scripts/tests/workflow.xml diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index d434c4a795..d0199091e4 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -10,7 +10,6 @@ logger = Logger(level=os.environ.get("LOGGING_LEVEL", "DEBUG"), colored_log=False) - def input_args(): """ Parse command-line arguments. @@ -40,47 +39,38 @@ def input_args(): return args - -def rocoto_statcount(): - """ - Run rocotostat and process its output. - """ - - args = input_args() - - try: - rocotostat = which("rocotostat") - except CommandNotFoundError: - logger.exception("rocotostat not found in PATH") - raise CommandNotFoundError("rocotostat not found in PATH") - - rocotostat_all = which("rocotostat") - rocotostat.add_default_arg(['-w', os.path.abspath(args.w.name), '-d', os.path.abspath(args.d.name), '-s']) - rocotostat_all.add_default_arg(['-w', os.path.abspath(args.w.name), '-d', os.path.abspath(args.d.name), '-a']) - +def rocotostat_summary(rocotostat): + rocotostat.add_default_arg('--summary') rocotostat_output = rocotostat(output=str) rocotostat_output = rocotostat_output.splitlines()[1:] rocotostat_output = [line.split()[0:2] for line in rocotostat_output] - rocotostat_output_all = rocotostat_all(output=str) - rocotostat_output_all = rocotostat_output_all.splitlines()[1:] - rocotostat_output_all = [line.split()[0:4] for line in rocotostat_output_all] - rocotostat_output_all = [line for line in rocotostat_output_all if len(line) != 1] - rocoto_status = { 'CYCLES_TOTAL': len(rocotostat_output), 'CYCLES_DONE': sum([sublist.count('Done') for sublist in rocotostat_output]) } + return rocoto_status + + +def rocoto_statcount(rocotostat): + """ + Run rocotostat and process its output. + """ + + rocotostat.add_default_arg('--all') + + rocotostat_output = rocotostat(output=str) + rocotostat_output = rocotostat_output.splitlines()[1:] + rocotostat_output = [line.split()[0:4] for line in rocotostat_output] + rocotostat_output = [line for line in rocotostat_output if len(line) != 1] status_cases = ['SUCCEEDED', 'FAIL', 'DEAD', 'RUNNING', 'SUBMITTING', 'QUEUED'] - status_counts = Counter(case for sublist in rocotostat_output_all for case in sublist) + rocoto_status = {} + status_counts = Counter(case for sublist in rocotostat_output for case in sublist) for case in status_cases: rocoto_status[case] = status_counts[case] - #for case in status_cases: - # rocoto_status[case] = sum([sublist.count(case) for sublist in rocotostat_output_all]) - return rocoto_status @@ -88,8 +78,17 @@ def rocoto_statcount(): args = input_args() + try: + rocotostat = which("rocotostat") + except CommandNotFoundError: + logger.exception("rocotostat not found in PATH") + raise CommandNotFoundError("rocotostat not found in PATH") + + rocotostat.add_default_arg(['-w', os.path.abspath(args.w.name), '-d', os.path.abspath(args.d.name)]) + error_return = 0 - rocoto_status = rocoto_statcount() + rocoto_status = rocoto_statcount(rocotostat) + rocoto_status.update(rocotostat_summary(rocotostat)) if rocoto_status['CYCLES_TOTAL'] == rocoto_status['CYCLES_DONE']: rocoto_state = 'DONE' diff --git a/ci/scripts/utils/test_rocotostat.py b/ci/scripts/utils/test_rocotostat.py deleted file mode 100755 index 39d8dae1d1..0000000000 --- a/ci/scripts/utils/test_rocotostat.py +++ /dev/null @@ -1,16 +0,0 @@ - -import pytest -from rocotostat import rocoto_statcount, CommandNotFoundError - -import os - -workflow_file = os.path.join(os.getcwd(), "workflow.xml") -database_file = os.path.join(os.getcwd(), "database.db") - -def test_rocoto_statcount(): - result = rocoto_statcount(w=workflow_file, d=database_file) - - assert result['CYCLES_TOTAL'] == 1 - assert result['CYCLES_DONE'] == 1 - assert result['SUCCEDED'] == 20 - assert result['ROCOTO_STATE'] == 'DONE' From a6508f563f2c5b6783872013e0b451950dcb612d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 17:53:38 +0000 Subject: [PATCH 009/158] added ci unit tests using pytest --- .github/workflows/linters.yaml | 43 ++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml index 488b6a1407..2f934bb134 100644 --- a/.github/workflows/linters.yaml +++ b/.github/workflows/linters.yaml @@ -36,6 +36,49 @@ jobs: name: Differential ShellCheck SARIF path: ${{ steps.ShellCheck.outputs.sarif }} + ci_pytest: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: 3.8 + + - name: Install dependencies + run: | + sudo apt-get update + sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl + python -m pip install --upgrade pip + pip install pytest wxflow + # If you have a requirements.txt file, you can install all dependencies using: + # pip install -r requirements.txt + + - name: Install Rocoto + run: | + git clone https://github.com/christopherwharrop/rocoto.git + cd rocoto + ./install.sh + + - name: Run tests + run: pytest ci/scripts/tests/test_rocotostat.py + + - name: Upload pytest results as artifact + if: always() + uses: actions/upload-artifact@v2 + with: + name: Pytest Results + path: ./**/test-results.xml + + - name: Upload SARIF to GitHub using github/codeql-action/upload-sarif + if: failure() + uses: github/codeql-action/upload-sarif@v1 + with: + sarif_file: ./**/test-results.xml + # lint-python: # runs-on: ubuntu-latest From ce9af99b8d59f05fded096cd0eeee308d3dd4895 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 17:59:06 +0000 Subject: [PATCH 010/158] chris H has install.h spelled INSTALL --- .github/workflows/linters.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml index 2f934bb134..a83d4bc3af 100644 --- a/.github/workflows/linters.yaml +++ b/.github/workflows/linters.yaml @@ -61,7 +61,7 @@ jobs: run: | git clone https://github.com/christopherwharrop/rocoto.git cd rocoto - ./install.sh + ./INSTALL - name: Run tests run: pytest ci/scripts/tests/test_rocotostat.py From 060aed65ac81a21cc796207c5660ad8836993692 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 18:13:25 +0000 Subject: [PATCH 011/158] added path to rocotostat in GitHub runner --- .github/workflows/linters.yaml | 3 ++- ci/scripts/tests/test-results.xml | 0 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 ci/scripts/tests/test-results.xml diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml index a83d4bc3af..cd378c7db1 100644 --- a/.github/workflows/linters.yaml +++ b/.github/workflows/linters.yaml @@ -62,6 +62,7 @@ jobs: git clone https://github.com/christopherwharrop/rocoto.git cd rocoto ./INSTALL + echo "$(pwd)/bin" >> $GITHUB_PATH - name: Run tests run: pytest ci/scripts/tests/test_rocotostat.py @@ -77,7 +78,7 @@ jobs: if: failure() uses: github/codeql-action/upload-sarif@v1 with: - sarif_file: ./**/test-results.xml + sarif_file: ci/scripts/tests/test-results.xml # lint-python: # runs-on: ubuntu-latest diff --git a/ci/scripts/tests/test-results.xml b/ci/scripts/tests/test-results.xml new file mode 100644 index 0000000000..e69de29bb2 From 336cbc4df218fbc77681269548c050d9bc991db2 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 18:25:58 +0000 Subject: [PATCH 012/158] added path relative to sript for input data --- ci/scripts/tests/test_rocotostat.py | 19 +++++++++++-------- ci/scripts/utils/rocotostat.py | 2 ++ 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index 781db64e9c..d0931ab73f 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -1,13 +1,14 @@ import sys import os -sys.path.append(os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'utils')) +script_dir = os.path.dirname(os.path.abspath(__file__)) +sys.path.append(os.path.join(os.path.dirname(script_dir), 'utils')) from rocotostat import rocoto_statcount, rocotostat_summary, CommandNotFoundError from wxflow import which -workflow_file = os.path.join(os.getcwd(), "workflow.xml") -database_file = os.path.join(os.getcwd(), "database.db") +workflow_file = os.path.join(script_dir, "workflow.xml") +database_file = os.path.join(script_dir, "database.db") try: rocotostat = which("rocotostat") @@ -15,6 +16,7 @@ raise CommandNotFoundError("rocotostat not found in PATH") rocotostat.add_default_arg(['-w', workflow_file, '-d', database_file]) + def test_rocoto_statcount(): result = rocoto_statcount(rocotostat) @@ -26,9 +28,10 @@ def test_rocoto_statcount(): assert result['SUBMITTING'] == 0 assert result['QUEUED'] == 0 + def test_rocoto_summary(): - - result = rocotostat_summary(rocotostat) - - assert result['CYCLES_TOTAL'] == 1 - assert result['CYCLES_DONE'] == 1 + + result = rocotostat_summary(rocotostat) + + assert result['CYCLES_TOTAL'] == 1 + assert result['CYCLES_DONE'] == 1 diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index d0199091e4..ed43274809 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -10,6 +10,7 @@ logger = Logger(level=os.environ.get("LOGGING_LEVEL", "DEBUG"), colored_log=False) + def input_args(): """ Parse command-line arguments. @@ -39,6 +40,7 @@ def input_args(): return args + def rocotostat_summary(rocotostat): rocotostat.add_default_arg('--summary') rocotostat_output = rocotostat(output=str) From 0a3561d98267482b78bc91f3e2a7a4543bf4a69a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 18:34:26 +0000 Subject: [PATCH 013/158] did not put in path for artifacts on success to unittess --- .github/workflows/linters.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml index cd378c7db1..66a8120a78 100644 --- a/.github/workflows/linters.yaml +++ b/.github/workflows/linters.yaml @@ -72,7 +72,7 @@ jobs: uses: actions/upload-artifact@v2 with: name: Pytest Results - path: ./**/test-results.xml + path: ci/scripts/tests/test-results.xml - name: Upload SARIF to GitHub using github/codeql-action/upload-sarif if: failure() From c36ef99a88bf1c69d7dc87cfff87cfda7f8ea164 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 19:07:10 +0000 Subject: [PATCH 014/158] details for artifacts and new actions file --- .github/workflows/ci-unit_tests.yaml | 52 ++++++++++++++++++++++++++++ .github/workflows/linters.yaml | 44 ----------------------- ci/scripts/tests/test-results.xml | 0 3 files changed, 52 insertions(+), 44 deletions(-) create mode 100644 .github/workflows/ci-unit_tests.yaml delete mode 100644 ci/scripts/tests/test-results.xml diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml new file mode 100644 index 0000000000..77c588ef57 --- /dev/null +++ b/.github/workflows/ci-unit_tests.yaml @@ -0,0 +1,52 @@ +name: CI Unit Tests +on: + pull_request: + +permissions: + contents: read + +jobs: + + ci_pytest: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: 3.8 + + - name: Install dependencies + run: | + sudo apt-get update + sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl + python -m pip install --upgrade pip + pip install pytest wxflow + # If you have a requirements.txt file, you can install all dependencies using: + # pip install -r requirements.txt + + - name: Install Rocoto + run: | + git clone https://github.com/christopherwharrop/rocoto.git + cd rocoto + ./INSTALL + echo "$(pwd)/bin" >> $GITHUB_PATH + + - name: Run tests + run: pytest -v --junitxml ci/scripts/tests/test-results.xml - ci/scripts/tests/test_rocotostat.py + + - name: Upload pytest results as artifact + if: always() + uses: actions/upload-artifact@v2 + with: + name: Pytest Results + path: ci/scripts/tests/test-results.xml + + - name: Upload SARIF to GitHub using github/codeql-action/upload-sarif + if: failure() + uses: github/codeql-action/upload-sarif@v1 + with: + sarif_file: ci/scripts/tests/test-results.xml \ No newline at end of file diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml index 66a8120a78..488b6a1407 100644 --- a/.github/workflows/linters.yaml +++ b/.github/workflows/linters.yaml @@ -36,50 +36,6 @@ jobs: name: Differential ShellCheck SARIF path: ${{ steps.ShellCheck.outputs.sarif }} - ci_pytest: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: 3.8 - - - name: Install dependencies - run: | - sudo apt-get update - sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl - python -m pip install --upgrade pip - pip install pytest wxflow - # If you have a requirements.txt file, you can install all dependencies using: - # pip install -r requirements.txt - - - name: Install Rocoto - run: | - git clone https://github.com/christopherwharrop/rocoto.git - cd rocoto - ./INSTALL - echo "$(pwd)/bin" >> $GITHUB_PATH - - - name: Run tests - run: pytest ci/scripts/tests/test_rocotostat.py - - - name: Upload pytest results as artifact - if: always() - uses: actions/upload-artifact@v2 - with: - name: Pytest Results - path: ci/scripts/tests/test-results.xml - - - name: Upload SARIF to GitHub using github/codeql-action/upload-sarif - if: failure() - uses: github/codeql-action/upload-sarif@v1 - with: - sarif_file: ci/scripts/tests/test-results.xml - # lint-python: # runs-on: ubuntu-latest diff --git a/ci/scripts/tests/test-results.xml b/ci/scripts/tests/test-results.xml deleted file mode 100644 index e69de29bb2..0000000000 From 4e89645e84c66d343081b1a90af190f6716404f2 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 19:12:29 +0000 Subject: [PATCH 015/158] syntax errors in ci unit tests actions yaml file --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 77c588ef57..dd4a9f26c1 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -36,7 +36,7 @@ jobs: echo "$(pwd)/bin" >> $GITHUB_PATH - name: Run tests - run: pytest -v --junitxml ci/scripts/tests/test-results.xml - ci/scripts/tests/test_rocotostat.py + run: pytest -v --junitxml ci/scripts/tests/test-results.xml ci/scripts/tests/test_rocotostat.py - name: Upload pytest results as artifact if: always() From c59c9971b67a68f4555f4a2af141b75fa0565d97 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 19:40:32 +0000 Subject: [PATCH 016/158] added report in UI --- .github/workflows/ci-unit_tests.yaml | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index dd4a9f26c1..4aeb2533ad 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -5,7 +5,7 @@ on: permissions: contents: read -jobs: +jobs: ci_pytest: runs-on: ubuntu-latest @@ -36,17 +36,14 @@ jobs: echo "$(pwd)/bin" >> $GITHUB_PATH - name: Run tests - run: pytest -v --junitxml ci/scripts/tests/test-results.xml ci/scripts/tests/test_rocotostat.py + run: pytest -v --junitxml test-results.xml ci/scripts/tests/test_rocotostat.py - - name: Upload pytest results as artifact + - name: Surface failing tests if: always() - uses: actions/upload-artifact@v2 + uses: pmeier/pytest-results-action@main with: - name: Pytest Results - path: ci/scripts/tests/test-results.xml - - - name: Upload SARIF to GitHub using github/codeql-action/upload-sarif - if: failure() - uses: github/codeql-action/upload-sarif@v1 - with: - sarif_file: ci/scripts/tests/test-results.xml \ No newline at end of file + path: test-results.xml + summary: true + display-options: fEX + fail-on-empty: true + title: Test results \ No newline at end of file From cb3c3e50cb701115be816acdd653456c29b54b43 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 19:58:20 +0000 Subject: [PATCH 017/158] trying another reportor --- .github/workflows/ci-unit_tests.yaml | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 4aeb2533ad..5cbc27b9a2 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -12,10 +12,10 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: 3.8 @@ -38,12 +38,8 @@ jobs: - name: Run tests run: pytest -v --junitxml test-results.xml ci/scripts/tests/test_rocotostat.py - - name: Surface failing tests + - name: Publish Unit Test Results + uses: EnricoMi/publish-unit-test-result-action@v1 if: always() - uses: pmeier/pytest-results-action@main with: - path: test-results.xml - summary: true - display-options: fEX - fail-on-empty: true - title: Test results \ No newline at end of file + files: test-results.xml \ No newline at end of file From 2dfe779fc3caa80e5bc4a64ea43905dec0a3a00f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 20:21:14 +0000 Subject: [PATCH 018/158] needed update permitions for report --- .github/workflows/ci-unit_tests.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 5cbc27b9a2..2a4824ef26 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -3,7 +3,8 @@ on: pull_request: permissions: - contents: read + checks: write + pull-requests: write jobs: @@ -15,7 +16,7 @@ jobs: uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.8 From ed29a28a64cbc85452b61ddef04ef5876f8d5cbe Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 20:31:35 +0000 Subject: [PATCH 019/158] added conclution to pytest ci --- .github/workflows/ci-unit_tests.yaml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 2a4824ef26..fde4eddd82 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -39,8 +39,12 @@ jobs: - name: Run tests run: pytest -v --junitxml test-results.xml ci/scripts/tests/test_rocotostat.py - - name: Publish Unit Test Results - uses: EnricoMi/publish-unit-test-result-action@v1 - if: always() - with: - files: test-results.xml \ No newline at end of file + - name: Publish Test Results + uses: EnricoMi/publish-unit-test-result-action@v2 + id: test-results + if: always() + with: + files: "test-results.xml" + + - name: Conclusion + run: echo "Conclusion is ${{ fromJSON( steps.test-results.outputs.json ).conclusion }}" \ No newline at end of file From b22801a3d6714ef16528ccccd9048ccaff82f4ab Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 20:33:45 +0000 Subject: [PATCH 020/158] indetation error in ci-pyunit acdtion file --- .github/workflows/ci-unit_tests.yaml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index fde4eddd82..a6fde7bd72 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -39,12 +39,12 @@ jobs: - name: Run tests run: pytest -v --junitxml test-results.xml ci/scripts/tests/test_rocotostat.py - - name: Publish Test Results - uses: EnricoMi/publish-unit-test-result-action@v2 - id: test-results - if: always() - with: - files: "test-results.xml" - - - name: Conclusion - run: echo "Conclusion is ${{ fromJSON( steps.test-results.outputs.json ).conclusion }}" \ No newline at end of file + - name: Publish Test Results + uses: EnricoMi/publish-unit-test-result-action@v2 + id: test-results + if: always() + with: + files: "test-results.xml" + + - name: Conclusion + run: echo "Conclusion is ${{ fromJSON( steps.test-results.outputs.json ).conclusion }}" \ No newline at end of file From f86862824047d4821aa665ec7404f3160949020a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 21:08:18 +0000 Subject: [PATCH 021/158] removed conclution in messages --- .github/workflows/ci-unit_tests.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index a6fde7bd72..d741b69277 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -43,8 +43,6 @@ jobs: uses: EnricoMi/publish-unit-test-result-action@v2 id: test-results if: always() + job_summary: true with: - files: "test-results.xml" - - - name: Conclusion - run: echo "Conclusion is ${{ fromJSON( steps.test-results.outputs.json ).conclusion }}" \ No newline at end of file + files: "test-results.xml" \ No newline at end of file From dfdcf7a843cbd60c174e18c7d6d7b8c114df202f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 21:16:27 +0000 Subject: [PATCH 022/158] job_summary did not work --- .github/workflows/ci-unit_tests.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index d741b69277..0bf2cf887f 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -40,9 +40,10 @@ jobs: run: pytest -v --junitxml test-results.xml ci/scripts/tests/test_rocotostat.py - name: Publish Test Results - uses: EnricoMi/publish-unit-test-result-action@v2 + uses: EnricoMi/publish-unit-test-result-action@vv2.16.1 id: test-results - if: always() job_summary: true + comment_mode: off + if: always() with: files: "test-results.xml" \ No newline at end of file From ca60b1345494040401ceb17dd55e96f9ec8b49cb Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 21:35:48 +0000 Subject: [PATCH 023/158] more publish and config report --- .github/workflows/ci-unit_tests.yaml | 41 ++++++++++++++++++++-------- 1 file changed, 30 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 0bf2cf887f..6a91dbf65a 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -2,10 +2,6 @@ name: CI Unit Tests on: pull_request: -permissions: - checks: write - pull-requests: write - jobs: ci_pytest: @@ -37,13 +33,36 @@ jobs: echo "$(pwd)/bin" >> $GITHUB_PATH - name: Run tests - run: pytest -v --junitxml test-results.xml ci/scripts/tests/test_rocotostat.py + run: python -m pytest ci/scripts/tests/test_rocotostat.py --junitxml test-results.xml - - name: Publish Test Results - uses: EnricoMi/publish-unit-test-result-action@vv2.16.1 - id: test-results - job_summary: true - comment_mode: off + - name: Upload Test Results if: always() + uses: actions/upload-artifact@v4 + with: + name: Test Results + path: test-results.xml + + publish-test-results: + name: "Publish Tests Results" + needs: ci_pytest + runs-on: ubuntu-latest + permissions: + checks: write + pull-requests: write + contents: read + issues: read + if: always() + + steps: + - name: Download Artifacts + uses: actions/download-artifact@v4 + with: + path: ci/scripts/tests + + - name: Publish Test Results + uses: EnricoMi/publish-unit-test-result-action@v2 with: - files: "test-results.xml" \ No newline at end of file + files: "ci/scripts/tests/*.xml" + job_summary: true + comment_mode: off + \ No newline at end of file From c29acdf46395203e84bd7c0cf052f34e765fddf3 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 21:43:47 +0000 Subject: [PATCH 024/158] more publish and config report path update --- .github/workflows/ci-unit_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 6a91dbf65a..514c026895 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -57,12 +57,12 @@ jobs: - name: Download Artifacts uses: actions/download-artifact@v4 with: - path: ci/scripts/tests + path: test-results.xml - name: Publish Test Results uses: EnricoMi/publish-unit-test-result-action@v2 with: - files: "ci/scripts/tests/*.xml" + files: "test-results.xml" job_summary: true comment_mode: off \ No newline at end of file From 74fe7ee90e5e897596dadcd17142441b342904a1 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 21:55:05 +0000 Subject: [PATCH 025/158] added full path to xml output --- .github/workflows/ci-unit_tests.yaml | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 514c026895..8696d9b412 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -33,14 +33,14 @@ jobs: echo "$(pwd)/bin" >> $GITHUB_PATH - name: Run tests - run: python -m pytest ci/scripts/tests/test_rocotostat.py --junitxml test-results.xml + run: python -m pytest ci/scripts/tests/test_rocotostat.py --junitxml ci/scripts/tests/test-results.xml - name: Upload Test Results if: always() uses: actions/upload-artifact@v4 with: name: Test Results - path: test-results.xml + path: ci/scripts/tests/test-results.xml publish-test-results: name: "Publish Tests Results" @@ -49,20 +49,11 @@ jobs: permissions: checks: write pull-requests: write - contents: read - issues: read if: always() - - steps: - - name: Download Artifacts - uses: actions/download-artifact@v4 - with: - path: test-results.xml - - name: Publish Test Results uses: EnricoMi/publish-unit-test-result-action@v2 with: - files: "test-results.xml" + files: ci/scripts/tests/test-results.xml job_summary: true comment_mode: off \ No newline at end of file From 10b0489d4920ee45385e0b376869d4c166c6f838 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 21:56:37 +0000 Subject: [PATCH 026/158] needed space for name --- .github/workflows/ci-unit_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 8696d9b412..d43cfdf126 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -50,6 +50,7 @@ jobs: checks: write pull-requests: write if: always() + - name: Publish Test Results uses: EnricoMi/publish-unit-test-result-action@v2 with: From 58ad8532dc01925c78392351b35272bf2663005d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 22:03:36 +0000 Subject: [PATCH 027/158] needed space for name --- .github/workflows/ci-unit_tests.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index d43cfdf126..46ad82f4ae 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -50,7 +50,11 @@ jobs: checks: write pull-requests: write if: always() - + steps: + - name: Download Artifacts + uses: actions/download-artifact@v4 + with: + path: ci/scripts/tests - name: Publish Test Results uses: EnricoMi/publish-unit-test-result-action@v2 with: From ca985a27f16458775063dd7ced7f1c4f73f2469a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 22:13:25 +0000 Subject: [PATCH 028/158] had name wrong was file name up upload --- .github/workflows/ci-unit_tests.yaml | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 46ad82f4ae..eea16e9e97 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -6,6 +6,9 @@ jobs: ci_pytest: runs-on: ubuntu-latest + permissions: + checks: write + pull-requests: write steps: - name: Checkout code @@ -39,23 +42,17 @@ jobs: if: always() uses: actions/upload-artifact@v4 with: - name: Test Results - path: ci/scripts/tests/test-results.xml + name: test-results.xml + path: ci/scripts/tests - publish-test-results: - name: "Publish Tests Results" - needs: ci_pytest - runs-on: ubuntu-latest - permissions: - checks: write - pull-requests: write - if: always() - steps: - name: Download Artifacts + if: always() uses: actions/download-artifact@v4 with: path: ci/scripts/tests + - name: Publish Test Results + if: always() uses: EnricoMi/publish-unit-test-result-action@v2 with: files: ci/scripts/tests/test-results.xml From 316d2ee22a5d5cbc1f4f9e9571fcfc1f4f956e7d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 22:22:20 +0000 Subject: [PATCH 029/158] took out upload --- .github/workflows/ci-unit_tests.yaml | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index eea16e9e97..8595a21276 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -38,19 +38,6 @@ jobs: - name: Run tests run: python -m pytest ci/scripts/tests/test_rocotostat.py --junitxml ci/scripts/tests/test-results.xml - - name: Upload Test Results - if: always() - uses: actions/upload-artifact@v4 - with: - name: test-results.xml - path: ci/scripts/tests - - - name: Download Artifacts - if: always() - uses: actions/download-artifact@v4 - with: - path: ci/scripts/tests - - name: Publish Test Results if: always() uses: EnricoMi/publish-unit-test-result-action@v2 From 0cb4a6d2215680ad294364cc64fb745132e1bd0f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 23:08:20 +0000 Subject: [PATCH 030/158] added docstrings to functions --- ci/scripts/utils/rocotostat.py | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index ed43274809..28e3fad707 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -42,6 +42,19 @@ def input_args(): def rocotostat_summary(rocotostat): + """ + ROCOTO_SUMMARY Run rocotostat and process its output. + + ROCOTO_SUMMARY(ROCOTOSTAT) adds a default argument '--summary' to the rocotostat + command, runs it, and processes its output to return a dictionary with the total + number of cycles and the number of cycles marked as 'Done'. + + Input: + ROCOTOSTAT - The rocotostat command. + + Output: + ROCOTO_STATUS - A dictionary with the total number of cycles and the number of cycles marked as 'Done'. + """ rocotostat.add_default_arg('--summary') rocotostat_output = rocotostat(output=str) rocotostat_output = rocotostat_output.splitlines()[1:] @@ -56,7 +69,17 @@ def rocotostat_summary(rocotostat): def rocoto_statcount(rocotostat): """ - Run rocotostat and process its output. + ROCOTO_STATCOUNT Run rocotostat and process its output. + + ROCOTO_STATCOUNT(ROCOTOSTAT) adds a default argument '--all' to the rocotostat + command, runs it, and processes its output to return a dictionary with the count + of each status case. + + Input: + ROCOTOSTAT - The rocotostat command. + + Output: + ROCOTO_STATUS - A dictionary with the count of each status case. """ rocotostat.add_default_arg('--all') From 2534fed325a38de9b687c1f773f70b805e8b52ae Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 23:11:30 +0000 Subject: [PATCH 031/158] removing Jenkins dispatch file --- ci/Jenkinsfile_dispatch | 294 ---------------------------------------- 1 file changed, 294 deletions(-) delete mode 100644 ci/Jenkinsfile_dispatch diff --git a/ci/Jenkinsfile_dispatch b/ci/Jenkinsfile_dispatch deleted file mode 100644 index ec3c41d67c..0000000000 --- a/ci/Jenkinsfile_dispatch +++ /dev/null @@ -1,294 +0,0 @@ -def Machine = 'none' -def machine = 'none' -def HOME = 'none' -def caseList = '' -// Location of the custom workspaces for each machine in the CI system. They are persitent for each iteration of the PR. -def custom_workspace = [hera: '/scratch1/NCEPDEV/global/CI', orion: '/work2/noaa/stmp/CI/ORION', hercules: '/work2/noaa/stmp/CI/HERCULES'] -def repo_url = 'git@github.com:TerrenceMcGUinness-NOAA/global-workflow.git' -def STATUS = 'Passed' - - -pipeline { - - agent { label 'built-in' } - - options { - skipDefaultCheckout() - //parallelsAlwaysFailFast() - } - - stages { // This initial stage is used to get the Machine name from the GitHub labels on the PR - // which is used to designate the Nodes in the Jenkins Controler by the agent label - // Each Jenknis Node is connected to said machine via an JAVA agent via an ssh tunnel - // no op 2 - - stage('1. Get Machine') { - agent { label 'built-in' } - steps { - script { - - def causes = currentBuild.rawBuild.getCauses() - def isSpawnedFromAnotherJob = causes.any { cause -> - cause instanceof hudson.model.Cause.UpstreamCause - } - - def run_nodes = [] - if (isSpawnedFromAnotherJob) { - echo "machine being set to value passed to this spawned job" - echo "passed machine: ${params.machine}" - machine = params.machine - } else { - echo "This is parent job so getting list of nodes from dispatched inputs" - echo "machine: ${params.machine}" - echo "Node: ${params.Node}" - run_nodes.add(params.Node) - - // for (label in pullRequest.labels) { - // if (label.matches("CI-(.*?)-Ready")) { - // def Machine_name = label.split('-')[1].toString() - // jenkins.model.Jenkins.get().computers.each { c -> - // if (c.node.selfLabel.name == "${Machine_name}-EMC") { - // run_nodes.add(c.node.selfLabel.name) - // } - // } - // } - // } - // Spawning all the jobs on the nodes matching the labels - if (run_nodes.size() > 1) { - run_nodes.init().each { node -> - def machine_name = node.split('-')[0].toLowerCase() - echo "Spawning job on node: ${node} with machine name: ${machine_name}" - build job: "/global-workflow/EMC-Global-Pipeline/PR-${env.CHANGE_ID}", parameters: [ - string(name: 'machine', value: machine_name), - string(name: 'Node', value: node) ], - wait: false - } - machine = run_nodes.last().split('-')[0].toLowerCase() - echo "Running parent job: ${machine}" - } else { - machine = run_nodes[0].split('-')[0].toLowerCase() - echo "Running only the parent job: ${machine}" - } - } - } - } - } - - stage('2. Get Common Workspace') { - agent { label "${machine}-emc" } - steps { - script { - Machine = machine[0].toUpperCase() + machine.substring(1) - echo "Getting Common Workspace for ${Machine}" - ws("${custom_workspace[machine]}/${env.CHANGE_ID}") { - properties([ - parameters([ - [$class: 'NodeParameterDefinition', - allowedSlaves: ['built-in', 'Hera-EMC', 'Orion-EMC'], - defaultSlaves: ['built-in'], name: 'Node', - nodeEligibility: [$class: 'AllNodeEligibility'], - triggerIfResult: 'allCases'], - string(name: 'machine', defaultValue: 'hera', description: 'Machine to run the job on') - ]) - ]) - HOME = "${WORKSPACE}" - sh(script: "mkdir -p ${HOME}/RUNTESTS;rm -Rf ${HOME}/RUNTESTS/error.logs") - sh(script: """${GH} pr edit ${env.CHANGE_ID} --repo ${repo_url} --add-label "CI-${Machine}-Building" --remove-label "CI-${Machine}-Ready" """) - } - echo "Building and running on ${Machine} in directory ${HOME}" - } - } - } - - stage('3. Build System') { - matrix { - agent { label "${machine}-emc" } - //options { - // throttle(['global_matrix_build']) - //} - axes { - axis { - name 'system' - values 'gfs', 'gefs' - } - } - stages { - stage('build system') { - steps { - script { - def HOMEgfs = "${HOME}/${system}" // local HOMEgfs is used to build the system on per system basis under the common workspace HOME - sh(script: "mkdir -p ${HOMEgfs}") - ws(HOMEgfs) { - if (fileExists("${HOMEgfs}/sorc/BUILT_semaphor")) { // if the system is already built, skip the build in the case of re-runs - sh(script: "cat ${HOMEgfs}/sorc/BUILT_semaphor", returnStdout: true).trim() // TODO: and user configurable control to manage build semphore - checkout scm - dir('sorc') { - sh(script: './link_workflow.sh') - } - } else { - checkout scm - def gist_url = "" - def error_logs = "" - def error_logs_message = "" - def builds_file = readYaml file: 'ci/cases/yamls/build.yaml' - def build_args_list = builds_file['builds'] - def build_args = build_args_list[system].join(' ').trim().replaceAll('null', '') - dir("${HOMEgfs}/sorc") { - try { - sh(script: "${build_args}") - } catch (Exception error_build) { - echo "Failed to build system: ${error_build.getMessage()}" - if ( fileExists("logs/error.logs") ) { - def fileContent = readFile 'logs/error.logs' - def lines = fileContent.readLines() - for (line in lines) { - echo "archiving: ${line}" - if (fileExists("${line}") && readFile("${line}").length() > 0 ){ - try { - archiveArtifacts artifacts: "${line}", fingerprint: true - error_logs = error_logs + "${HOMEgfs}/sorc/${line} " - error_logs_message = error_logs_message + "${HOMEgfs}/sorc/${line}\n" - } - catch (Exception error_arch) { echo "Failed to archive error log ${line}: ${error_arch.getMessage()}" } - } - } - try { - sh(script: "${HOMEgfs}/ci/scripts/utils/publish_logs.py --file ${error_logs} --repo PR_BUILD_${env.CHANGE_ID}") - gist_url=sh(script: "${HOMEgfs}/ci/scripts/utils/publish_logs.py --file ${error_logs} --gist PR_BUILD_${env.CHANGE_ID}", returnStdout: true).trim() - sh(script: """${GH} pr comment ${env.CHANGE_ID} --repo ${repo_url} --body "Build **FAILED** on **${Machine}** with error logs:\n\\`\\`\\`\n${error_logs_message}\\`\\`\\`\n\nFollow link here to view the contents of the above file(s): [(link)](${gist_url})" """) - } catch (Exception error_comment) { - echo "Failed to comment on PR: ${error_comment.getMessage()}" - } - error("Failed to build system on ${Machine}") - } - } - sh(script: './link_workflow.sh') - sh(script: "echo ${HOMEgfs} > BUILT_semaphor") - } - } - if (env.CHANGE_ID && system == 'gfs') { - try { - sh(script: """${GH} pr edit ${env.CHANGE_ID} --repo ${repo_url} --add-label "CI-${Machine}-Running" --remove-label "CI-${Machine}-Building" """) - } catch (Exception e) { - echo "Failed to update label from Buildng to Running: ${e.getMessage()}" - } - } - if (system == 'gfs') { - caseList = sh(script: "${HOMEgfs}/ci/scripts/utils/get_host_case_list.py ${machine}", returnStdout: true).trim().split() - } - } - } - } - } - } - } - } - - stage('4. Run Tests') { - failFast false - matrix { - agent { label "${machine}-emc" } - axes { - axis { - name 'Case' - // TODO add dynamic list of cases from env vars (needs addtional plugins) - values 'C48C48_ufs_hybatmDA', 'C48_ATM', 'C48_S2SW', 'C48_S2SWA_gefs', 'C48mx500_3DVarAOWCDA', 'C96C48_hybatmDA', 'C96_atm3DVar', 'C96_atmaerosnowDA' - } - } - stages { - - stage('Create Experiments') { - when { - expression { return caseList.contains(Case) } - } - steps { - script { - sh(script: "sed -n '/{.*}/!p' ${HOME}/gfs/ci/cases/pr/${Case}.yaml > ${HOME}/gfs/ci/cases/pr/${Case}.yaml.tmp") - def yaml_case = readYaml file: "${HOME}/gfs/ci/cases/pr/${Case}.yaml.tmp" - system = yaml_case.experiment.system - def HOMEgfs = "${HOME}/${system}" // local HOMEgfs is used to populate the XML on per system basis - env.RUNTESTS = "${HOME}/RUNTESTS" - sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh create_experiment ${HOMEgfs}/ci/cases/pr/${Case}.yaml") - } - } - } - - stage('Run Experiments') { - when { - expression { return caseList.contains(Case) } - } - failFast false - steps { - script { - HOMEgfs = "${HOME}/gfs" // common HOMEgfs is used to launch the scripts that run the experiments - def pslot = sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh get_pslot ${HOME}/RUNTESTS ${Case}", returnStdout: true).trim() - def error_file = "${HOME}/RUNTESTS/${pslot}_error.logs" - sh(script: " rm -f ${error_file}") - try { - sh(script: "${HOMEgfs}/ci/scripts/run-check_ci.sh ${HOME} ${pslot} ${system}") - } catch (Exception error_experment) { - sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh cancel_batch_jobs ${pslot}") - ws(HOME) { - def error_logs = "" - def error_logs_message = "" - if (fileExists(error_file)) { - def fileContent = readFile error_file - def lines = fileContent.readLines() - for (line in lines) { - echo "archiving: ${line}" - if (fileExists("${HOME}/${line}") && readFile("${HOME}/${line}").length() > 0) { - try { - archiveArtifacts artifacts: "${line}", fingerprint: true - error_logs = error_logs + "${HOME}/${line} " - error_logs_message = error_logs_message + "${HOME}/${line}\n" - } catch (Exception error_arch) { - echo "Failed to archive error log ${line}: ${error_arch.getMessage()}" - } - } - } - try { - gist_url = sh(script: "${HOMEgfs}/ci/scripts/utils/publish_logs.py --file ${error_logs} --gist PR_${env.CHANGE_ID}", returnStdout: true).trim() - sh(script: """${GH} pr comment ${env.CHANGE_ID} --repo ${repo_url} --body "Experiment ${Case} **FAILED** on ${Machine} with error logs:\n\\`\\`\\`\n${error_logs_message}\\`\\`\\`\n\nFollow link here to view the contents of the above file(s): [(link)](${gist_url})" """) - sh(script: "${HOMEgfs}/ci/scripts/utils/publish_logs.py --file ${error_logs} --repo PR_${env.CHANGE_ID}") - } catch (Exception error_comment) { - echo "Failed to comment on PR: ${error_comment.getMessage()}" - } - } else { - echo "No error logs found for failed cases in $HOME/RUNTESTS/${pslot}_error.logs" - } - STATUS = 'Failed' - try { - sh(script: """${GH} pr edit ${env.CHANGE_ID} --repo ${repo_url} --remove-label "CI-${Machine}-Running" --add-label "CI-${Machine}-${STATUS}" """, returnStatus: true) - sh(script: """${GH} pr comment ${env.CHANGE_ID} --repo ${repo_url} --body "Experiment ${Case} **FAILED** on ${Machine} in\n\\`${HOME}/RUNTESTS/${pslot}\\`" """) - } catch (Exception e) { - echo "Failed to update label from Running to ${STATUS}: ${e.getMessage()}" - } - error("Failed to run experiments ${Case} on ${Machine}") - } - } - } - } - } - } - } - } - stage( '5. FINALIZE' ) { - when { - expression { - STATUS == 'Passed' - } - } - agent { label "${machine}-emc" } - steps { - script { - try { - sh(script: """${GH} pr edit ${env.CHANGE_ID} --repo ${repo_url} --remove-label "CI-${Machine}-Running" --remove-label "CI-${Machine}-Building" --add-label "CI-${Machine}-${STATUS}" """, returnStatus: true) - sh(script: """${GH} pr comment ${env.CHANGE_ID} --repo ${repo_url} --body "**CI ${STATUS}** ${Machine} at
Built and ran in directory \\`${HOME}\\`" """, returnStatus: true) - } catch (Exception e) { - echo "Failed to update label from Running to ${STATUS}: ${e.getMessage()}" - } - } - } - } - } -} From 89d60586d6e745070a2a856d6ba40d612d96631b Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 8 May 2024 23:23:36 +0000 Subject: [PATCH 032/158] added verbose in the pytest argument to list each test --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 8595a21276..5dfb062726 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -36,7 +36,7 @@ jobs: echo "$(pwd)/bin" >> $GITHUB_PATH - name: Run tests - run: python -m pytest ci/scripts/tests/test_rocotostat.py --junitxml ci/scripts/tests/test-results.xml + run: python -m pytest ci/scripts/tests/test_rocotostat.py -v --junitxml ci/scripts/tests/test-results.xml - name: Publish Test Results if: always() From a53445b1a6e96b3bbebc6bd50a3f72e44f51cbf3 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 10 May 2024 14:34:16 +0000 Subject: [PATCH 033/158] moved test data specfic to rocotostat tests in test directory and neutered XML file --- ci/scripts/tests/test_rocotostat.py | 4 +- .../{ => testdata/rocotostat}/database.db | Bin .../{ => testdata/rocotostat}/workflow.xml | 104 ++++++++---------- 3 files changed, 48 insertions(+), 60 deletions(-) rename ci/scripts/tests/{ => testdata/rocotostat}/database.db (100%) rename ci/scripts/tests/{ => testdata/rocotostat}/workflow.xml (52%) diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index d0931ab73f..8deb88ca0e 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -7,8 +7,8 @@ from rocotostat import rocoto_statcount, rocotostat_summary, CommandNotFoundError from wxflow import which -workflow_file = os.path.join(script_dir, "workflow.xml") -database_file = os.path.join(script_dir, "database.db") +workflow_file = os.path.join(script_dir, "testdata/rocotostat/workflow.xml") +database_file = os.path.join(script_dir, "testdata/rocotostat/database.db") try: rocotostat = which("rocotostat") diff --git a/ci/scripts/tests/database.db b/ci/scripts/tests/testdata/rocotostat/database.db similarity index 100% rename from ci/scripts/tests/database.db rename to ci/scripts/tests/testdata/rocotostat/database.db diff --git a/ci/scripts/tests/workflow.xml b/ci/scripts/tests/testdata/rocotostat/workflow.xml similarity index 52% rename from ci/scripts/tests/workflow.xml rename to ci/scripts/tests/testdata/rocotostat/workflow.xml index 5c8a64651f..d5171f647a 100644 --- a/ci/scripts/tests/workflow.xml +++ b/ci/scripts/tests/testdata/rocotostat/workflow.xml @@ -9,21 +9,21 @@ This workflow was automatically generated at 2024-05-01 14:24:16.515689 --> - - + + ]> - /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1/logs/@Y@m@d@H.log + STUB 202103231200 202103231200 24:00:00 - /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/stage_ic.sh + stage_ic.sh C48_ATM_0ad155f1_gfsstage_ic_@H nems @@ -33,35 +33,23 @@ 1:ppn=1:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsstage_ic.log + /RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsstage_ic.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs - EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + HOMEgfsgfs + EXPDIRRUNTESTS/EXPDIR/C48_ATM_0ad155f1 NETgfs CDUMPgfs RUNgfs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + COMROOT/RUNTESTS/COMROOT + DATAROOT/RUNDIRS/C48_ATM_0ad155f1 - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_ctrl.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile1.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile2.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile3.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile4.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile5.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_data.tile6.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile1.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile2.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile3.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile4.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile5.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/sfc_data.tile6.nc + /ICSDIR/prototype_ICs/workflow_C48_refactored/@Y@m@d@H/atmos/gfs_ctrl.nc @@ -69,7 +57,7 @@ - /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/fcst.sh + /CI/ORION/2555/gfs/jobs/rocoto/fcst.sh C48_ATM_0ad155f1_gfsfcst_@H nems @@ -79,19 +67,19 @@ 1:ppn=40:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsfcst.log + /CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsfcst.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs - EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + HOMEgfs/CI/ORION/2555/gfs + EXPDIR/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 NETgfs CDUMPgfs RUNgfs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + COMROOT/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/RUNDIRS/C48_ATM_0ad155f1 @@ -109,7 +97,7 @@ - /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/atmos_products.sh + /CI/ORION/2555/gfs/jobs/rocoto/atmos_products.sh C48_ATM_0ad155f1_gfsatmos_prod#grp#_@H nems @@ -119,19 +107,19 @@ 1:ppn=24:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsatmos_prod#grp#.log + /RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsatmos_prod#grp#.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs - EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + HOMEgfs/CI/ORION/2555/gfs + EXPDIR/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 NETgfs CDUMPgfs RUNgfs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + COMROOT/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/RUNDIRS/C48_ATM_0ad155f1 FHRLST#lst# COMPONENTatmos @@ -145,7 +133,7 @@ - /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/tracker.sh + /CI/ORION/2555/gfs/jobs/rocoto/tracker.sh C48_ATM_0ad155f1_gfstracker_@H nems @@ -156,19 +144,19 @@ 4G --export=NONE - /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfstracker.log + /CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfstracker.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs - EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + HOMEgfs/CI/ORION/2555/gfs + EXPDIR/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 NETgfs CDUMPgfs RUNgfs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + COMROOT/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/RUNDIRS/C48_ATM_0ad155f1 @@ -178,7 +166,7 @@ - /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/genesis.sh + /CI/ORION/2555/gfs/jobs/rocoto/genesis.sh C48_ATM_0ad155f1_gfsgenesis_@H nems @@ -189,19 +177,19 @@ 10G --export=NONE - /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsgenesis.log + /CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsgenesis.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs - EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + HOMEgfs/CI/ORION/2555/gfs + EXPDIR/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 NETgfs CDUMPgfs RUNgfs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + COMROOT/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/RUNDIRS/C48_ATM_0ad155f1 @@ -211,7 +199,7 @@ - /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/arch.sh + /CI/ORION/2555/gfs/jobs/rocoto/arch.sh C48_ATM_0ad155f1_gfsarch_@H nems @@ -222,19 +210,19 @@ 4096M --export=NONE - /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsarch.log + /CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfsarch.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs - EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + HOMEgfs/CI/ORION/2555/gfs + EXPDIR/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 NETgfs CDUMPgfs RUNgfs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + COMROOT/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/RUNDIRS/C48_ATM_0ad155f1 @@ -248,7 +236,7 @@ - /work2/noaa/stmp/CI/ORION/2555/gfs/jobs/rocoto/cleanup.sh + /CI/ORION/2555/gfs/jobs/rocoto/cleanup.sh C48_ATM_0ad155f1_gfscleanup_@H nems @@ -259,19 +247,19 @@ 4096M --export=NONE - /work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfscleanup.log + /CI/ORION/2555/RUNTESTS/COMROOT/C48_ATM_0ad155f1/logs/@Y@m@d@H/gfscleanup.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2555/gfs - EXPDIR/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 + HOMEgfs/CI/ORION/2555/gfs + EXPDIR/CI/ORION/2555/RUNTESTS/EXPDIR/C48_ATM_0ad155f1 NETgfs CDUMPgfs RUNgfs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2555/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_ATM_0ad155f1 + COMROOT/CI/ORION/2555/RUNTESTS/COMROOT + DATAROOT/RUNDIRS/C48_ATM_0ad155f1 From eafc6cc3840f227213d9fe311889b0014e6a7874 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 10 May 2024 14:51:39 +0000 Subject: [PATCH 034/158] cashed install of Rocoto in actions runner --- .github/workflows/ci-unit_tests.yaml | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 5dfb062726..a8293bcd51 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -28,12 +28,20 @@ jobs: # If you have a requirements.txt file, you can install all dependencies using: # pip install -r requirements.txt + - name: Cache Rocoto + uses: actions/cache@v3 + with: + path: ~/rocoto + key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} + - name: Install Rocoto run: | - git clone https://github.com/christopherwharrop/rocoto.git - cd rocoto - ./INSTALL - echo "$(pwd)/bin" >> $GITHUB_PATH + if [ ! -d "$HOME/rocoto" ]; then + git clone https://github.com/christopherwharrop/rocoto.git $HOME/rocoto + cd $HOME/rocoto + ./INSTALL + fi + echo "$HOME/rocoto/bin" >> $GITHUB_PATH - name: Run tests run: python -m pytest ci/scripts/tests/test_rocotostat.py -v --junitxml ci/scripts/tests/test-results.xml @@ -45,4 +53,3 @@ jobs: files: ci/scripts/tests/test-results.xml job_summary: true comment_mode: off - \ No newline at end of file From 6ed8e71443d476af5fae55eb01c204d69cce281a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 10 May 2024 15:02:16 +0000 Subject: [PATCH 035/158] update cashe action to version 4 --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index a8293bcd51..caf03c3279 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -29,7 +29,7 @@ jobs: # pip install -r requirements.txt - name: Cache Rocoto - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: ~/rocoto key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} From e81512b8073d7d530b09af5e05715e0f79198dc7 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Fri, 10 May 2024 10:46:47 -0500 Subject: [PATCH 036/158] added test data for rocotocheck stalled case --- .../testdata/rocotostat_stalled/stalled.db | Bin 0 -> 36864 bytes 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24:00:00 + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/stage_ic.sh + + C48_S2SWA_gefs_c6c24a90_stage_ic_@H + nems + batch + orion + 00:15:00 + 1:ppn=1:tpp=1 + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/stage_ic.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + + + + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_ctrl.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile1.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile2.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile3.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile4.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile5.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile6.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile1.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile2.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile3.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile4.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile5.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile6.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/ocean/@Y@m@d.@H0000.MOM.res.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/ice/@Y@m@d.@H0000.cice_model.res.nc + /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/wave/@Y@m@d.@H0000.restart.glo_500 + + + + + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/waveinit.sh + + C48_S2SWA_gefs_c6c24a90_wave_init_@H + nems + batch + orion + 00:10:00 + 1:ppn=40:tpp=1 + 2GB + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/wave_init.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + + + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/fcst.sh + + C48_S2SWA_gefs_c6c24a90_fcst_mem000_@H + nems + batch + orion + 03:00:00 + 1:ppn=40:tpp=1 + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/fcst_mem000.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + + + + + + + + + + + + + 001 002 + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/fcst.sh + + C48_S2SWA_gefs_c6c24a90_fcst_mem#member#_@H + nems + batch + orion + 03:00:00 + 1:ppn=40:tpp=1 + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/fcst_mem#member#.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + ENSMEM#member# + MEMDIRmem#member# + + + + + + + + + + + + + + + 000 001 002 + + + + 000 006 012 018 024 030 036 042 048 054 060 066 072 078 084 090 096 102 108 114 120 + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/atmos_products.sh + + C48_S2SWA_gefs_c6c24a90_atmos_prod_mem#member#_f#fhr#_@H + nems + batch + orion + 00:15:00 + 1:ppn=24:tpp=1 + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/atmos_prod_mem#member#_f#fhr#.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + ENSMEM#member# + MEMDIRmem#member# + FHRLST#fhr# + COMPONENTatmos + + + &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/atmos/master/gefs.t@Hz.master.grb2f#fhr# + + + + + + + + + + + 000 006 012 018 024 030 036 042 048 054 060 066 072 078 084 090 096 102 108 114 120 + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/atmos_ensstat.sh + + C48_S2SWA_gefs_c6c24a90_atmos_ensstat_f#fhr#_@H + nems + batch + orion + 00:30:00 + 1:ppn=6:tpp=1 + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/atmos_ensstat_f#fhr#.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + FHRLST#fhr# + + + + + + + + + + + + + + + + 000 001 002 + + + + 006 012 018 024 030 036 042 048 054 060 066 072 078 084 090 096 102 108 114 120 + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/oceanice_products.sh + + C48_S2SWA_gefs_c6c24a90_ocean_prod_mem#member#_f#fhr#_@H + nems + batch + orion + 00:15:00 + 1:ppn=1:tpp=1 + 96GB + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/ocean_prod_mem#member#_f#fhr#.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + ENSMEM#member# + MEMDIRmem#member# + FHRLST#fhr# + COMPONENTocean + + + + &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ocean/history/gefs.ocean.t@Hz.24hr_avg.f#fhr#.nc + /work2/noaa/stmp/CI/ORION/2561/gefs/ush/check_netcdf.sh &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ocean/history/gefs.ocean.t@Hz.24hr_avg.f#fhr#.nc + + + + + + + + + + + + 000 001 002 + + + + 006 012 018 024 030 036 042 048 054 060 066 072 078 084 090 096 102 108 114 120 + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/oceanice_products.sh + + C48_S2SWA_gefs_c6c24a90_ice_prod_mem#member#_f#fhr#_@H + nems + batch + orion + 00:15:00 + 1:ppn=1:tpp=1 + 96GB + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/ice_prod_mem#member#_f#fhr#.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + ENSMEM#member# + MEMDIRmem#member# + FHRLST#fhr# + COMPONENTice + + + &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ice/history/gefs.ice.t@Hz.24hr_avg.f#fhr#.nc + + + + + + + + + + + 000 001 002 + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/wavepostsbs.sh + + C48_S2SWA_gefs_c6c24a90_wave_post_grid_mem#member#_@H + nems + batch + orion + 03:00:00 + 1:ppn=40:tpp=1 + 10GB + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/wave_post_grid_mem#member#.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + ENSMEM#member# + MEMDIRmem#member# + + + + &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/wave/history/gefswave.out_grd.glo_500.@Y@m@d.@H0000 + + + + + + + + + + 000 001 002 + + + + /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/wavepostpnt.sh + + C48_S2SWA_gefs_c6c24a90_wave_post_pnt_mem#member#_@H + nems + batch + orion + 04:00:00 + 5:ppn=40:tpp=1 + --export=NONE + + /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/wave_post_pnt_mem#member#.log + + RUN_ENVIRemc + HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs + EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + NETgefs + CDUMPgefs + RUNgefs + CDATE@Y@m@d@H + PDY@Y@m@d + cyc@H + COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + ENSMEM#member# + MEMDIRmem#member# + + + + + + + + + + + + From 14b1622c0a585d4711d4f4b0cab2291dcb81b81e Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 10 May 2024 16:03:25 +0000 Subject: [PATCH 037/158] added stalled and done as functions and added two more unit tests for each in rocotostatus --- .github/workflows/ci-unit_tests.yaml | 2 +- ci/scripts/tests/test_rocotostat.py | 17 +- .../testdata/rocotostat_stalled/stalled.xml | 164 ++++++++---------- ci/scripts/utils/rocotostat.py | 16 +- 4 files changed, 106 insertions(+), 93 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index caf03c3279..a46e2fd55c 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -44,7 +44,7 @@ jobs: echo "$HOME/rocoto/bin" >> $GITHUB_PATH - name: Run tests - run: python -m pytest ci/scripts/tests/test_rocotostat.py -v --junitxml ci/scripts/tests/test-results.xml + run: python -m pytest ci/scripts/tests/ -v --junitxml ci/scripts/tests/test-results.xml - name: Publish Test Results if: always() diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index 8deb88ca0e..bbbe0ca467 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -4,7 +4,7 @@ script_dir = os.path.dirname(os.path.abspath(__file__)) sys.path.append(os.path.join(os.path.dirname(script_dir), 'utils')) -from rocotostat import rocoto_statcount, rocotostat_summary, CommandNotFoundError +from rocotostat import rocoto_statcount, rocotostat_summary, is_done, is_stalled, CommandNotFoundError from wxflow import which workflow_file = os.path.join(script_dir, "testdata/rocotostat/workflow.xml") @@ -35,3 +35,18 @@ def test_rocoto_summary(): assert result['CYCLES_TOTAL'] == 1 assert result['CYCLES_DONE'] == 1 + +def test_rocoto_done(): + + result = rocotostat_summary(rocotostat) + + assert is_done(result) == True + +def test_rocoto_stalled(): + + workflow_file = os.path.join(script_dir, "testdata/rocotostat_stalled/stalled.xml") + database_file = os.path.join(script_dir, "testdata/rocotostat_stalled/stalled.db") + + result = rocoto_statcount(rocotostat) + + assert is_stalled(result) == True diff --git a/ci/scripts/tests/testdata/rocotostat_stalled/stalled.xml b/ci/scripts/tests/testdata/rocotostat_stalled/stalled.xml index cf7b449cb8..dd4e5a6a68 100644 --- a/ci/scripts/tests/testdata/rocotostat_stalled/stalled.xml +++ b/ci/scripts/tests/testdata/rocotostat_stalled/stalled.xml @@ -8,24 +8,24 @@ NOTES: This workflow was automatically generated at 2024-05-08 19:53:07.741175 --> - - - + + + ]> - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H.log + /RUNTESTS/EXPDIR/C48_S2SWA_gefs/logs/@Y@m@d@H.log 202103231200 202103231200 24:00:00 - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/stage_ic.sh + /gefs/jobs/rocoto/stage_ic.sh - C48_S2SWA_gefs_c6c24a90_stage_ic_@H + C48_S2SWA_gefs_stage_ic_@H nems batch orion @@ -33,37 +33,23 @@ 1:ppn=1:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/stage_ic.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/stage_ic.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_ctrl.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile1.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile2.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile3.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile4.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile5.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_data.tile6.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile1.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile2.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile3.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile4.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile5.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/sfc_data.tile6.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/ocean/@Y@m@d.@H0000.MOM.res.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/ice/@Y@m@d.@H0000.cice_model.res.nc /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/wave/@Y@m@d.@H0000.restart.glo_500 @@ -72,9 +58,9 @@ - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/waveinit.sh + /gefs/jobs/rocoto/waveinit.sh - C48_S2SWA_gefs_c6c24a90_wave_init_@H + C48_S2SWA_gefs_wave_init_@H nems batch orion @@ -83,27 +69,27 @@ 2GB --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/wave_init.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/wave_init.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/fcst.sh + /gefs/jobs/rocoto/fcst.sh - C48_S2SWA_gefs_c6c24a90_fcst_mem000_@H + C48_S2SWA_gefs_fcst_mem000_@H nems batch orion @@ -111,19 +97,19 @@ 1:ppn=40:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/fcst_mem000.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/fcst_mem000.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs @@ -140,9 +126,9 @@ - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/fcst.sh + /gefs/jobs/rocoto/fcst.sh - C48_S2SWA_gefs_c6c24a90_fcst_mem#member#_@H + C48_S2SWA_gefs_fcst_mem#member#_@H nems batch orion @@ -150,19 +136,19 @@ 1:ppn=40:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/fcst_mem#member#.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/fcst_mem#member#.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs ENSMEM#member# MEMDIRmem#member# @@ -187,9 +173,9 @@ - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/atmos_products.sh + /gefs/jobs/rocoto/atmos_products.sh - C48_S2SWA_gefs_c6c24a90_atmos_prod_mem#member#_f#fhr#_@H + C48_S2SWA_gefs_atmos_prod_mem#member#_f#fhr#_@H nems batch orion @@ -197,19 +183,19 @@ 1:ppn=24:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/atmos_prod_mem#member#_f#fhr#.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/atmos_prod_mem#member#_f#fhr#.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs ENSMEM#member# MEMDIRmem#member# FHRLST#fhr# @@ -231,9 +217,9 @@ - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/atmos_ensstat.sh + /gefs/jobs/rocoto/atmos_ensstat.sh - C48_S2SWA_gefs_c6c24a90_atmos_ensstat_f#fhr#_@H + C48_S2SWA_gefs_atmos_ensstat_f#fhr#_@H nems batch orion @@ -241,19 +227,19 @@ 1:ppn=6:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/atmos_ensstat_f#fhr#.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/atmos_ensstat_f#fhr#.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs FHRLST#fhr# @@ -278,9 +264,9 @@ - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/oceanice_products.sh + /gefs/jobs/rocoto/oceanice_products.sh - C48_S2SWA_gefs_c6c24a90_ocean_prod_mem#member#_f#fhr#_@H + C48_S2SWA_gefs_ocean_prod_mem#member#_f#fhr#_@H nems batch orion @@ -289,19 +275,19 @@ 96GB --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/ocean_prod_mem#member#_f#fhr#.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/ocean_prod_mem#member#_f#fhr#.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs ENSMEM#member# MEMDIRmem#member# FHRLST#fhr# @@ -310,7 +296,7 @@ &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ocean/history/gefs.ocean.t@Hz.24hr_avg.f#fhr#.nc - /work2/noaa/stmp/CI/ORION/2561/gefs/ush/check_netcdf.sh &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ocean/history/gefs.ocean.t@Hz.24hr_avg.f#fhr#.nc + /gefs/ush/check_netcdf.sh &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ocean/history/gefs.ocean.t@Hz.24hr_avg.f#fhr#.nc @@ -330,9 +316,9 @@ - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/oceanice_products.sh + /gefs/jobs/rocoto/oceanice_products.sh - C48_S2SWA_gefs_c6c24a90_ice_prod_mem#member#_f#fhr#_@H + C48_S2SWA_gefs_ice_prod_mem#member#_f#fhr#_@H nems batch orion @@ -341,19 +327,19 @@ 96GB --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/ice_prod_mem#member#_f#fhr#.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/ice_prod_mem#member#_f#fhr#.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs ENSMEM#member# MEMDIRmem#member# FHRLST#fhr# @@ -375,9 +361,9 @@ - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/wavepostsbs.sh + /gefs/jobs/rocoto/wavepostsbs.sh - C48_S2SWA_gefs_c6c24a90_wave_post_grid_mem#member#_@H + C48_S2SWA_gefs_wave_post_grid_mem#member#_@H nems batch orion @@ -386,19 +372,19 @@ 10GB --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/wave_post_grid_mem#member#.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/wave_post_grid_mem#member#.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs ENSMEM#member# MEMDIRmem#member# @@ -418,9 +404,9 @@ - /work2/noaa/stmp/CI/ORION/2561/gefs/jobs/rocoto/wavepostpnt.sh + /gefs/jobs/rocoto/wavepostpnt.sh - C48_S2SWA_gefs_c6c24a90_wave_post_pnt_mem#member#_@H + C48_S2SWA_gefs_wave_post_pnt_mem#member#_@H nems batch orion @@ -428,19 +414,19 @@ 5:ppn=40:tpp=1 --export=NONE - /work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT/C48_S2SWA_gefs_c6c24a90/logs/@Y@m@d@H/wave_post_pnt_mem#member#.log + /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/wave_post_pnt_mem#member#.log RUN_ENVIRemc - HOMEgfs/work2/noaa/stmp/CI/ORION/2561/gefs - EXPDIR/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/EXPDIR/C48_S2SWA_gefs_c6c24a90 + HOMEgfs/gefs + EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs NETgefs CDUMPgefs RUNgefs CDATE@Y@m@d@H PDY@Y@m@d cyc@H - COMROOT/work2/noaa/stmp/CI/ORION/2561/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs_c6c24a90 + COMROOT/RUNTESTS/COMROOT + DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs ENSMEM#member# MEMDIRmem#member# diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 28e3fad707..88b7faa8e9 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -98,6 +98,18 @@ def rocoto_statcount(rocotostat): return rocoto_status +def is_done(rocoto_status): + if rocoto_status['CYCLES_TOTAL'] == rocoto_status['CYCLES_DONE']: + return True + else: + return False + +def is_stalled(rocoto_status): + if rocoto_status['RUNNING'] + rocoto_status['SUBMITTING'] + rocoto_status['QUEUED'] == 0: + return True + else: + return False + if __name__ == '__main__': @@ -115,7 +127,7 @@ def rocoto_statcount(rocotostat): rocoto_status = rocoto_statcount(rocotostat) rocoto_status.update(rocotostat_summary(rocotostat)) - if rocoto_status['CYCLES_TOTAL'] == rocoto_status['CYCLES_DONE']: + if is_done(rocoto_status): rocoto_state = 'DONE' elif rocoto_status['DEAD'] > 0: error_return = rocoto_status['FAIL'] + rocoto_status['DEAD'] @@ -123,7 +135,7 @@ def rocoto_statcount(rocotostat): elif 'UNKNOWN' in rocoto_status: error_return = rocoto_status['UNKNOWN'] rocoto_state = 'UNKNOWN' - elif rocoto_status['RUNNING'] + rocoto_status['SUBMITTING'] + rocoto_status['QUEUED'] == 0: + elif is_stalled(rocoto_status): # # TODO for now a STALLED state will be just a warning as it can # produce a false negative if there is a timestamp on a file dependency. From 5901d513b22f044c27d813be14526f9d726d4fd7 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 10 May 2024 16:18:13 +0000 Subject: [PATCH 038/158] added doctrings to new functions in rocotstat --- ci/scripts/utils/rocotostat.py | 39 ++++++++++++++++++++++++++++++++-- 1 file changed, 37 insertions(+), 2 deletions(-) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 88b7faa8e9..40f10c6aa8 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -55,6 +55,7 @@ def rocotostat_summary(rocotostat): Output: ROCOTO_STATUS - A dictionary with the total number of cycles and the number of cycles marked as 'Done'. """ + rocotostat.add_default_arg('--summary') rocotostat_output = rocotostat(output=str) rocotostat_output = rocotostat_output.splitlines()[1:] @@ -99,19 +100,53 @@ def rocoto_statcount(rocotostat): return rocoto_status def is_done(rocoto_status): + """ + IS_DONE Check if all cycles are done. + + IS_DONE(ROCOTO_STATUS) checks if the total number of cycles equals the number of + done cycles in the ROCOTO_STATUS dictionary. + + Input: + ROCOTO_STATUS - A dictionary with the count of each status case. + + Output: + BOOLEAN - True if all cycles are done, False otherwise. + """ + if rocoto_status['CYCLES_TOTAL'] == rocoto_status['CYCLES_DONE']: return True else: return False + def is_stalled(rocoto_status): - if rocoto_status['RUNNING'] + rocoto_status['SUBMITTING'] + rocoto_status['QUEUED'] == 0: + """ + IS_STALLED Check if all cycles are stalled. + + IS_STALLED(ROCOTO_STATUS) checks if all cycles are stalled by verifying if + there are no jobs that are RUNNING, SUBMITTING, or QUEUED. + + Input: + ROCOTO_STATUS - A dictionary with the count of each status case. + + Output: + BOOLEAN - True if all cycles are stalled, False otherwise. + """ + + if rocoto_status['RUNNING'] + rocoto_status['SUBMITTING'] + rocoto_status['QUEUED'] == 0: return True - else: + else: return False if __name__ == '__main__': + """ + MAIN Execute the script. + + MAIN() parses the input arguments, checks if the rocotostat command is available, + adds default arguments to the rocotostat command, and runs it and reports + out to stdout spcific information of rocoto workflow. + """ args = input_args() From 9fe4f629c3d87fe7ef6dcc239caef15f060d73d6 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 10 May 2024 16:24:34 +0000 Subject: [PATCH 039/158] updated pynorm spaces --- ci/scripts/tests/test_rocotostat.py | 10 ++++++---- ci/scripts/utils/rocotostat.py | 5 +++-- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index bbbe0ca467..5fd1655677 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -36,17 +36,19 @@ def test_rocoto_summary(): assert result['CYCLES_TOTAL'] == 1 assert result['CYCLES_DONE'] == 1 + def test_rocoto_done(): result = rocotostat_summary(rocotostat) assert is_done(result) == True + def test_rocoto_stalled(): - workflow_file = os.path.join(script_dir, "testdata/rocotostat_stalled/stalled.xml") - database_file = os.path.join(script_dir, "testdata/rocotostat_stalled/stalled.db") + workflow_file = os.path.join(script_dir, "testdata/rocotostat_stalled/stalled.xml") + database_file = os.path.join(script_dir, "testdata/rocotostat_stalled/stalled.db") - result = rocoto_statcount(rocotostat) + result = rocoto_statcount(rocotostat) - assert is_stalled(result) == True + assert is_stalled(result) == True diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 40f10c6aa8..fe8c84b5e7 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -99,6 +99,7 @@ def rocoto_statcount(rocotostat): return rocoto_status + def is_done(rocoto_status): """ IS_DONE Check if all cycles are done. @@ -134,9 +135,9 @@ def is_stalled(rocoto_status): """ if rocoto_status['RUNNING'] + rocoto_status['SUBMITTING'] + rocoto_status['QUEUED'] == 0: - return True + return True else: - return False + return False if __name__ == '__main__': From 2f3cd87003deb28c9bbc7fb74f04222e50088e52 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 10 May 2024 16:26:48 +0000 Subject: [PATCH 040/158] do not need to assert is set to true, it just is --- ci/scripts/tests/test_rocotostat.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index 5fd1655677..52737c4e8f 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -41,7 +41,7 @@ def test_rocoto_done(): result = rocotostat_summary(rocotostat) - assert is_done(result) == True + assert is_done(result) def test_rocoto_stalled(): @@ -51,4 +51,4 @@ def test_rocoto_stalled(): result = rocoto_statcount(rocotostat) - assert is_stalled(result) == True + assert is_stalled(result) From 7f7f705dd5b0940f0e008f48054366a4bc362431 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 10 May 2024 23:04:10 +0000 Subject: [PATCH 041/158] cashe after intall or Rocoto silly --- .github/workflows/ci-unit_tests.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index caf03c3279..841ecf674c 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -28,12 +28,6 @@ jobs: # If you have a requirements.txt file, you can install all dependencies using: # pip install -r requirements.txt - - name: Cache Rocoto - uses: actions/cache@v4 - with: - path: ~/rocoto - key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} - - name: Install Rocoto run: | if [ ! -d "$HOME/rocoto" ]; then @@ -43,6 +37,12 @@ jobs: fi echo "$HOME/rocoto/bin" >> $GITHUB_PATH + - name: Cache Rocoto + uses: actions/cache@v4 + with: + path: ~/rocoto + key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} + - name: Run tests run: python -m pytest ci/scripts/tests/test_rocotostat.py -v --junitxml ci/scripts/tests/test-results.xml From 4566503532a151a6c8dfbe6b7a33b3439f03fa3a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 19:04:40 +0000 Subject: [PATCH 042/158] removded all rocoto test data and put them in S3 bucket and have them downloaded using curl when not present --- ci/scripts/tests/test_rocotostat.py | 33 +- .../tests/testdata/rocotostat/database.db | Bin 28672 -> 0 bytes ci/scripts/tests/testdata/rocotostat/stub | 0 .../tests/testdata/rocotostat/workflow.xml | 272 ----------- .../testdata/rocotostat_stalled/stalled.db | Bin 36864 -> 0 bytes .../testdata/rocotostat_stalled/stalled.xml | 443 ------------------ .../tests/testdata/rocotostat_stalled/stub | 0 ci/scripts/utils/rocotostat.py | 2 +- 8 files changed, 28 insertions(+), 722 deletions(-) delete mode 100644 ci/scripts/tests/testdata/rocotostat/database.db create mode 100644 ci/scripts/tests/testdata/rocotostat/stub delete mode 100644 ci/scripts/tests/testdata/rocotostat/workflow.xml delete mode 100644 ci/scripts/tests/testdata/rocotostat_stalled/stalled.db delete mode 100644 ci/scripts/tests/testdata/rocotostat_stalled/stalled.xml create mode 100644 ci/scripts/tests/testdata/rocotostat_stalled/stub diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index 52737c4e8f..caf9ae4e6b 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -7,15 +7,25 @@ from rocotostat import rocoto_statcount, rocotostat_summary, is_done, is_stalled, CommandNotFoundError from wxflow import which -workflow_file = os.path.join(script_dir, "testdata/rocotostat/workflow.xml") -database_file = os.path.join(script_dir, "testdata/rocotostat/database.db") +test_data_url ='https://noaa-nws-global-pds.s3.amazonaws.com/data/CI/' + +testdata_path = 'testdata/rocotostat' +testdata_full_path = os.path.join(script_dir, testdata_path) + +wget = which('wget') +if not os.listdir(os.path.join(testdata_full_path)): + wget.add_default_arg(['-P', testdata_full_path, + test_data_url + str(testdata_path) + '/workflow.xml', + test_data_url + str(testdata_path) + '/database.db', + ]) + wget() try: - rocotostat = which("rocotostat") + rocotostat = which('rocotostat') except CommandNotFoundError: raise CommandNotFoundError("rocotostat not found in PATH") -rocotostat.add_default_arg(['-w', workflow_file, '-d', database_file]) +rocotostat.add_default_arg(['-w', os.path.join(testdata_path,'workflow.xml'), '-d', os.path.join(testdata_path, 'database.db')]) def test_rocoto_statcount(): @@ -45,10 +55,21 @@ def test_rocoto_done(): def test_rocoto_stalled(): + testdata_path = 'testdata/rocotostat_stalled' + testdata_full_path = os.path.join(script_dir, testdata_path) + + wget = which('wget') + if not os.listdir(os.path.join(testdata_full_path)): + wget.add_default_arg(['-P', testdata_full_path, + test_data_url + str(testdata_path) + '/stalled.xml', + test_data_url + str(testdata_path) + '/stalled.db', + ]) + wget() - workflow_file = os.path.join(script_dir, "testdata/rocotostat_stalled/stalled.xml") - database_file = os.path.join(script_dir, "testdata/rocotostat_stalled/stalled.db") + rocotostat = which('rocotostat') + rocotostat.add_default_arg(['-w', os.path.join(testdata_path,'stalled.xml'), '-d', os.path.join(testdata_path, 'stalled.db')]) result = rocoto_statcount(rocotostat) + assert result['SUCCEEDED'] == 110 assert is_stalled(result) diff --git a/ci/scripts/tests/testdata/rocotostat/database.db b/ci/scripts/tests/testdata/rocotostat/database.db deleted file mode 100644 index baca6c7513b04755ae034ac7db45b1336d936935..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 28672 zcmeI4&u`mg7{_0yX_Ga-wr*3Is;aJvpb>5N`e&MQSzB9MMVfYL2dWV2+}P>NTBq1f zw<2+9kq{CW4hSJ6E*y~fC%Az)a2P^J69?{S9LE*$yiSwGbuEF!R84!VB(`6_&-Zzr z&-=Vd9mid}U9o+OZ#3Oq!{;S(k#HQj!SjTWBY39Z*;&|jvawb$ zA_JMHB=a=?YwmHbmHj>YWt;)FBLO6U1dsp{Kmter2_OL^@c$AxoZwQ!qodr>HQ(6U zvFZo)9m}*DopoZdrq8eI{QCStMdv%M{G@I2OVxG#re5P$YfH=XwGI9aePfE>cAKp| z$Jn*_H|J}Mx8`e;s$85pG3>O8iVDr9?fM7&!pcfTpRZ2wM%}mf4c~4$o6SbUv;2;a z;=;hd@U?545yZG})LX6H_G>B>U%QQ;+%Y_V^LR&t@Yk1?_2S``{?zc;7vcE!Ls4~`_^#b6=(L>s z4lwWOVYb|$h{bjn<7l-PuK)Jte?bpJ`=E*gIKu2F9aUAAOR$R1dsp{Kmter2_OL^ zfCP{L5OWQ z&kd)w$NnN+yR*2c>zb}Dt}L%s^mSd!iQ* zqki9V&o*1uE`r(XNiK*m!6GcpN(yu3?>4>7J-2CYHUyzG-GFOpOyi|!yySbWaE1!Y zGo(UiK}C>bRJd_17g13ZmO`%zEz{`+Evs=VA8DD0id>4QltfS|&Bm#Gko%6L85ea3 z)H);B=2I?95Yx8hSf1@MfhdtgLd!>@P)orO_Hd=;G7zCkTof;B*@%jw2&ak63Xsce zDNf~8Egeyjgoui)fQll-sZ_KJ5fwSAqR614##IVuY6B4!F;Z_-gnFZr6c@{Seu(7R z=(OjaHW<;AOOgCkiA7e9)11hEOejn`Ze)bb=U^sKfdcDB-Se5%WbID1x>UV+ywdt3 zUPbA2%~Jtt9`2Ti^GXU|wChYxfEsx3nTMymN2_eGUrR+|kb;;)Ge%M&23d@YVMR+u zR0Ne}9#WxDt5k@sRZiqPHcrCL_l{DgZfwyjOO z&a#f88)Dc0;ii95cvN`wf`5=<`bYo?AOR$R1dsp{Kmter2_OL^fCSEsz)Yf#)X)4< zb>`OU;>@zQ#{Rp)jBd8(;9Dq3o$34c{pB)MJLmuBmLNJt0!RP}AOR$R1dsp{Kmter s2_OL^fCQd70X+YI=7`Y&5 - 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- - - - - -]> - - - - /RUNTESTS/EXPDIR/C48_S2SWA_gefs/logs/@Y@m@d@H.log - - - 202103231200 202103231200 24:00:00 - - - - /gefs/jobs/rocoto/stage_ic.sh - - C48_S2SWA_gefs_stage_ic_@H - nems - batch - orion - 00:15:00 - 1:ppn=1:tpp=1 - --export=NONE - - /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/stage_ic.log - - RUN_ENVIRemc - HOMEgfs/gefs - EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs - NETgefs - CDUMPgefs - RUNgefs - CDATE@Y@m@d@H - PDY@Y@m@d - cyc@H - COMROOT/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - - - - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/atmos/gfs_ctrl.nc - /work/noaa/global/glopara/data/ICSDIR/prototype_ICs/gefs_test/@Y@m@d@H/mem000/wave/@Y@m@d.@H0000.restart.glo_500 - - - - - - - - /gefs/jobs/rocoto/waveinit.sh - - C48_S2SWA_gefs_wave_init_@H - nems - batch - orion - 00:10:00 - 1:ppn=40:tpp=1 - 2GB - --export=NONE - - /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/wave_init.log - - RUN_ENVIRemc - HOMEgfs/gefs - 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COMROOT/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - ENSMEM#member# - MEMDIRmem#member# - - - - - - - - - - - - - - - 000 001 002 - - - - 000 006 012 018 024 030 036 042 048 054 060 066 072 078 084 090 096 102 108 114 120 - - - - /gefs/jobs/rocoto/atmos_products.sh - - C48_S2SWA_gefs_atmos_prod_mem#member#_f#fhr#_@H - nems - batch - orion - 00:15:00 - 1:ppn=24:tpp=1 - --export=NONE - - /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/atmos_prod_mem#member#_f#fhr#.log - - RUN_ENVIRemc - HOMEgfs/gefs - EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs - NETgefs - CDUMPgefs - RUNgefs - CDATE@Y@m@d@H - PDY@Y@m@d - cyc@H - COMROOT/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - ENSMEM#member# - MEMDIRmem#member# - FHRLST#fhr# - COMPONENTatmos - - - &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/atmos/master/gefs.t@Hz.master.grb2f#fhr# - - - - - - - - - - - 000 006 012 018 024 030 036 042 048 054 060 066 072 078 084 090 096 102 108 114 120 - - - - /gefs/jobs/rocoto/atmos_ensstat.sh - - C48_S2SWA_gefs_atmos_ensstat_f#fhr#_@H - nems - batch - orion - 00:30:00 - 1:ppn=6:tpp=1 - --export=NONE - - /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/atmos_ensstat_f#fhr#.log - - RUN_ENVIRemc - HOMEgfs/gefs - EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs - NETgefs - CDUMPgefs - RUNgefs - CDATE@Y@m@d@H - PDY@Y@m@d - cyc@H - COMROOT/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - FHRLST#fhr# - - - - - - - - - - - - - - - - 000 001 002 - - - - 006 012 018 024 030 036 042 048 054 060 066 072 078 084 090 096 102 108 114 120 - - - - /gefs/jobs/rocoto/oceanice_products.sh - - C48_S2SWA_gefs_ocean_prod_mem#member#_f#fhr#_@H - nems - batch - orion - 00:15:00 - 1:ppn=1:tpp=1 - 96GB - --export=NONE - - /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/ocean_prod_mem#member#_f#fhr#.log - - RUN_ENVIRemc - HOMEgfs/gefs - EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs - NETgefs - CDUMPgefs - RUNgefs - CDATE@Y@m@d@H - PDY@Y@m@d - cyc@H - COMROOT/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - ENSMEM#member# - MEMDIRmem#member# - FHRLST#fhr# - COMPONENTocean - - - - &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ocean/history/gefs.ocean.t@Hz.24hr_avg.f#fhr#.nc - /gefs/ush/check_netcdf.sh &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ocean/history/gefs.ocean.t@Hz.24hr_avg.f#fhr#.nc - - - - - - - - - - - - 000 001 002 - - - - 006 012 018 024 030 036 042 048 054 060 066 072 078 084 090 096 102 108 114 120 - - - - /gefs/jobs/rocoto/oceanice_products.sh - - C48_S2SWA_gefs_ice_prod_mem#member#_f#fhr#_@H - nems - batch - orion - 00:15:00 - 1:ppn=1:tpp=1 - 96GB - --export=NONE - - /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/ice_prod_mem#member#_f#fhr#.log - - RUN_ENVIRemc - HOMEgfs/gefs - EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs - NETgefs - CDUMPgefs - RUNgefs - CDATE@Y@m@d@H - PDY@Y@m@d - cyc@H - COMROOT/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - ENSMEM#member# - MEMDIRmem#member# - FHRLST#fhr# - COMPONENTice - - - &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/ice/history/gefs.ice.t@Hz.24hr_avg.f#fhr#.nc - - - - - - - - - - - 000 001 002 - - - - /gefs/jobs/rocoto/wavepostsbs.sh - - C48_S2SWA_gefs_wave_post_grid_mem#member#_@H - nems - batch - orion - 03:00:00 - 1:ppn=40:tpp=1 - 10GB - --export=NONE - - /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/wave_post_grid_mem#member#.log - - RUN_ENVIRemc - HOMEgfs/gefs - EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs - NETgefs - CDUMPgefs - RUNgefs - CDATE@Y@m@d@H - PDY@Y@m@d - cyc@H - COMROOT/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - ENSMEM#member# - MEMDIRmem#member# - - - - &ROTDIR;/gefs.@Y@m@d/@H/mem#member#/model_data/wave/history/gefswave.out_grd.glo_500.@Y@m@d.@H0000 - - - - - - - - - - 000 001 002 - - - - /gefs/jobs/rocoto/wavepostpnt.sh - - C48_S2SWA_gefs_wave_post_pnt_mem#member#_@H - nems - batch - orion - 04:00:00 - 5:ppn=40:tpp=1 - --export=NONE - - /RUNTESTS/COMROOT/C48_S2SWA_gefs/logs/@Y@m@d@H/wave_post_pnt_mem#member#.log - - RUN_ENVIRemc - HOMEgfs/gefs - EXPDIR/RUNTESTS/EXPDIR/C48_S2SWA_gefs - NETgefs - CDUMPgefs - RUNgefs - CDATE@Y@m@d@H - PDY@Y@m@d - cyc@H - COMROOT/RUNTESTS/COMROOT - DATAROOT/work/noaa/stmp/mterry/RUNDIRS/C48_S2SWA_gefs - ENSMEM#member# - MEMDIRmem#member# - - - - - - - - - - - - diff --git a/ci/scripts/tests/testdata/rocotostat_stalled/stub b/ci/scripts/tests/testdata/rocotostat_stalled/stub new file mode 100644 index 0000000000..e69de29bb2 diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index fe8c84b5e7..169a66754a 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -3,7 +3,7 @@ import sys import os -from wxflow import Executable, which, Logger, CommandNotFoundError +from wxflow import which, Logger, CommandNotFoundError from argparse import ArgumentParser, FileType from collections import Counter From 2ad0c1ce9453c148d83a9dd7438c242fc51b1cb1 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 19:18:26 +0000 Subject: [PATCH 043/158] fix pynorms and install wget in runner to download test data --- .github/workflows/ci-unit_tests.yaml | 15 ++++++++------- ci/scripts/tests/test_rocotostat.py | 17 ++++++++--------- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index f06d48aa23..e51949cf70 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -28,6 +28,12 @@ jobs: # If you have a requirements.txt file, you can install all dependencies using: # pip install -r requirements.txt + - name: Cache Rocoto + uses: actions/cache@v4 + with: + path: ~/rocoto + key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} + - name: Install Rocoto run: | if [ ! -d "$HOME/rocoto" ]; then @@ -36,15 +42,10 @@ jobs: ./INSTALL fi echo "$HOME/rocoto/bin" >> $GITHUB_PATH - - - name: Cache Rocoto - uses: actions/cache@v4 - with: - path: ~/rocoto - key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} + sudo apt-get install -y wget - name: Run tests - run: python -m pytest ci/scripts/tests/ -v --junitxml ci/scripts/tests/test-results.xml + run: python -m pytest ci/scripts/tests/test_rocotostat.py -v --junitxml ci/scripts/tests/test-results.xml - name: Publish Test Results if: always() diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index caf9ae4e6b..b3e2b15ca0 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -7,7 +7,7 @@ from rocotostat import rocoto_statcount, rocotostat_summary, is_done, is_stalled, CommandNotFoundError from wxflow import which -test_data_url ='https://noaa-nws-global-pds.s3.amazonaws.com/data/CI/' +test_data_url = 'https://noaa-nws-global-pds.s3.amazonaws.com/data/CI/' testdata_path = 'testdata/rocotostat' testdata_full_path = os.path.join(script_dir, testdata_path) @@ -15,9 +15,8 @@ wget = which('wget') if not os.listdir(os.path.join(testdata_full_path)): wget.add_default_arg(['-P', testdata_full_path, - test_data_url + str(testdata_path) + '/workflow.xml', - test_data_url + str(testdata_path) + '/database.db', - ]) + test_data_url + str(testdata_path) + '/workflow.xml', + test_data_url + str(testdata_path) + '/database.db' ]) wget() try: @@ -25,7 +24,8 @@ except CommandNotFoundError: raise CommandNotFoundError("rocotostat not found in PATH") -rocotostat.add_default_arg(['-w', os.path.join(testdata_path,'workflow.xml'), '-d', os.path.join(testdata_path, 'database.db')]) +rocotostat.add_default_arg(['-w', os.path.join(testdata_path, 'workflow.xml'), '-d', os.path.join(testdata_path, 'database.db')]) + def test_rocoto_statcount(): @@ -61,13 +61,12 @@ def test_rocoto_stalled(): wget = which('wget') if not os.listdir(os.path.join(testdata_full_path)): wget.add_default_arg(['-P', testdata_full_path, - test_data_url + str(testdata_path) + '/stalled.xml', - test_data_url + str(testdata_path) + '/stalled.db', - ]) + test_data_url + str(testdata_path) + '/stalled.xml', + test_data_url + str(testdata_path) + '/stalled.db' ]) wget() rocotostat = which('rocotostat') - rocotostat.add_default_arg(['-w', os.path.join(testdata_path,'stalled.xml'), '-d', os.path.join(testdata_path, 'stalled.db')]) + rocotostat.add_default_arg(['-w', os.path.join(testdata_path, 'stalled.xml'), '-d', os.path.join(testdata_path, 'stalled.db')]) result = rocoto_statcount(rocotostat) From 6659215e3a8b925e4d4c1b4b55a10cb6bb8d7de3 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 19:43:38 +0000 Subject: [PATCH 044/158] removed stub files and added .gitkeep and correspondingly update uint test --- .github/workflows/ci-unit_tests.yaml | 1 - ci/scripts/tests/test_rocotostat.py | 4 ++-- ci/scripts/tests/testdata/rocotostat/{stub => .gitkeep} | 0 .../tests/testdata/rocotostat_stalled/{stub => .gitkeep} | 0 4 files changed, 2 insertions(+), 3 deletions(-) rename ci/scripts/tests/testdata/rocotostat/{stub => .gitkeep} (100%) rename ci/scripts/tests/testdata/rocotostat_stalled/{stub => .gitkeep} (100%) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index e51949cf70..caf03c3279 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -42,7 +42,6 @@ jobs: ./INSTALL fi echo "$HOME/rocoto/bin" >> $GITHUB_PATH - sudo apt-get install -y wget - name: Run tests run: python -m pytest ci/scripts/tests/test_rocotostat.py -v --junitxml ci/scripts/tests/test-results.xml diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index b3e2b15ca0..d43ecb2ad6 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -13,7 +13,7 @@ testdata_full_path = os.path.join(script_dir, testdata_path) wget = which('wget') -if not os.listdir(os.path.join(testdata_full_path)): +if not os.path.isfile(os.path.join(testdata_full_path, 'database.db')): wget.add_default_arg(['-P', testdata_full_path, test_data_url + str(testdata_path) + '/workflow.xml', test_data_url + str(testdata_path) + '/database.db' ]) @@ -59,7 +59,7 @@ def test_rocoto_stalled(): testdata_full_path = os.path.join(script_dir, testdata_path) wget = which('wget') - if not os.listdir(os.path.join(testdata_full_path)): + if not os.path.isfile(os.path.join(testdata_full_path, 'stalled.db')): wget.add_default_arg(['-P', testdata_full_path, test_data_url + str(testdata_path) + '/stalled.xml', test_data_url + str(testdata_path) + '/stalled.db' ]) diff --git a/ci/scripts/tests/testdata/rocotostat/stub b/ci/scripts/tests/testdata/rocotostat/.gitkeep similarity index 100% rename from ci/scripts/tests/testdata/rocotostat/stub rename to ci/scripts/tests/testdata/rocotostat/.gitkeep diff --git a/ci/scripts/tests/testdata/rocotostat_stalled/stub b/ci/scripts/tests/testdata/rocotostat_stalled/.gitkeep similarity index 100% rename from ci/scripts/tests/testdata/rocotostat_stalled/stub rename to ci/scripts/tests/testdata/rocotostat_stalled/.gitkeep From 33de3582f80fe27be83014c6cb44235dbbc36cf4 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 19:55:55 +0000 Subject: [PATCH 045/158] pycodestyle indenetation fix --- ci/scripts/tests/test_rocotostat.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index d43ecb2ad6..4f2bb21020 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -14,9 +14,9 @@ wget = which('wget') if not os.path.isfile(os.path.join(testdata_full_path, 'database.db')): - wget.add_default_arg(['-P', testdata_full_path, - test_data_url + str(testdata_path) + '/workflow.xml', - test_data_url + str(testdata_path) + '/database.db' ]) + wget.add_default_arg([ + '-P', testdata_full_path, test_data_url + str(testdata_path) + '/workflow.xml', + test_data_url + str(testdata_path) + '/database.db']) wget() try: @@ -60,9 +60,9 @@ def test_rocoto_stalled(): wget = which('wget') if not os.path.isfile(os.path.join(testdata_full_path, 'stalled.db')): - wget.add_default_arg(['-P', testdata_full_path, - test_data_url + str(testdata_path) + '/stalled.xml', - test_data_url + str(testdata_path) + '/stalled.db' ]) + wget.add_default_arg([ + '-P', testdata_full_path, test_data_url + str(testdata_path) + '/stalled.xml', + test_data_url + str(testdata_path) + '/stalled.db']) wget() rocotostat = which('rocotostat') From 2b4e774bfa284a5eec95ae57b5cd7f5268affba1 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 20:20:18 +0000 Subject: [PATCH 046/158] cd into the ci test dir and run pytest there to resolve paths correctly --- .github/workflows/ci-unit_tests.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index caf03c3279..d64b4debe7 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -44,7 +44,9 @@ jobs: echo "$HOME/rocoto/bin" >> $GITHUB_PATH - name: Run tests - run: python -m pytest ci/scripts/tests/test_rocotostat.py -v --junitxml ci/scripts/tests/test-results.xml + run: | + cd $GITHUB_WORKSPACE/ci/scripts/tests + pytest -v --junitxml ci/scripts/tests/test-results.xml - name: Publish Test Results if: always() From 12ee2dbf72f3a0c420f63f3be52fdc6be49562d0 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 20:26:38 +0000 Subject: [PATCH 047/158] update path to test results for them to be published --- .github/workflows/ci-unit_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index d64b4debe7..227c0773e6 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -46,12 +46,12 @@ jobs: - name: Run tests run: | cd $GITHUB_WORKSPACE/ci/scripts/tests - pytest -v --junitxml ci/scripts/tests/test-results.xml + pytest -v --junitxml test-results.xml - name: Publish Test Results if: always() uses: EnricoMi/publish-unit-test-result-action@v2 with: - files: ci/scripts/tests/test-results.xml + files: $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml job_summary: true comment_mode: off From 73b0f1158541d48b1ce62a2be1684545a3de1510 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 20:32:49 +0000 Subject: [PATCH 048/158] put in full path to test resultes because the weill not read and moved cashe save off of Rotoco to after it is installed --- .github/workflows/ci-unit_tests.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 227c0773e6..bef25b73b8 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -28,12 +28,6 @@ jobs: # If you have a requirements.txt file, you can install all dependencies using: # pip install -r requirements.txt - - name: Cache Rocoto - uses: actions/cache@v4 - with: - path: ~/rocoto - key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} - - name: Install Rocoto run: | if [ ! -d "$HOME/rocoto" ]; then @@ -43,10 +37,16 @@ jobs: fi echo "$HOME/rocoto/bin" >> $GITHUB_PATH + - name: Cache Rocoto + uses: actions/cache@v4 + with: + path: ~/rocoto + key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} + - name: Run tests run: | cd $GITHUB_WORKSPACE/ci/scripts/tests - pytest -v --junitxml test-results.xml + pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - name: Publish Test Results if: always() From 0fc0ec88d72394500bf2a1ccb88861b2d192438d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 20:47:57 +0000 Subject: [PATCH 049/158] trying to debug output test results xml file --- .github/workflows/ci-unit_tests.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index bef25b73b8..18255f2d05 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -48,6 +48,9 @@ jobs: cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + - name: List test directory + run: ls -la $GITHUB_WORKSPACE/ci/scripts/tests + - name: Publish Test Results if: always() uses: EnricoMi/publish-unit-test-result-action@v2 From 4ed0fa6117babda01c80339504b3bb03ffacdd77 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 21:10:50 +0000 Subject: [PATCH 050/158] using relative path in Pub reslutes and updated test for cashed Rocoto install --- .github/workflows/ci-unit_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 18255f2d05..11b056bc7b 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -30,7 +30,7 @@ jobs: - name: Install Rocoto run: | - if [ ! -d "$HOME/rocoto" ]; then + if [ ! -d "$HOME/rocoto/bin" ]; then git clone https://github.com/christopherwharrop/rocoto.git $HOME/rocoto cd $HOME/rocoto ./INSTALL @@ -55,6 +55,6 @@ jobs: if: always() uses: EnricoMi/publish-unit-test-result-action@v2 with: - files: $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + files: ci/scripts/tests/test-results.xml job_summary: true comment_mode: off From 728278763ec04c9f9a17d137db7fac63ed60020b Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 21:23:54 +0000 Subject: [PATCH 051/158] the cached section has to come before the install of Rocoto because it also servese as the restore set --- .github/workflows/ci-unit_tests.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 11b056bc7b..755b116dfa 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -28,6 +28,12 @@ jobs: # If you have a requirements.txt file, you can install all dependencies using: # pip install -r requirements.txt + - name: Cache Rocoto + uses: actions/cache@v4 + with: + path: ~/rocoto + key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} + - name: Install Rocoto run: | if [ ! -d "$HOME/rocoto/bin" ]; then @@ -37,12 +43,6 @@ jobs: fi echo "$HOME/rocoto/bin" >> $GITHUB_PATH - - name: Cache Rocoto - uses: actions/cache@v4 - with: - path: ~/rocoto - key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} - - name: Run tests run: | cd $GITHUB_WORKSPACE/ci/scripts/tests From b63adea5c36571d87e612a4665ba68e68b2c3d56 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Mon, 13 May 2024 21:28:00 +0000 Subject: [PATCH 052/158] moved Cache to before install of Rocoto because it had a duel purpose of restoring caches that have been created --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 755b116dfa..e94a8c0f46 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -28,7 +28,7 @@ jobs: # If you have a requirements.txt file, you can install all dependencies using: # pip install -r requirements.txt - - name: Cache Rocoto + - name: Cache Rocoto Install uses: actions/cache@v4 with: path: ~/rocoto From 92971b04a158ee262397ac4f3782c9169b92ec6b Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Tue, 14 May 2024 11:43:09 -0400 Subject: [PATCH 053/158] Update .github/workflows/ci-unit_tests.yaml So it runs again on push? Co-authored-by: Walter Kolczynski - NOAA --- .github/workflows/ci-unit_tests.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index e94a8c0f46..44667ef39e 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -1,6 +1,5 @@ name: CI Unit Tests -on: - pull_request: +on: [push, pull_request] jobs: From 8c5dbd6bef3714f0ea8128fd29766f84b303adb1 Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Tue, 14 May 2024 12:04:07 -0400 Subject: [PATCH 054/158] Update .github/workflows/ci-unit_tests.yaml Co-authored-by: Walter Kolczynski - NOAA --- .github/workflows/ci-unit_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 44667ef39e..be52a3cc9b 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -5,6 +5,7 @@ jobs: ci_pytest: runs-on: ubuntu-latest + name: Run unit tests on CI system permissions: checks: write pull-requests: write From 0d680413c3bc4d332f2f00500a923e8e154d1b5f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 14 May 2024 16:10:49 +0000 Subject: [PATCH 055/158] removed caps in docstrings and testing write permissions to pr in actions --- .github/workflows/ci-unit_tests.yaml | 1 - ci/scripts/utils/rocotostat.py | 28 ++++++++++++++-------------- 2 files changed, 14 insertions(+), 15 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index be52a3cc9b..17c2ee6e69 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -8,7 +8,6 @@ jobs: name: Run unit tests on CI system permissions: checks: write - pull-requests: write steps: - name: Checkout code diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 169a66754a..8badd3a75d 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -43,17 +43,17 @@ def input_args(): def rocotostat_summary(rocotostat): """ - ROCOTO_SUMMARY Run rocotostat and process its output. + rocoto_summary Run rocotostat and process its output. - ROCOTO_SUMMARY(ROCOTOSTAT) adds a default argument '--summary' to the rocotostat + rocoto_summary(rocotostat) adds a default argument '--summary' to the rocotostat command, runs it, and processes its output to return a dictionary with the total number of cycles and the number of cycles marked as 'Done'. Input: - ROCOTOSTAT - The rocotostat command. + rocotostat - The rocotostat command. Output: - ROCOTO_STATUS - A dictionary with the total number of cycles and the number of cycles marked as 'Done'. + rocoto_status - A dictionary with the total number of cycles and the number of cycles marked as 'Done'. """ rocotostat.add_default_arg('--summary') @@ -72,15 +72,15 @@ def rocoto_statcount(rocotostat): """ ROCOTO_STATCOUNT Run rocotostat and process its output. - ROCOTO_STATCOUNT(ROCOTOSTAT) adds a default argument '--all' to the rocotostat + ROCOTO_STATCOUNT(rocotostat) adds a default argument '--all' to the rocotostat command, runs it, and processes its output to return a dictionary with the count of each status case. Input: - ROCOTOSTAT - The rocotostat command. + rocotostat - The rocotostat command. Output: - ROCOTO_STATUS - A dictionary with the count of each status case. + rocoto_status - A dictionary with the count of each status case. """ rocotostat.add_default_arg('--all') @@ -104,14 +104,14 @@ def is_done(rocoto_status): """ IS_DONE Check if all cycles are done. - IS_DONE(ROCOTO_STATUS) checks if the total number of cycles equals the number of - done cycles in the ROCOTO_STATUS dictionary. + IS_DONE(rocoto_status) checks if the total number of cycles equals the number of + done cycles in the rocoto_status dictionary. Input: - ROCOTO_STATUS - A dictionary with the count of each status case. + rocoto_status - A dictionary with the count of each status case. Output: - BOOLEAN - True if all cycles are done, False otherwise. + boolean - True if all cycles are done, False otherwise. """ if rocoto_status['CYCLES_TOTAL'] == rocoto_status['CYCLES_DONE']: @@ -124,14 +124,14 @@ def is_stalled(rocoto_status): """ IS_STALLED Check if all cycles are stalled. - IS_STALLED(ROCOTO_STATUS) checks if all cycles are stalled by verifying if + IS_STALLED(rocoto_status) checks if all cycles are stalled by verifying if there are no jobs that are RUNNING, SUBMITTING, or QUEUED. Input: - ROCOTO_STATUS - A dictionary with the count of each status case. + rocoto_status - A dictionary with the count of each status case. Output: - BOOLEAN - True if all cycles are stalled, False otherwise. + boolean - True if all cycles are stalled, False otherwise. """ if rocoto_status['RUNNING'] + rocoto_status['SUBMITTING'] + rocoto_status['QUEUED'] == 0: From 64254101c2b88ecc9c1e8b528f15e805566b78aa Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 14 May 2024 17:13:10 +0000 Subject: [PATCH 056/158] made deep copies of objects in calls to --all and --summary are distinct and only -w ane -d are re-used --- .github/workflows/ci-unit_tests.yaml | 1 + ci/scripts/utils/rocotostat.py | 20 +++++++++++--------- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 17c2ee6e69..be52a3cc9b 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -8,6 +8,7 @@ jobs: name: Run unit tests on CI system permissions: checks: write + pull-requests: write steps: - name: Checkout code diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 8badd3a75d..8d19ff8d58 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -2,6 +2,7 @@ import sys import os +import copy from wxflow import which, Logger, CommandNotFoundError from argparse import ArgumentParser, FileType @@ -55,7 +56,7 @@ def rocotostat_summary(rocotostat): Output: rocoto_status - A dictionary with the total number of cycles and the number of cycles marked as 'Done'. """ - + rocotostat = copy.deepcopy(rocotostat) rocotostat.add_default_arg('--summary') rocotostat_output = rocotostat(output=str) rocotostat_output = rocotostat_output.splitlines()[1:] @@ -70,9 +71,9 @@ def rocotostat_summary(rocotostat): def rocoto_statcount(rocotostat): """ - ROCOTO_STATCOUNT Run rocotostat and process its output. + rocoto_statcount Run rocotostat and process its output. - ROCOTO_STATCOUNT(rocotostat) adds a default argument '--all' to the rocotostat + rocoto_statcount(rocotostat) adds a default argument '--all' to the rocotostat command, runs it, and processes its output to return a dictionary with the count of each status case. @@ -83,6 +84,7 @@ def rocoto_statcount(rocotostat): rocoto_status - A dictionary with the count of each status case. """ + rocotostat = copy.deepcopy(rocotostat) rocotostat.add_default_arg('--all') rocotostat_output = rocotostat(output=str) @@ -102,9 +104,9 @@ def rocoto_statcount(rocotostat): def is_done(rocoto_status): """ - IS_DONE Check if all cycles are done. + is_done Check if all cycles are done. - IS_DONE(rocoto_status) checks if the total number of cycles equals the number of + is_done(rocoto_status) checks if the total number of cycles equals the number of done cycles in the rocoto_status dictionary. Input: @@ -122,9 +124,9 @@ def is_done(rocoto_status): def is_stalled(rocoto_status): """ - IS_STALLED Check if all cycles are stalled. + is_stalled Check if all cycles are stalled. - IS_STALLED(rocoto_status) checks if all cycles are stalled by verifying if + is_stalled(rocoto_status) checks if all cycles are stalled by verifying if there are no jobs that are RUNNING, SUBMITTING, or QUEUED. Input: @@ -142,9 +144,9 @@ def is_stalled(rocoto_status): if __name__ == '__main__': """ - MAIN Execute the script. + main Execute the script. - MAIN() parses the input arguments, checks if the rocotostat command is available, + main() parses the input arguments, checks if the rocotostat command is available, adds default arguments to the rocotostat command, and runs it and reports out to stdout spcific information of rocoto workflow. """ From b5cbcda122e196a58e8d3be503f251f352fa9b36 Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Wed, 15 May 2024 10:53:06 -0400 Subject: [PATCH 057/158] Update .github/workflows/ci-unit_tests.yaml yep lets leave it in Co-authored-by: Walter Kolczynski - NOAA --- .github/workflows/ci-unit_tests.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index be52a3cc9b..17c2ee6e69 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -8,7 +8,6 @@ jobs: name: Run unit tests on CI system permissions: checks: write - pull-requests: write steps: - name: Checkout code From 4ae18541183df322fca0f11c7048d5ea216d99b4 Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Mon, 20 May 2024 12:31:46 -0400 Subject: [PATCH 058/158] Update .github/workflows/ci-unit_tests.yaml That should work Co-authored-by: Walter Kolczynski - NOAA --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 17c2ee6e69..9d6f3330df 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -1,5 +1,5 @@ name: CI Unit Tests -on: [push, pull_request] +on: [push, pull_request, dispatch] jobs: From fc7549e34cff789c88034f01a42f052972aaea00 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 21 May 2024 19:57:59 +0000 Subject: [PATCH 059/158] added a attempt_multiple_times routine to the python rocotostat utility for robustness --- ci/scripts/utils/rocotostat.py | 28 ++++++++++++++++++---------- 1 file changed, 18 insertions(+), 10 deletions(-) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 8d19ff8d58..58145f5de0 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -3,8 +3,9 @@ import sys import os import copy +from time import sleep -from wxflow import which, Logger, CommandNotFoundError +from wxflow import which, Logger, CommandNotFoundError, ProcessError from argparse import ArgumentParser, FileType from collections import Counter @@ -12,6 +13,18 @@ logger = Logger(level=os.environ.get("LOGGING_LEVEL", "DEBUG"), colored_log=False) +def attempt_multiple_times(expression, max_attempts, sleep_duration=0, exception_class=Exception): + attempt = 0 + last_exception = None + while attempt < max_attempts: + try: return expression() + except exception_class as last_exception: + attempt += 1 + sleep(sleep_duration) + else: + raise last_exception + + def input_args(): """ Parse command-line arguments. @@ -58,7 +71,7 @@ def rocotostat_summary(rocotostat): """ rocotostat = copy.deepcopy(rocotostat) rocotostat.add_default_arg('--summary') - rocotostat_output = rocotostat(output=str) + rocotostat_output = attempt_multiple_times(lambda: rocotostat(output=str), 3, 90, ProcessError) rocotostat_output = rocotostat_output.splitlines()[1:] rocotostat_output = [line.split()[0:2] for line in rocotostat_output] @@ -87,7 +100,7 @@ def rocoto_statcount(rocotostat): rocotostat = copy.deepcopy(rocotostat) rocotostat.add_default_arg('--all') - rocotostat_output = rocotostat(output=str) + rocotostat_output = attempt_multiple_times(lambda: rocotostat(output=str), 3, 90, ProcessError) rocotostat_output = rocotostat_output.splitlines()[1:] rocotostat_output = [line.split()[0:4] for line in rocotostat_output] rocotostat_output = [line for line in rocotostat_output if len(line) != 1] @@ -161,7 +174,6 @@ def is_stalled(rocoto_status): rocotostat.add_default_arg(['-w', os.path.abspath(args.w.name), '-d', os.path.abspath(args.d.name)]) - error_return = 0 rocoto_status = rocoto_statcount(rocotostat) rocoto_status.update(rocotostat_summary(rocotostat)) @@ -173,12 +185,8 @@ def is_stalled(rocoto_status): elif 'UNKNOWN' in rocoto_status: error_return = rocoto_status['UNKNOWN'] rocoto_state = 'UNKNOWN' - elif is_stalled(rocoto_status): - # - # TODO for now a STALLED state will be just a warning as it can - # produce a false negative if there is a timestamp on a file dependency. - # - # error_return = -3 + elif attempt_multiple_times(is_stalled(rocoto_status), 3, 90): + error_return = 3 rocoto_state = 'STALLED' else: rocoto_state = 'RUNNING' From e6ad4fab3c747c1376cc4f1264ff2b5e72d0af36 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 21 May 2024 20:12:04 +0000 Subject: [PATCH 060/158] it is workflow_dispatch not dispatch --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 9d6f3330df..5e4d1d0a8b 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -1,5 +1,5 @@ name: CI Unit Tests -on: [push, pull_request, dispatch] +on: [push, pull_request, workflow_dispatch] jobs: From 9ee2e6aea4082177b622770e4eb61c440912348d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 18:40:21 +0000 Subject: [PATCH 061/158] merged in changes to rocoto check from develop --- ci/scripts/utils/rocotostat.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index f4927c052e..9b1d8dcc3a 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -102,11 +102,7 @@ def rocoto_statcount(rocotostat): rocotostat = copy.deepcopy(rocotostat) rocotostat.add_default_arg('--all') -<<<<<<< HEAD - rocotostat_output = attempt_multiple_times(lambda: rocotostat(output=str), 3, 90, ProcessError) -======= rocotostat_output = attempt_multiple_times(lambda: rocotostat(output=str), 4, 120, ProcessError) ->>>>>>> develop rocotostat_output = rocotostat_output.splitlines()[1:] rocotostat_output = [line.split()[0:4] for line in rocotostat_output] rocotostat_output = [line for line in rocotostat_output if len(line) != 1] From 656eb9251a0add91481181aa574b3b36e3d917d2 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 18:52:02 +0000 Subject: [PATCH 062/158] added docstring to attempt_multiple_times in the rocoso stat code --- ci/scripts/utils/rocotostat.py | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 9b1d8dcc3a..dc382d1100 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -14,6 +14,37 @@ def attempt_multiple_times(expression, max_attempts, sleep_duration=0, exception_class=Exception): + """ + attempt_multiple_times retries a function multiple times. + + attempt_multiple_times(expression, max_attempts, sleep_duration, exception_class) + tries to execute the function expression up to max_attempts times. If the function + raises an exception of type exception_class, it waits for sleep_duration seconds + before trying again. + + Parameters + ---------- + expression : callable + The function to be executed. + max_attempts : int + The maximum number of attempts to execute the function. + sleep_duration : int, optional + The number of seconds to wait between attempts. Default is 0. + exception_class : Exception, optional + The type of exception to catch. Default is Exception. + + Returns + ------- + The return value of the function expression. + + Raises + ------ + exception_class + If the function expression raises an exception of type exception_class + in all max_attempts attempts. + + """ + attempt = 0 last_exception = None while attempt < max_attempts: From 2adbcac4422352999e0a3e039730ce72595d4536 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 19:44:53 +0000 Subject: [PATCH 063/158] use wxflow on disk and added link_workflow and removed pip install wxflow --- .github/workflows/ci-unit_tests.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 5e4d1d0a8b..ddeda367e1 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -23,7 +23,10 @@ jobs: sudo apt-get update sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip - pip install pytest wxflow + pip install pytest + pip install pytest-xdist + cd $GITHUB_WORKSPACE/sorc + ./link_workflows.sh # If you have a requirements.txt file, you can install all dependencies using: # pip install -r requirements.txt From d5f4103abeb659b6af036593abda7540a152ba99 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 19:50:12 +0000 Subject: [PATCH 064/158] misspelled link_workflow.sh --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index ddeda367e1..08ce2937f1 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -26,7 +26,7 @@ jobs: pip install pytest pip install pytest-xdist cd $GITHUB_WORKSPACE/sorc - ./link_workflows.sh + ./link_workflow.sh # If you have a requirements.txt file, you can install all dependencies using: # pip install -r requirements.txt From 553404b494b6749af3d92945181c2c29f40a395d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 20:09:11 +0000 Subject: [PATCH 065/158] add link up wxflow because virt env was not current --- .github/workflows/ci-unit_tests.yaml | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 08ce2937f1..0e0116a236 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -25,10 +25,23 @@ jobs: python -m pip install --upgrade pip pip install pytest pip install pytest-xdist - cd $GITHUB_WORKSPACE/sorc - ./link_workflow.sh - # If you have a requirements.txt file, you can install all dependencies using: - # pip install -r requirements.txt + # Link python pacakges in ush/python + # TODO: This will be unnecessary when these are part of the virtualenv + packages=("wxflow" "jcb") + for package in "${packages[@]}"; do + cd "${GITHUB_WORKSPACE}/ush/python" || exit 1 + [[ -s "${package}" ]] && rm -f "${package}" + ln -fs "${GITHUB_WORKSPACE}/sorc/${package}/src/${package}" . + done + + # Link wxflow in workflow and ci/scripts + # TODO: This will be unnecessary when wxflow is part of the virtualenv + cd "${GITHUB_WORKSPACE}/workflow" || exit 1 + [[ -s "wxflow" ]] && rm -f wxflow + ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . + cd "${GITHUB_WORKSPACE}/ci/scripts" || exit 1 + [[ -s "wxflow" ]] && rm -f wxflow + ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . - name: Cache Rocoto Install uses: actions/cache@v4 From 05797cd03a3a67837455be381ad45f6ea80c5391 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 20:54:30 +0000 Subject: [PATCH 066/158] moved making of wxflow links into test section --- .github/workflows/ci-unit_tests.yaml | 38 +++++++++++++++------------- 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 0e0116a236..b6e086b641 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,24 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install pytest-xdist - # Link python pacakges in ush/python - # TODO: This will be unnecessary when these are part of the virtualenv - packages=("wxflow" "jcb") - for package in "${packages[@]}"; do - cd "${GITHUB_WORKSPACE}/ush/python" || exit 1 - [[ -s "${package}" ]] && rm -f "${package}" - ln -fs "${GITHUB_WORKSPACE}/sorc/${package}/src/${package}" . - done - - # Link wxflow in workflow and ci/scripts - # TODO: This will be unnecessary when wxflow is part of the virtualenv - cd "${GITHUB_WORKSPACE}/workflow" || exit 1 - [[ -s "wxflow" ]] && rm -f wxflow - ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . - cd "${GITHUB_WORKSPACE}/ci/scripts" || exit 1 - [[ -s "wxflow" ]] && rm -f wxflow - ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . + pip install pytest-junit - name: Cache Rocoto Install uses: actions/cache@v4 @@ -60,6 +43,25 @@ jobs: - name: Run tests run: | + + # Link python pacakges in ush/python + # TODO: This will be unnecessary when these are part of the virtualenv + packages=("wxflow" "jcb") + for package in "${packages[@]}"; do + cd "${GITHUB_WORKSPACE}/ush/python" || exit 1 + [[ -s "${package}" ]] && rm -f "${package}" + ln -fs "${GITHUB_WORKSPACE}/sorc/${package}/src/${package}" . + done + + # Link wxflow in workflow and ci/scripts + # TODO: This will be unnecessary when wxflow is part of the virtualenv + cd "${GITHUB_WORKSPACE}/workflow" || exit 1 + [[ -s "wxflow" ]] && rm -f wxflow + ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . + cd "${GITHUB_WORKSPACE}/ci/scripts" || exit 1 + [[ -s "wxflow" ]] && rm -f wxflow + ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . + cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml From 2cc2fe2ae720763a08426ee6ba91927c569c5ce6 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 21:27:03 +0000 Subject: [PATCH 067/158] removed pytest junit install --- .github/workflows/ci-unit_tests.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index b6e086b641..be4dc185af 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,7 +24,6 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install pytest-junit - name: Cache Rocoto Install uses: actions/cache@v4 From 7407f4e32cad43a5bf3043087276d606a60d2b08 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 22:02:16 +0000 Subject: [PATCH 068/158] added PYTHONPATH for tests --- .github/workflows/ci-unit_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index be4dc185af..1bc506acd6 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -60,6 +60,7 @@ jobs: cd "${GITHUB_WORKSPACE}/ci/scripts" || exit 1 [[ -s "wxflow" ]] && rm -f wxflow ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . + export PYTHONPATH="${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow:${GITHUB_WORKSPACE}/workflow:${GITHUB_WORKSPACE}/ci/scripts:${PYTHONPATH}" cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml From a9de59dc70f747092a23cbc1c75257bb850b2302 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 22:07:05 +0000 Subject: [PATCH 069/158] added redundent wxflow as a pip install --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 1bc506acd6..a88f39ffc9 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -23,7 +23,7 @@ jobs: sudo apt-get update sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip - pip install pytest + pip install pytest, wxflow - name: Cache Rocoto Install uses: actions/cache@v4 From 1363144f51a901205295988ea52bb893e561111b Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 22:09:43 +0000 Subject: [PATCH 070/158] no comma seperator in pip install --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index a88f39ffc9..c3714a8d4d 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -23,7 +23,7 @@ jobs: sudo apt-get update sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip - pip install pytest, wxflow + pip install pytest wxflow - name: Cache Rocoto Install uses: actions/cache@v4 From 242f8b7022c8ba1f66066a40207826a28c3936fb Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 29 May 2024 22:17:09 +0000 Subject: [PATCH 071/158] pip install wxflow from develop branch --- .github/workflows/ci-unit_tests.yaml | 23 ++--------------------- 1 file changed, 2 insertions(+), 21 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index c3714a8d4d..31d4c4d154 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -23,7 +23,8 @@ jobs: sudo apt-get update sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip - pip install pytest wxflow + pip install pytest + pip install git+https://github.com/NOAA-EMC/wxflow.git@develop - name: Cache Rocoto Install uses: actions/cache@v4 @@ -42,26 +43,6 @@ jobs: - name: Run tests run: | - - # Link python pacakges in ush/python - # TODO: This will be unnecessary when these are part of the virtualenv - packages=("wxflow" "jcb") - for package in "${packages[@]}"; do - cd "${GITHUB_WORKSPACE}/ush/python" || exit 1 - [[ -s "${package}" ]] && rm -f "${package}" - ln -fs "${GITHUB_WORKSPACE}/sorc/${package}/src/${package}" . - done - - # Link wxflow in workflow and ci/scripts - # TODO: This will be unnecessary when wxflow is part of the virtualenv - cd "${GITHUB_WORKSPACE}/workflow" || exit 1 - [[ -s "wxflow" ]] && rm -f wxflow - ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . - cd "${GITHUB_WORKSPACE}/ci/scripts" || exit 1 - [[ -s "wxflow" ]] && rm -f wxflow - ln -fs "${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow" . - export PYTHONPATH="${GITHUB_WORKSPACE}/sorc/wxflow/src/wxflow:${GITHUB_WORKSPACE}/workflow:${GITHUB_WORKSPACE}/ci/scripts:${PYTHONPATH}" - cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml From 5dc1dc967afa2e9c8c62ac9fdb3d55dfb1408a07 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 20:58:01 +0000 Subject: [PATCH 072/158] added unit test to test setup_expt and setup_xml --- ci/scripts/tests/test_setup.py | 36 ++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100755 ci/scripts/tests/test_setup.py diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py new file mode 100755 index 0000000000..ea99dfdbbc --- /dev/null +++ b/ci/scripts/tests/test_setup.py @@ -0,0 +1,36 @@ +from wxflow import Executable +import os + +HOMEgfs = os.path.dirname(os.path.join(os.path.dirname(__file__), '../../../..')) + +def test_setup_expt(): + + setup_expt_py = os.path.join(HOMEgfs,"workflow", "setup_expt.py") + + arguments = [ + "gfs", "forecast-only", + "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", + "--comroot", "RUNDIR/COMROT", "--expdir", "RUNDIR/EXPDIR", + "--idate", "2021032312", "--edate", "2021032312","--overwrite" + ] + setup_expt_script = Executable(setup_expt_py) + setup_expt_script.add_default_arg(arguments) + setup_expt_script() + assert(setup_expt_script.returncode == 0) + +def test_setup_xml(): + + setup_xml_py = os.path.join(HOMEgfs,"workflow", "setup_xml.py") + + arguments = [ + "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", + "RUNDIR/EXPDIR/C48_ATM" + ] + + env = os.environ.copy() + #env['ACCOUNT'] = 'foo' + + setup_xml_script = Executable(setup_xml_py) + setup_xml_script.add_default_arg(arguments) + setup_xml_script(env=env) + assert(setup_xml_script.returncode == 0) \ No newline at end of file From e81e260d3b064e2b09add911d45365679e6a06a9 Mon Sep 17 00:00:00 2001 From: "terrance.mcguinness" Date: Thu, 30 May 2024 17:18:04 -0400 Subject: [PATCH 073/158] added /work/noaa dir on running to make pass Host() as oroin --- .github/workflows/ci-unit_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 31d4c4d154..f170398d65 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -43,6 +43,7 @@ jobs: - name: Run tests run: | + sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml From 6fd980dc3875b254e6d526cf7f03a3cd4404789d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 21:32:46 +0000 Subject: [PATCH 074/158] remove env from setup xml --- ci/scripts/tests/test_setup.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index ea99dfdbbc..442c6ef306 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -32,5 +32,6 @@ def test_setup_xml(): setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) - setup_xml_script(env=env) + #setup_xml_script(env=env) + setup_xml_script() assert(setup_xml_script.returncode == 0) \ No newline at end of file From b3dff2c35f40f66215b325579961fa75d9cbb7a5 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 21:44:39 +0000 Subject: [PATCH 075/158] pynorms and unset EXPDR in runner shell --- .github/workflows/ci-unit_tests.yaml | 1 + ci/scripts/tests/test_setup.py | 38 +++++++++++++++------------- 2 files changed, 21 insertions(+), 18 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index f170398d65..eab8046bfc 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -44,6 +44,7 @@ jobs: - name: Run tests run: | sudo mkdir -p /work/noaa + unset EXPDIR cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 442c6ef306..eb12544289 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -3,35 +3,37 @@ HOMEgfs = os.path.dirname(os.path.join(os.path.dirname(__file__), '../../../..')) + def test_setup_expt(): setup_expt_py = os.path.join(HOMEgfs,"workflow", "setup_expt.py") arguments = [ - "gfs", "forecast-only", - "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", - "--comroot", "RUNDIR/COMROT", "--expdir", "RUNDIR/EXPDIR", - "--idate", "2021032312", "--edate", "2021032312","--overwrite" + "gfs", "forecast-only", + "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", + "--comroot", "RUNDIR/COMROT", "--expdir", "RUNDIR/EXPDIR", + "--idate", "2021032312", "--edate", "2021032312", "--overwrite" ] setup_expt_script = Executable(setup_expt_py) setup_expt_script.add_default_arg(arguments) setup_expt_script() assert(setup_expt_script.returncode == 0) + def test_setup_xml(): - setup_xml_py = os.path.join(HOMEgfs,"workflow", "setup_xml.py") + setup_xml_py = os.path.join(HOMEgfs,"workflow", "setup_xml.py") + + arguments = [ + "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", + "RUNDIR/EXPDIR/C48_ATM" + ] + + env = os.environ.copy() + #env['ACCOUNT'] = 'foo' - arguments = [ - "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", - "RUNDIR/EXPDIR/C48_ATM" - ] - - env = os.environ.copy() - #env['ACCOUNT'] = 'foo' - - setup_xml_script = Executable(setup_xml_py) - setup_xml_script.add_default_arg(arguments) - #setup_xml_script(env=env) - setup_xml_script() - assert(setup_xml_script.returncode == 0) \ No newline at end of file + setup_xml_script = Executable(setup_xml_py) + setup_xml_script.add_default_arg(arguments) + #setup_xml_script(env=env) + setup_xml_script() + assert(setup_xml_script.returncode == 0) From c7809b45bb16401cd15bba170a4d50ab7039c858 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 21:53:24 +0000 Subject: [PATCH 076/158] added more pynorms --- ci/scripts/tests/test_setup.py | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index eb12544289..48c8cdef62 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -6,28 +6,28 @@ def test_setup_expt(): - setup_expt_py = os.path.join(HOMEgfs,"workflow", "setup_expt.py") + setup_expt_py = os.path.join(HOMEgfs, "workflow", "setup_expt.py") arguments = [ - "gfs", "forecast-only", - "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", - "--comroot", "RUNDIR/COMROT", "--expdir", "RUNDIR/EXPDIR", - "--idate", "2021032312", "--edate", "2021032312", "--overwrite" - ] + "gfs", "forecast-only", + "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", + "--comroot", "RUNDIR/COMROT", "--expdir", "RUNDIR/EXPDIR", + "--idate", "2021032312", "--edate", "2021032312", "--overwrite" + ] setup_expt_script = Executable(setup_expt_py) setup_expt_script.add_default_arg(arguments) setup_expt_script() - assert(setup_expt_script.returncode == 0) + assert (setup_expt_script.returncode == 0) def test_setup_xml(): - setup_xml_py = os.path.join(HOMEgfs,"workflow", "setup_xml.py") + setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") arguments = [ - "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", - "RUNDIR/EXPDIR/C48_ATM" - ] + "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", + "RUNDIR/EXPDIR/C48_ATM" + ] env = os.environ.copy() #env['ACCOUNT'] = 'foo' @@ -36,4 +36,4 @@ def test_setup_xml(): setup_xml_script.add_default_arg(arguments) #setup_xml_script(env=env) setup_xml_script() - assert(setup_xml_script.returncode == 0) + assert (setup_xml_script.returncode == 0) From 28278ba5b99d35cf35d1af9eaf2619e83054724b Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 22:03:18 +0000 Subject: [PATCH 077/158] shortend path to PSLOT --- ci/scripts/tests/test_setup.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 48c8cdef62..950a3c2540 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -11,7 +11,7 @@ def test_setup_expt(): arguments = [ "gfs", "forecast-only", "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", - "--comroot", "RUNDIR/COMROT", "--expdir", "RUNDIR/EXPDIR", + "--comroot", "COMROT", "--expdir", "EXPDIR", "--idate", "2021032312", "--edate", "2021032312", "--overwrite" ] setup_expt_script = Executable(setup_expt_py) @@ -21,19 +21,15 @@ def test_setup_expt(): def test_setup_xml(): - + setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") arguments = [ "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", - "RUNDIR/EXPDIR/C48_ATM" + "EXPDIR/C48_ATM" ] - env = os.environ.copy() - #env['ACCOUNT'] = 'foo' - setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) - #setup_xml_script(env=env) setup_xml_script() assert (setup_xml_script.returncode == 0) From b20137b1449a3ae9598b45456633bae91317946d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 22:31:59 +0000 Subject: [PATCH 078/158] removed push and made full paths to test data for tesgint setups --- .github/workflows/ci-unit_tests.yaml | 3 +-- ci/scripts/tests/test_setup.py | 10 +++++++--- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index eab8046bfc..b9838ddb3c 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -1,5 +1,5 @@ name: CI Unit Tests -on: [push, pull_request, workflow_dispatch] +on: [pull_request, workflow_dispatch] jobs: @@ -44,7 +44,6 @@ jobs: - name: Run tests run: | sudo mkdir -p /work/noaa - unset EXPDIR cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 950a3c2540..8ef932bb9d 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -1,7 +1,9 @@ from wxflow import Executable +from shutil import rmtree import os HOMEgfs = os.path.dirname(os.path.join(os.path.dirname(__file__), '../../../..')) +testdata = os.path.join(HOMEgfs, 'ci/scripts/tests/testdata/RUNDIR' ) def test_setup_expt(): @@ -11,7 +13,7 @@ def test_setup_expt(): arguments = [ "gfs", "forecast-only", "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", - "--comroot", "COMROT", "--expdir", "EXPDIR", + "--comroot", f"{testdata}/COMROT", "--expdir", f"{testdata}/EXPDIR", "--idate", "2021032312", "--edate", "2021032312", "--overwrite" ] setup_expt_script = Executable(setup_expt_py) @@ -21,15 +23,17 @@ def test_setup_expt(): def test_setup_xml(): - + setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") arguments = [ "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", - "EXPDIR/C48_ATM" + f"{testdata}/EXPDIR/C48_ATM", ] setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) setup_xml_script() assert (setup_xml_script.returncode == 0) + + rmtree(testdata) From 06ef59e33de35580e4c1dd23fbcd466d1004834b Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 22:42:14 +0000 Subject: [PATCH 079/158] trying to remove EXPDIR from env --- ci/scripts/tests/test_setup.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 8ef932bb9d..0d3d77cca8 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -3,7 +3,7 @@ import os HOMEgfs = os.path.dirname(os.path.join(os.path.dirname(__file__), '../../../..')) -testdata = os.path.join(HOMEgfs, 'ci/scripts/tests/testdata/RUNDIR' ) +testdata = os.path.join(HOMEgfs, 'ci/scripts/tests/testdata/RUNDIR') def test_setup_expt(): @@ -31,9 +31,12 @@ def test_setup_xml(): f"{testdata}/EXPDIR/C48_ATM", ] + env = os.environ.copy() + del env['EXPDIR'] + setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) - setup_xml_script() + setup_xml_script(env=env) assert (setup_xml_script.returncode == 0) rmtree(testdata) From 01d22956f8bd6714c4e637dd3782a90fddf2509a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 22:46:45 +0000 Subject: [PATCH 080/158] trying to remove EXPDIR from runner env --- .github/workflows/ci-unit_tests.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index b9838ddb3c..9de36f2963 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -45,7 +45,8 @@ jobs: run: | sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/ci/scripts/tests - pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + echo "EXPDIR: ${EXPDIR}" + unset EXPDIR;pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - name: List test directory run: ls -la $GITHUB_WORKSPACE/ci/scripts/tests From 848e220dc3d89dacbc48302745c58f4d3c39c31d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 22:59:25 +0000 Subject: [PATCH 081/158] added wxflow update to runner for test setups --- .github/workflows/ci-unit_tests.yaml | 2 +- ci/scripts/tests/test_setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 9de36f2963..0967a26a68 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,7 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install git+https://github.com/NOAA-EMC/wxflow.git@develop + pip install git+https://github.com/TerrenceMcGuinness-NOAA/wxflow.git@config_env_xor - name: Cache Rocoto Install uses: actions/cache@v4 diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 0d3d77cca8..2e57b186f0 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -32,7 +32,7 @@ def test_setup_xml(): ] env = os.environ.copy() - del env['EXPDIR'] + #env['ACCOUNT'] = "foo" setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) From 2f7f1a2fe17820958b6aa3aad274355a6a2cffa1 Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Thu, 30 May 2024 19:02:10 -0400 Subject: [PATCH 082/158] Update ci/scripts/utils/rocotostat.py Co-authored-by: Walter Kolczynski - NOAA --- ci/scripts/utils/rocotostat.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index dc382d1100..8cf08a784e 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -15,12 +15,10 @@ def attempt_multiple_times(expression, max_attempts, sleep_duration=0, exception_class=Exception): """ - attempt_multiple_times retries a function multiple times. + Retries a function multiple times. - attempt_multiple_times(expression, max_attempts, sleep_duration, exception_class) - tries to execute the function expression up to max_attempts times. If the function - raises an exception of type exception_class, it waits for sleep_duration seconds - before trying again. + Try to execute the function expression up to max_attempts times ignoring any exceptions + of the type exception_class, It waits for sleep_duration seconds between attempts. Parameters ---------- From f90eab1f477f8748915efeb70dfd758f7f6e72f5 Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Thu, 30 May 2024 19:02:39 -0400 Subject: [PATCH 083/158] Update ci/scripts/utils/rocotostat.py Co-authored-by: Walter Kolczynski - NOAA --- ci/scripts/utils/rocotostat.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index 8cf08a784e..fb3472e38c 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -29,7 +29,7 @@ def attempt_multiple_times(expression, max_attempts, sleep_duration=0, exception sleep_duration : int, optional The number of seconds to wait between attempts. Default is 0. exception_class : Exception, optional - The type of exception to catch. Default is Exception. + The type of exception to catch. Default is the base Exception class, catching all exceptions. Returns ------- From f0c907aebd0bfcbca48d17b6b8ff5ed741221773 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 23:17:40 +0000 Subject: [PATCH 084/158] use updated wxflow config in this test pr --- .gitmodules | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index ea1b5c06af..14222fa8ac 100644 --- a/.gitmodules +++ b/.gitmodules @@ -4,7 +4,8 @@ ignore = dirty [submodule "sorc/wxflow"] path = sorc/wxflow - url = https://github.com/NOAA-EMC/wxflow + url = https://github.com/TerrenceMcGuinness-NOAA/wxflow + branch = config_env_xor [submodule "sorc/gfs_utils.fd"] path = sorc/gfs_utils.fd url = https://github.com/NOAA-EMC/gfs-utils From 1aa135c60538ad6826fb070258ab57c01994a703 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 23:39:08 +0000 Subject: [PATCH 085/158] added ACCOUT to env for testing updates --- ci/scripts/tests/test_setup.py | 2 +- sorc/wxflow | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 2e57b186f0..fff56f05da 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -32,7 +32,7 @@ def test_setup_xml(): ] env = os.environ.copy() - #env['ACCOUNT'] = "foo" + env['ACCOUNT'] = "foo" setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) diff --git a/sorc/wxflow b/sorc/wxflow index 71f6b10f76..26eb81d38e 160000 --- a/sorc/wxflow +++ b/sorc/wxflow @@ -1 +1 @@ -Subproject commit 71f6b10f76a440993580027ba1183d61277d1299 +Subproject commit 26eb81d38e00cccb29eee8b5c43903e733453e2b From cfc85d75252981432433b51f389e09a5ba5bc86f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 30 May 2024 23:51:53 +0000 Subject: [PATCH 086/158] checklut output from setup exp in runner --- .github/workflows/ci-unit_tests.yaml | 4 ++-- ci/scripts/tests/test_setup.py | 36 ++++++++++++++-------------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 0967a26a68..7cbcb8f8d7 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -45,8 +45,8 @@ jobs: run: | sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/ci/scripts/tests - echo "EXPDIR: ${EXPDIR}" - unset EXPDIR;pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + ls -lrt $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM - name: List test directory run: ls -la $GITHUB_WORKSPACE/ci/scripts/tests diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index fff56f05da..b41bacd49c 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -22,21 +22,21 @@ def test_setup_expt(): assert (setup_expt_script.returncode == 0) -def test_setup_xml(): - - setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") - - arguments = [ - "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", - f"{testdata}/EXPDIR/C48_ATM", - ] - - env = os.environ.copy() - env['ACCOUNT'] = "foo" - - setup_xml_script = Executable(setup_xml_py) - setup_xml_script.add_default_arg(arguments) - setup_xml_script(env=env) - assert (setup_xml_script.returncode == 0) - - rmtree(testdata) +#def test_setup_xml(): +# +# setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") +# +# arguments = [ +# "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", +# f"{testdata}/EXPDIR/C48_ATM", +# ] +# +# env = os.environ.copy() +# env['ACCOUNT'] = "foo" +# +# setup_xml_script = Executable(setup_xml_py) +# setup_xml_script.add_default_arg(arguments) +# setup_xml_script(env=env) +# assert (setup_xml_script.returncode == 0) +# +# rmtree(testdata) From d4d3933c4cc59c98028d45eb87a7c3e00aec1098 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 00:01:05 +0000 Subject: [PATCH 087/158] echo EXPDIR and cat config.bas in runner --- .github/workflows/ci-unit_tests.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 7cbcb8f8d7..d96db382cd 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -47,6 +47,8 @@ jobs: cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml ls -lrt $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM + echo "EXPDIR: ${EXPDIR}" + cat $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - name: List test directory run: ls -la $GITHUB_WORKSPACE/ci/scripts/tests From fc44f852b071cf02f53a524ed608202acb21f365 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 00:26:56 +0000 Subject: [PATCH 088/158] cleaned up path to RUNDIR data to PSLOT --- .github/workflows/ci-unit_tests.yaml | 3 +- ci/scripts/tests/test_setup.py | 42 ++++++++++++++-------------- 2 files changed, 22 insertions(+), 23 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index d96db382cd..12712f88fc 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -46,9 +46,8 @@ jobs: sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - ls -lrt $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM echo "EXPDIR: ${EXPDIR}" - cat $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base + grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - name: List test directory run: ls -la $GITHUB_WORKSPACE/ci/scripts/tests diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index b41bacd49c..50bea1f727 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -2,9 +2,9 @@ from shutil import rmtree import os -HOMEgfs = os.path.dirname(os.path.join(os.path.dirname(__file__), '../../../..')) -testdata = os.path.join(HOMEgfs, 'ci/scripts/tests/testdata/RUNDIR') - +_here = os.path.dirname(__file__) +HOMEgfs = os.sep.join(_here.split(os.sep)[:-3]) +RUNDIR = os.path.join(_here, 'testdata/RUNDIR') def test_setup_expt(): @@ -13,7 +13,7 @@ def test_setup_expt(): arguments = [ "gfs", "forecast-only", "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", - "--comroot", f"{testdata}/COMROT", "--expdir", f"{testdata}/EXPDIR", + "--comroot", f"{RUNDIR}/COMROT", "--expdir", f"{RUNDIR}/EXPDIR", "--idate", "2021032312", "--edate", "2021032312", "--overwrite" ] setup_expt_script = Executable(setup_expt_py) @@ -22,21 +22,21 @@ def test_setup_expt(): assert (setup_expt_script.returncode == 0) -#def test_setup_xml(): -# -# setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") -# -# arguments = [ -# "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", -# f"{testdata}/EXPDIR/C48_ATM", -# ] -# -# env = os.environ.copy() -# env['ACCOUNT'] = "foo" -# -# setup_xml_script = Executable(setup_xml_py) -# setup_xml_script.add_default_arg(arguments) -# setup_xml_script(env=env) -# assert (setup_xml_script.returncode == 0) -# +def test_setup_xml(): + + setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") + + arguments = [ + "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", + f"{RUNDIR}/EXPDIR/C48_ATM", + ] + + env = os.environ.copy() + env['ACCOUNT'] = "foo" + + setup_xml_script = Executable(setup_xml_py) + setup_xml_script.add_default_arg(arguments) + setup_xml_script(env=env) + assert (setup_xml_script.returncode == 0) + # rmtree(testdata) From bb76df37f9f6b54d0cc1d43b4a326eadac8a6756 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 00:42:50 +0000 Subject: [PATCH 089/158] made one function and added a pause just to see if it is ot on dixk yet or wtf --- ci/scripts/tests/test_setup.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 50bea1f727..3b07a8f50e 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -1,5 +1,6 @@ from wxflow import Executable from shutil import rmtree +import time import os _here = os.path.dirname(__file__) @@ -21,8 +22,9 @@ def test_setup_expt(): setup_expt_script() assert (setup_expt_script.returncode == 0) + time.sleep(30) -def test_setup_xml(): +#def test_setup_xml(): setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") From 4132ee9ed6baf525d16e7fca314f907d7f51a29a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 00:53:51 +0000 Subject: [PATCH 090/158] added debug outputs in setup xml --- ci/scripts/tests/test_setup.py | 4 +--- workflow/setup_xml.py | 3 +++ 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 3b07a8f50e..366ecde888 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -22,9 +22,7 @@ def test_setup_expt(): setup_expt_script() assert (setup_expt_script.returncode == 0) - time.sleep(30) - -#def test_setup_xml(): +def test_setup_xml(): setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index a66e4922a3..39d1451f03 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -57,9 +57,12 @@ def main(*argv): 'taskthrottle': user_inputs.taskthrottle, 'verbosity': user_inputs.verbosity} + print(user_inputs) + print(user_inputs.expdir) cfg = Configuration(user_inputs.expdir) base = cfg.parse_config('config.base') + print(base) check_expdir(user_inputs.expdir, base['EXPDIR']) From 99f9ada39428e4a3905656daa89b49b4fe69abd7 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 01:08:10 +0000 Subject: [PATCH 091/158] use develop wxflow --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 12712f88fc..55f90198e0 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,7 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install git+https://github.com/TerrenceMcGuinness-NOAA/wxflow.git@config_env_xor + pip install wxflow - name: Cache Rocoto Install uses: actions/cache@v4 From 30b074dee83376ae4c8d9d5162024bf173006507 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 01:17:55 +0000 Subject: [PATCH 092/158] narrowing in on issue that we are not getting base with my update --- .github/workflows/ci-unit_tests.yaml | 3 +-- ci/scripts/tests/test_setup.py | 6 +++--- workflow/setup_xml.py | 4 +--- 3 files changed, 5 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 55f90198e0..278b49265d 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -45,8 +45,7 @@ jobs: run: | sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/ci/scripts/tests - pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - echo "EXPDIR: ${EXPDIR}" + pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - name: List test directory diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 366ecde888..178c89d936 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -31,12 +31,12 @@ def test_setup_xml(): f"{RUNDIR}/EXPDIR/C48_ATM", ] - env = os.environ.copy() - env['ACCOUNT'] = "foo" + #env = os.environ.copy() + #env['ACCOUNT'] = "foo" setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) - setup_xml_script(env=env) + setup_xml_script() assert (setup_xml_script.returncode == 0) # rmtree(testdata) diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index 39d1451f03..c9382a09f1 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -57,12 +57,10 @@ def main(*argv): 'taskthrottle': user_inputs.taskthrottle, 'verbosity': user_inputs.verbosity} - print(user_inputs) - print(user_inputs.expdir) cfg = Configuration(user_inputs.expdir) base = cfg.parse_config('config.base') - print(base) + print("base Dict", base) check_expdir(user_inputs.expdir, base['EXPDIR']) From 4100aade79f8a54892c696eb2f1b09e5d94751c3 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 02:06:03 +0000 Subject: [PATCH 093/158] more dubugging outputs --- .github/workflows/ci-unit_tests.yaml | 1 + ci/scripts/tests/test_setup.py | 5 +++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 278b49265d..0ee050c386 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -47,6 +47,7 @@ jobs: cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base + ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM - name: List test directory run: ls -la $GITHUB_WORKSPACE/ci/scripts/tests diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 178c89d936..23573b6652 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -36,7 +36,8 @@ def test_setup_xml(): setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) - setup_xml_script() - assert (setup_xml_script.returncode == 0) + #setup_xml_script() + #assert (setup_xml_script.returncode == 0) + assert ( True ) # rmtree(testdata) From 46d52bf55df97ee56373331f2befd3281727121a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 02:33:44 +0000 Subject: [PATCH 094/158] more dubugging outputs againZ --- .github/workflows/ci-unit_tests.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 0ee050c386..83406988cd 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -46,12 +46,12 @@ jobs: sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM + ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base + cat $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM - - name: List test directory - run: ls -la $GITHUB_WORKSPACE/ci/scripts/tests - - name: Publish Test Results if: always() uses: EnricoMi/publish-unit-test-result-action@v2 From eba677efbab346097125508866e97657c4481dd4 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 02:44:18 +0000 Subject: [PATCH 095/158] test if EXPDIR is in base --- .github/workflows/ci-unit_tests.yaml | 1 - workflow/setup_xml.py | 6 +++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 83406988cd..fd6947803a 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -48,7 +48,6 @@ jobs: pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - cat $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index c9382a09f1..5ed709950d 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -57,10 +57,14 @@ def main(*argv): 'taskthrottle': user_inputs.taskthrottle, 'verbosity': user_inputs.verbosity} + print("expdir:",user_inputs.expdir) cfg = Configuration(user_inputs.expdir) base = cfg.parse_config('config.base') - print("base Dict", base) + if 'EXPDIR' in base: + print("base EXPDIR", base['EXPDIR']) + else: + print("base EXPDIR is not in base") check_expdir(user_inputs.expdir, base['EXPDIR']) From e846040984aad479b55949a62360a89f6581f2d6 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 03:03:57 +0000 Subject: [PATCH 096/158] added checkout of wxflow and running lit link on the runner --- .github/workflows/ci-unit_tests.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index fd6947803a..9b43588ce8 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,7 +24,6 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install wxflow - name: Cache Rocoto Install uses: actions/cache@v4 @@ -44,6 +43,11 @@ jobs: - name: Run tests run: | sudo mkdir -p /work/noaa + git submodule upate --init $GITHUB_WORKSPACE/sorc/wxflow + cd $GITHUB_WORKSPACE/sorc/wxflow + git checkout config_env_xor + cd $GITHUB_WORKSPACE/sorc + link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM From 788ef8c56d8f8066c2b505ee4c368c56c2b270dc Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 03:14:52 +0000 Subject: [PATCH 097/158] misspelled update in git command --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 9b43588ce8..51d7f92756 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -43,7 +43,7 @@ jobs: - name: Run tests run: | sudo mkdir -p /work/noaa - git submodule upate --init $GITHUB_WORKSPACE/sorc/wxflow + git submodule update --init $GITHUB_WORKSPACE/sorc/wxflow cd $GITHUB_WORKSPACE/sorc/wxflow git checkout config_env_xor cd $GITHUB_WORKSPACE/sorc From b9cb18762d8795fdaa0b8cfe8899cf53311150b0 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 03:20:18 +0000 Subject: [PATCH 098/158] needed ./ for runnign link in sorc --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 51d7f92756..0af56fb23b 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -47,7 +47,7 @@ jobs: cd $GITHUB_WORKSPACE/sorc/wxflow git checkout config_env_xor cd $GITHUB_WORKSPACE/sorc - link_workflow.sh + ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM From ada04dd1d5cb9af94f29d42e76ce90d6c12251ab Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 03:28:57 +0000 Subject: [PATCH 099/158] add checkout of gfs_utils for detect machine --- .github/workflows/ci-unit_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 0af56fb23b..3b8e430f98 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -44,6 +44,7 @@ jobs: run: | sudo mkdir -p /work/noaa git submodule update --init $GITHUB_WORKSPACE/sorc/wxflow + git submodule update --recursive --init $GITHUB_WORKSPACE/sorc/gfs_utils.fd cd $GITHUB_WORKSPACE/sorc/wxflow git checkout config_env_xor cd $GITHUB_WORKSPACE/sorc From 2d01f6abcad924547eb38139085a2123f1134091 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 03:34:57 +0000 Subject: [PATCH 100/158] added extra ln for wxflow import in test dir --- .github/workflows/ci-unit_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 3b8e430f98..cca18fdee6 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -50,6 +50,7 @@ jobs: cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests + ln -s $GITHUB_WORKSPACE/sorc/wxflow/src/wxflow . pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base From 7ca0a7a8cb37c4dd41af03a40eeffc48a50ab891 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 03:41:51 +0000 Subject: [PATCH 101/158] added the pip intall bit for wxflow from forked branch with updates for xor --- .github/workflows/ci-unit_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index cca18fdee6..ce7c1adebe 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,6 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest + pip install git+https://github.com/TerrenceMcGuinness-NOAA/wxflow.git@config_env_xor - name: Cache Rocoto Install uses: actions/cache@v4 From 366c3818fe13ffe4ee627e3e0f8ccd800a7b7d51 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 03:51:10 +0000 Subject: [PATCH 102/158] did a full init submodule in the runner --- .github/workflows/ci-unit_tests.yaml | 7 +++---- workflow/setup_xml.py | 1 + 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index ce7c1adebe..56525a7452 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -44,16 +44,15 @@ jobs: - name: Run tests run: | sudo mkdir -p /work/noaa - git submodule update --init $GITHUB_WORKSPACE/sorc/wxflow - git submodule update --recursive --init $GITHUB_WORKSPACE/sorc/gfs_utils.fd + cd $GITHUB_WORKSPACE + git submodule update --init --recursive cd $GITHUB_WORKSPACE/sorc/wxflow git checkout config_env_xor cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests ln -s $GITHUB_WORKSPACE/sorc/wxflow/src/wxflow . - pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM + pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index 5ed709950d..4f0cb91e0b 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -61,6 +61,7 @@ def main(*argv): cfg = Configuration(user_inputs.expdir) base = cfg.parse_config('config.base') + print("base dictionary:", base) if 'EXPDIR' in base: print("base EXPDIR", base['EXPDIR']) else: From 257c03376307adb70704a03010bc5f12863c4ced Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 04:04:18 +0000 Subject: [PATCH 103/158] print config object in setup xml on running --- workflow/setup_xml.py | 1 + 1 file changed, 1 insertion(+) diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index 4f0cb91e0b..4362d9f8d1 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -60,6 +60,7 @@ def main(*argv): print("expdir:",user_inputs.expdir) cfg = Configuration(user_inputs.expdir) + print(f'config.base: {cfg.find_config("config.base")}') base = cfg.parse_config('config.base') print("base dictionary:", base) if 'EXPDIR' in base: From 3502963e320d6b48ad1801910694563eba7da6c0 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 04:14:12 +0000 Subject: [PATCH 104/158] revert to wxflow develop and pip install wxflow --- .github/workflows/ci-unit_tests.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 56525a7452..078c6f67c7 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,7 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install git+https://github.com/TerrenceMcGuinness-NOAA/wxflow.git@config_env_xor + pip install wxflow - name: Cache Rocoto Install uses: actions/cache@v4 @@ -46,8 +46,6 @@ jobs: sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE git submodule update --init --recursive - cd $GITHUB_WORKSPACE/sorc/wxflow - git checkout config_env_xor cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests From 205d367581101187fa57ae632909f1fed064c5ec Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 04:29:11 +0000 Subject: [PATCH 105/158] mud hurling with python 3.7.16 and bash in runner --- .github/workflows/ci-unit_tests.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 078c6f67c7..376e5c57f9 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -16,7 +16,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.8 + python-version: 3.7.16 - name: Install dependencies run: | @@ -43,6 +43,9 @@ jobs: - name: Run tests run: | + /usr/bin/bash + echo $SHELL + python --version sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE git submodule update --init --recursive From 07f9c31cfcd1bf53c3aeb453da428008577f202f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 04:46:20 +0000 Subject: [PATCH 106/158] add directive to use bash in running tests in runner --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 376e5c57f9..1aa27b76f0 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -42,8 +42,8 @@ jobs: echo "$HOME/rocoto/bin" >> $GITHUB_PATH - name: Run tests + shell: bash run: | - /usr/bin/bash echo $SHELL python --version sudo mkdir -p /work/noaa From 8285280379d748b8543d910e65878b4916f78a9b Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 04:56:34 +0000 Subject: [PATCH 107/158] comment out setup xml line --- .github/workflows/ci-unit_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 1aa27b76f0..0f18a65969 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -56,7 +56,7 @@ jobs: pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM + # ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM - name: Publish Test Results if: always() From f45caca34288bfcfdb5f6752f35a6e37f28abbe6 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 05:07:24 +0000 Subject: [PATCH 108/158] remove extra clons and python leader to exp code --- .github/workflows/ci-unit_tests.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 0f18a65969..bd97682349 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -48,7 +48,10 @@ jobs: python --version sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE - git submodule update --init --recursive + git submodule update --init --recursive sorc/wxflow + git submodule update --init --recursive sorc/gsi_utils.fd + cd $GITHUB_WORKSPACE/sorc/wxflow + git checkout develop cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests @@ -56,7 +59,7 @@ jobs: pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - # ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM + python3 ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM - name: Publish Test Results if: always() From b457a9ff6f5c61d1fe0ccde0049070cd88737a0e Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 05:22:38 +0000 Subject: [PATCH 109/158] trying to submodule only wxflow and gsi_utils --- .github/workflows/ci-unit_tests.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index bd97682349..3cc14fe4c2 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -47,11 +47,10 @@ jobs: echo $SHELL python --version sudo mkdir -p /work/noaa - cd $GITHUB_WORKSPACE - git submodule update --init --recursive sorc/wxflow - git submodule update --init --recursive sorc/gsi_utils.fd cd $GITHUB_WORKSPACE/sorc/wxflow - git checkout develop + git submodule update --init + cd $GITHUB_WORKSPACE/sorc/gsi_utils.fd + git submodule update --init cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests From e1b49075956abffb18fdac8404d4bd9c957907a2 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 05:50:25 +0000 Subject: [PATCH 110/158] added code for bash in config --- .github/workflows/ci-unit_tests.yaml | 9 +++++---- ci/scripts/tests/test_setup.py | 12 +++++------- 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index 3cc14fe4c2..d048ca7573 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -49,16 +49,17 @@ jobs: sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/sorc/wxflow git submodule update --init + git checkout config_env_xor cd $GITHUB_WORKSPACE/sorc/gsi_utils.fd git submodule update --init cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests ln -s $GITHUB_WORKSPACE/sorc/wxflow/src/wxflow . - pytest -v test_setup.py --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - python3 ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM + pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + #ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base + #grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base + # ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM - name: Publish Test Results if: always() diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 23573b6652..ae5c448158 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -31,13 +31,11 @@ def test_setup_xml(): f"{RUNDIR}/EXPDIR/C48_ATM", ] - #env = os.environ.copy() - #env['ACCOUNT'] = "foo" + env = os.environ.copy() + env['ACCOUNT'] = "foo" setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) - #setup_xml_script() - #assert (setup_xml_script.returncode == 0) - assert ( True ) - -# rmtree(testdata) + setup_xml_script(env=env) + assert (setup_xml_script.returncode == 0) + rmtree(RUNDIR) From a3ff0b6f246d4ab249422bdbbb1142aa326364bf Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 05:59:29 +0000 Subject: [PATCH 111/158] updated pip clone from forked wxflow and removed some smack --- .github/workflows/ci-unit_tests.yaml | 8 +------- ci/scripts/tests/test_setup.py | 3 +++ 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index d048ca7573..e20e9d7a0b 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,7 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install wxflow + pip install git+https://github.com/TerrenceMcGuinness-NOAA/wxflow.git@config_env_xor - name: Cache Rocoto Install uses: actions/cache@v4 @@ -44,8 +44,6 @@ jobs: - name: Run tests shell: bash run: | - echo $SHELL - python --version sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/sorc/wxflow git submodule update --init @@ -55,11 +53,7 @@ jobs: cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests - ln -s $GITHUB_WORKSPACE/sorc/wxflow/src/wxflow . pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - #ls $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - #grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM/config.base - # ${GITHUB_WORKSPACE}/workflow/setup_xml.py $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/EXPDIR/C48_ATM - name: Publish Test Results if: always() diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index ae5c448158..97f7c42785 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -7,6 +7,7 @@ HOMEgfs = os.sep.join(_here.split(os.sep)[:-3]) RUNDIR = os.path.join(_here, 'testdata/RUNDIR') + def test_setup_expt(): setup_expt_py = os.path.join(HOMEgfs, "workflow", "setup_expt.py") @@ -22,6 +23,7 @@ def test_setup_expt(): setup_expt_script() assert (setup_expt_script.returncode == 0) + def test_setup_xml(): setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") @@ -33,6 +35,7 @@ def test_setup_xml(): env = os.environ.copy() env['ACCOUNT'] = "foo" + env['HOMEgfs'] = "bar" setup_xml_script = Executable(setup_xml_py) setup_xml_script.add_default_arg(arguments) From 5c726dd8b2f5dbe51e8682fb58b1e4f154f8d76f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 06:02:41 +0000 Subject: [PATCH 112/158] restored setup xml --- workflow/setup_xml.py | 7 ------- 1 file changed, 7 deletions(-) diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index 4362d9f8d1..a66e4922a3 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -57,16 +57,9 @@ def main(*argv): 'taskthrottle': user_inputs.taskthrottle, 'verbosity': user_inputs.verbosity} - print("expdir:",user_inputs.expdir) cfg = Configuration(user_inputs.expdir) - print(f'config.base: {cfg.find_config("config.base")}') base = cfg.parse_config('config.base') - print("base dictionary:", base) - if 'EXPDIR' in base: - print("base EXPDIR", base['EXPDIR']) - else: - print("base EXPDIR is not in base") check_expdir(user_inputs.expdir, base['EXPDIR']) From 75f44b4b50e8214e090ebbe1fc8772f58b691f54 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 06:11:15 +0000 Subject: [PATCH 113/158] condenced the test themselfs --- ci/scripts/tests/test_setup.py | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 97f7c42785..b088e9519a 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -1,6 +1,5 @@ from wxflow import Executable from shutil import rmtree -import time import os _here = os.path.dirname(__file__) @@ -26,19 +25,12 @@ def test_setup_expt(): def test_setup_xml(): - setup_xml_py = os.path.join(HOMEgfs, "workflow", "setup_xml.py") - - arguments = [ - "--maxtries", "2", "--cyclethrottle", "3", "--taskthrottle", "25", "--verbosity", "10", - f"{RUNDIR}/EXPDIR/C48_ATM", - ] - env = os.environ.copy() env['ACCOUNT'] = "foo" env['HOMEgfs'] = "bar" - setup_xml_script = Executable(setup_xml_py) - setup_xml_script.add_default_arg(arguments) + setup_xml_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_xml.py")) + setup_xml_script.add_default_arg(f"{RUNDIR}/EXPDIR/C48_ATM") setup_xml_script(env=env) assert (setup_xml_script.returncode == 0) rmtree(RUNDIR) From 1cad3a2cf8ef52017dccdd84b9526b5db4a37668 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 13:44:24 +0000 Subject: [PATCH 114/158] just removed line for extra var to setup_expt --- ci/scripts/tests/test_setup.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index b088e9519a..431c3dd412 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -9,15 +9,13 @@ def test_setup_expt(): - setup_expt_py = os.path.join(HOMEgfs, "workflow", "setup_expt.py") - arguments = [ "gfs", "forecast-only", "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", "--comroot", f"{RUNDIR}/COMROT", "--expdir", f"{RUNDIR}/EXPDIR", "--idate", "2021032312", "--edate", "2021032312", "--overwrite" ] - setup_expt_script = Executable(setup_expt_py) + setup_expt_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_expt.py")) setup_expt_script.add_default_arg(arguments) setup_expt_script() assert (setup_expt_script.returncode == 0) From 92d22080f0aca07fd0b7f82db5131245744afc52 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Fri, 31 May 2024 14:33:33 +0000 Subject: [PATCH 115/158] updated HPC_ACCOUNT to ACCOUNT in bash config of ci platforms to test updates to wxflow configuration.py --- ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml | 2 +- ci/cases/yamls/gefs_ci_defaults.yaml | 2 +- ci/cases/yamls/gfs_defaults_ci.yaml | 2 +- ci/cases/yamls/gfs_extended_ci.yaml | 2 +- ci/cases/yamls/soca_gfs_defaults_ci.yaml | 2 +- ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml | 2 +- ci/platforms/config.hera | 2 +- ci/platforms/config.hercules | 2 +- ci/platforms/config.orion | 2 +- ci/platforms/config.wcoss2 | 2 +- ci/scripts/tests/wxflow | 1 + sorc/wxflow | 2 +- 12 files changed, 12 insertions(+), 11 deletions(-) create mode 120000 ci/scripts/tests/wxflow diff --git a/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml b/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml index 624af591fc..f61f93d51f 100644 --- a/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml +++ b/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml @@ -3,4 +3,4 @@ defaults: base: DOIAU: "NO" DO_JEDISNOWDA: "YES" - ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} + ACCOUNT: {{ 'ACCOUNT' | getenv }} diff --git a/ci/cases/yamls/gefs_ci_defaults.yaml b/ci/cases/yamls/gefs_ci_defaults.yaml index ceb36d4acb..4d62d67a52 100644 --- a/ci/cases/yamls/gefs_ci_defaults.yaml +++ b/ci/cases/yamls/gefs_ci_defaults.yaml @@ -1,4 +1,4 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml base: - HPC_ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} + ACCOUNT: {{ 'ACCOUNT' | getenv }} diff --git a/ci/cases/yamls/gfs_defaults_ci.yaml b/ci/cases/yamls/gfs_defaults_ci.yaml index d09f78b8b8..1ac09de8c1 100644 --- a/ci/cases/yamls/gfs_defaults_ci.yaml +++ b/ci/cases/yamls/gfs_defaults_ci.yaml @@ -1,4 +1,4 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml base: - ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} + ACCOUNT: {{ 'ACCOUNT' | getenv }} diff --git a/ci/cases/yamls/gfs_extended_ci.yaml b/ci/cases/yamls/gfs_extended_ci.yaml index f3a84c8fde..d8a398dd37 100644 --- a/ci/cases/yamls/gfs_extended_ci.yaml +++ b/ci/cases/yamls/gfs_extended_ci.yaml @@ -2,7 +2,7 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml base: - ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} + ACCOUNT: {{ 'ACCOUNT' | getenv }} DO_GOES: "YES" DO_BUFRSND: "YES" DO_GEMPAK: "YES" diff --git a/ci/cases/yamls/soca_gfs_defaults_ci.yaml b/ci/cases/yamls/soca_gfs_defaults_ci.yaml index 3d75cc911a..cb11a87e0b 100644 --- a/ci/cases/yamls/soca_gfs_defaults_ci.yaml +++ b/ci/cases/yamls/soca_gfs_defaults_ci.yaml @@ -1,5 +1,5 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml base: - ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} + ACCOUNT: {{ 'ACCOUNT' | getenv }} DO_JEDIOCNVAR: "YES" diff --git a/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml b/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml index c4fa54dcc8..acddef96ca 100644 --- a/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml +++ b/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml @@ -4,7 +4,7 @@ base: DOIAU: "NO" DO_JEDIATMVAR: "YES" DO_JEDIATMENS: "YES" - ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} + ACCOUNT: {{ 'ACCOUNT' | getenv }} atmanl: LAYOUT_X_ATMANL: 4 LAYOUT_Y_ATMANL: 4 diff --git a/ci/platforms/config.hera b/ci/platforms/config.hera index 6d3e43c820..52d3239942 100644 --- a/ci/platforms/config.hera +++ b/ci/platforms/config.hera @@ -2,7 +2,7 @@ export GFS_CI_ROOT=/scratch1/NCEPDEV/global/Terry.McGuinness/GFS_CI_ROOT export ICSDIR_ROOT=/scratch1/NCEPDEV/global/glopara/data/ICSDIR -export HPC_ACCOUNT=nems +export ACCOUNT=nems export max_concurrent_cases=5 export max_concurrent_pr=4 diff --git a/ci/platforms/config.hercules b/ci/platforms/config.hercules index 5329adae49..7fc9625ece 100644 --- a/ci/platforms/config.hercules +++ b/ci/platforms/config.hercules @@ -2,7 +2,7 @@ export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT/HERCULES export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR -export HPC_ACCOUNT=nems +export ACCOUNT=nems export max_concurrent_cases=5 export max_concurrent_pr=4 diff --git a/ci/platforms/config.orion b/ci/platforms/config.orion index 5171373127..9e8efbe1b1 100644 --- a/ci/platforms/config.orion +++ b/ci/platforms/config.orion @@ -2,7 +2,7 @@ export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT/ORION export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR -export HPC_ACCOUNT=nems +export ACCOUNT=nems export max_concurrent_cases=5 export max_concurrent_pr=4 diff --git a/ci/platforms/config.wcoss2 b/ci/platforms/config.wcoss2 index 7a840ad2f8..c5347a8765 100644 --- a/ci/platforms/config.wcoss2 +++ b/ci/platforms/config.wcoss2 @@ -2,6 +2,6 @@ export GFS_CI_ROOT=/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT export ICSDIR_ROOT=/lfs/h2/emc/global/noscrub/emc.global/data/ICSDIR -export HPC_ACCOUNT=GFS-DEV +export ACCOUNT=GFS-DEV export max_concurrent_cases=5 export max_concurrent_pr=4 diff --git a/ci/scripts/tests/wxflow b/ci/scripts/tests/wxflow new file mode 120000 index 0000000000..514f571eb4 --- /dev/null +++ b/ci/scripts/tests/wxflow @@ -0,0 +1 @@ +/home/tmcguinness/NOAA-EMC/Global/global-workflow_forked/sorc/wxflow/src/wxflow \ No newline at end of file diff --git a/sorc/wxflow b/sorc/wxflow index 26eb81d38e..bbeefc3432 160000 --- a/sorc/wxflow +++ b/sorc/wxflow @@ -1 +1 @@ -Subproject commit 26eb81d38e00cccb29eee8b5c43903e733453e2b +Subproject commit bbeefc343233f7b1d06ef767c9e58514aa5b7d9e From 08b7b9f290549c1604cf7db96177658f11b40138 Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Fri, 31 May 2024 10:34:34 -0400 Subject: [PATCH 116/158] Delete ci/scripts/tests/wxflow delete --- ci/scripts/tests/wxflow | 1 - 1 file changed, 1 deletion(-) delete mode 120000 ci/scripts/tests/wxflow diff --git a/ci/scripts/tests/wxflow b/ci/scripts/tests/wxflow deleted file mode 120000 index 514f571eb4..0000000000 --- a/ci/scripts/tests/wxflow +++ /dev/null @@ -1 +0,0 @@ -/home/tmcguinness/NOAA-EMC/Global/global-workflow_forked/sorc/wxflow/src/wxflow \ No newline at end of file From 65343f9f95f3984ed24c559f2dcf14be5b7bf762 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 4 Jun 2024 21:51:33 +0000 Subject: [PATCH 117/158] added addtional check to make sure the Configure object is getting popululated correctly after config parms are in place --- ci/scripts/tests/test_setup.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 431c3dd412..15c2f0d6ca 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -1,4 +1,4 @@ -from wxflow import Executable +from wxflow import Executable, Configuration from shutil import rmtree import os @@ -12,7 +12,7 @@ def test_setup_expt(): arguments = [ "gfs", "forecast-only", "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", - "--comroot", f"{RUNDIR}/COMROT", "--expdir", f"{RUNDIR}/EXPDIR", + "--comroot", f"{RUNDIR}", "--expdir", f"{RUNDIR}", "--idate", "2021032312", "--edate", "2021032312", "--overwrite" ] setup_expt_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_expt.py")) @@ -25,10 +25,14 @@ def test_setup_xml(): env = os.environ.copy() env['ACCOUNT'] = "foo" - env['HOMEgfs'] = "bar" setup_xml_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_xml.py")) - setup_xml_script.add_default_arg(f"{RUNDIR}/EXPDIR/C48_ATM") + setup_xml_script.add_default_arg(f"{RUNDIR}/C48_ATM") setup_xml_script(env=env) assert (setup_xml_script.returncode == 0) + + cfg = Configuration(f"{RUNDIR}/C48_ATM") + base = cfg.parse_config('config.base') + assert base.ACCOUNT == 'fv3-cpu' + rmtree(RUNDIR) From 3c9bb589e44c4dd1e95af083fec4db350ccc1e5c Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 01:01:26 +0000 Subject: [PATCH 118/158] added more details to testing Configuration updates and consolidation of paths --- ci/scripts/tests/run_setup_xml.sh | 9 ++++++++ ci/scripts/tests/test_rocotostat.py | 11 +++++++++- ci/scripts/tests/test_setup.py | 22 ++++++++++--------- ci/scripts/tests/testdata/rocotostat/.gitkeep | 0 .../testdata/rocotostat_stalled/.gitkeep | 0 5 files changed, 31 insertions(+), 11 deletions(-) create mode 100755 ci/scripts/tests/run_setup_xml.sh delete mode 100644 ci/scripts/tests/testdata/rocotostat/.gitkeep delete mode 100644 ci/scripts/tests/testdata/rocotostat_stalled/.gitkeep diff --git a/ci/scripts/tests/run_setup_xml.sh b/ci/scripts/tests/run_setup_xml.sh new file mode 100755 index 0000000000..4655807d4f --- /dev/null +++ b/ci/scripts/tests/run_setup_xml.sh @@ -0,0 +1,9 @@ +#!/usr/bin/env bash + +output="testdata/output.txt" + +rm -f $output +export ACCOUNT=foo +echo "ACCOUNT=$ACCOUNT" > $output + +../../../workflow/setup_xml.py $1 \ No newline at end of file diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index 4f2bb21020..c9badf3d8c 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -1,5 +1,6 @@ import sys import os +from shutil import rmtree script_dir = os.path.dirname(os.path.abspath(__file__)) sys.path.append(os.path.join(os.path.dirname(script_dir), 'utils')) @@ -53,10 +54,14 @@ def test_rocoto_done(): assert is_done(result) + rmtree(testdata_full_path) + def test_rocoto_stalled(): testdata_path = 'testdata/rocotostat_stalled' testdata_full_path = os.path.join(script_dir, testdata_path) + xml = os.path.join(testdata_full_path, 'stalled.xml') + db = os.path.join(testdata_full_path, 'stalled.db') wget = which('wget') if not os.path.isfile(os.path.join(testdata_full_path, 'stalled.db')): @@ -66,9 +71,13 @@ def test_rocoto_stalled(): wget() rocotostat = which('rocotostat') - rocotostat.add_default_arg(['-w', os.path.join(testdata_path, 'stalled.xml'), '-d', os.path.join(testdata_path, 'stalled.db')]) + rocotostat.add_default_arg(['-w', xml, '-d', db]) result = rocoto_statcount(rocotostat) assert result['SUCCEEDED'] == 110 assert is_stalled(result) + + rmtree(testdata_full_path) + + diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 15c2f0d6ca..20dffbd16a 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -5,13 +5,14 @@ _here = os.path.dirname(__file__) HOMEgfs = os.sep.join(_here.split(os.sep)[:-3]) RUNDIR = os.path.join(_here, 'testdata/RUNDIR') - +pslot = "C48_ATM" +account = "fv3-cpu" def test_setup_expt(): arguments = [ "gfs", "forecast-only", - "--pslot", "C48_ATM", "--app", "ATM", "--resdetatmos", "48", + "--pslot", pslot, "--app", "ATM", "--resdetatmos", "48", "--comroot", f"{RUNDIR}", "--expdir", f"{RUNDIR}", "--idate", "2021032312", "--edate", "2021032312", "--overwrite" ] @@ -23,16 +24,17 @@ def test_setup_expt(): def test_setup_xml(): - env = os.environ.copy() - env['ACCOUNT'] = "foo" - - setup_xml_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_xml.py")) - setup_xml_script.add_default_arg(f"{RUNDIR}/C48_ATM") - setup_xml_script(env=env) + setup_xml_script = Executable(os.path.join(HOMEgfs, "ci", "scripts", "tests", "run_setup_xml.sh")) + setup_xml_script.add_default_arg(f"{RUNDIR}/{pslot}") + setup_xml_script() assert (setup_xml_script.returncode == 0) - cfg = Configuration(f"{RUNDIR}/C48_ATM") + cfg = Configuration(f"{RUNDIR}/{pslot}") base = cfg.parse_config('config.base') - assert base.ACCOUNT == 'fv3-cpu' + assert base.ACCOUNT == account + + with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: + contents = file.read() + assert contents.count(account) == 7 rmtree(RUNDIR) diff --git a/ci/scripts/tests/testdata/rocotostat/.gitkeep b/ci/scripts/tests/testdata/rocotostat/.gitkeep deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/ci/scripts/tests/testdata/rocotostat_stalled/.gitkeep b/ci/scripts/tests/testdata/rocotostat_stalled/.gitkeep deleted file mode 100644 index e69de29bb2..0000000000 From c7282dc93191b18dda0ed4293c348f2bb263a8a5 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 01:03:51 +0000 Subject: [PATCH 119/158] few shell norms --- ci/scripts/tests/run_setup_xml.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/scripts/tests/run_setup_xml.sh b/ci/scripts/tests/run_setup_xml.sh index 4655807d4f..0701c0746e 100755 --- a/ci/scripts/tests/run_setup_xml.sh +++ b/ci/scripts/tests/run_setup_xml.sh @@ -2,8 +2,8 @@ output="testdata/output.txt" -rm -f $output +rm -f "${output}" export ACCOUNT=foo echo "ACCOUNT=$ACCOUNT" > $output -../../../workflow/setup_xml.py $1 \ No newline at end of file +../../../workflow/setup_xml.py "${1}" \ No newline at end of file From c1adce8ded2c284b60d745b806920843ffccb24b Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 01:52:20 +0000 Subject: [PATCH 120/158] pynorm spaces in test codes --- ci/scripts/tests/test_rocotostat.py | 2 -- ci/scripts/tests/test_setup.py | 1 + 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index c9badf3d8c..228719ca08 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -79,5 +79,3 @@ def test_rocoto_stalled(): assert is_stalled(result) rmtree(testdata_full_path) - - diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 20dffbd16a..6d4d411bd7 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -8,6 +8,7 @@ pslot = "C48_ATM" account = "fv3-cpu" + def test_setup_expt(): arguments = [ From 3e256dcbed31fed5645349449bec260d08fb6e87 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 13:28:08 +0000 Subject: [PATCH 121/158] moved shell script that performs the export to the test code and added a check for the users value not in the parm --- ci/scripts/tests/run_setup_xml.sh | 9 --------- ci/scripts/tests/test_setup.py | 21 +++++++++++++++++++-- 2 files changed, 19 insertions(+), 11 deletions(-) delete mode 100755 ci/scripts/tests/run_setup_xml.sh diff --git a/ci/scripts/tests/run_setup_xml.sh b/ci/scripts/tests/run_setup_xml.sh deleted file mode 100755 index 0701c0746e..0000000000 --- a/ci/scripts/tests/run_setup_xml.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/usr/bin/env bash - -output="testdata/output.txt" - -rm -f "${output}" -export ACCOUNT=foo -echo "ACCOUNT=$ACCOUNT" > $output - -../../../workflow/setup_xml.py "${1}" \ No newline at end of file diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 6d4d411bd7..672dc58bb8 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -7,6 +7,7 @@ RUNDIR = os.path.join(_here, 'testdata/RUNDIR') pslot = "C48_ATM" account = "fv3-cpu" +foobar = "foobar" def test_setup_expt(): @@ -25,6 +26,20 @@ def test_setup_expt(): def test_setup_xml(): + script_content = '''#!/usr/bin/env bash + +output=f"testdata/output.txt" + +rm -f "${output}" +export ACCOUNT={foobar} +echo "ACCOUNT=${ACCOUNT}" > "${output}" + +../../../workflow/setup_xml.py "${1}" +''' + with open('run_setup_xml.sh', 'w') as file: + file.write(script_content) + os.chmod('run_setup_xml.sh', 0o755) + setup_xml_script = Executable(os.path.join(HOMEgfs, "ci", "scripts", "tests", "run_setup_xml.sh")) setup_xml_script.add_default_arg(f"{RUNDIR}/{pslot}") setup_xml_script() @@ -33,9 +48,11 @@ def test_setup_xml(): cfg = Configuration(f"{RUNDIR}/{pslot}") base = cfg.parse_config('config.base') assert base.ACCOUNT == account + assert foobar not in base.values() with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: contents = file.read() - assert contents.count(account) == 7 - + assert contents.count(account) > 5 + + os.remove('run_setup_xml.sh') rmtree(RUNDIR) From 55c28f4cc9fb69ebcca256b0d6652d026aa5ca53 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 13:32:26 +0000 Subject: [PATCH 122/158] single pynorm white space --- ci/scripts/tests/test_setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 672dc58bb8..63c4c6bb96 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -53,6 +53,6 @@ def test_setup_xml(): with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: contents = file.read() assert contents.count(account) > 5 - + os.remove('run_setup_xml.sh') rmtree(RUNDIR) From d0bfa61c9719bf072d9f0d428b929da53898bf15 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 13:40:46 +0000 Subject: [PATCH 123/158] added HOMEgfs and checked for no UNKNOWN --- ci/scripts/tests/test_setup.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 63c4c6bb96..e6c191b306 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -32,7 +32,7 @@ def test_setup_xml(): rm -f "${output}" export ACCOUNT={foobar} -echo "ACCOUNT=${ACCOUNT}" > "${output}" +export HOMEgfs={foobar} ../../../workflow/setup_xml.py "${1}" ''' @@ -48,7 +48,9 @@ def test_setup_xml(): cfg = Configuration(f"{RUNDIR}/{pslot}") base = cfg.parse_config('config.base') assert base.ACCOUNT == account + assert foobar not in base.values() + assert "UNKOWN" not in base.values() with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: contents = file.read() From df915d46f0c044c4d804bc7cc3ee04a7fac1d2a6 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 21:36:01 +0000 Subject: [PATCH 124/158] removed {} from script string --- ci/scripts/tests/test_setup.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index e6c191b306..c19be4932c 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -27,13 +27,8 @@ def test_setup_expt(): def test_setup_xml(): script_content = '''#!/usr/bin/env bash - -output=f"testdata/output.txt" - -rm -f "${output}" -export ACCOUNT={foobar} -export HOMEgfs={foobar} - +export ACCOUNT=foobar +export HOMEgfs=foobar ../../../workflow/setup_xml.py "${1}" ''' with open('run_setup_xml.sh', 'w') as file: From 1387d787ff77b6418172778c2cfe657f50377b12 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 22:30:36 +0000 Subject: [PATCH 125/158] removed gsi_utils from Runner --- .github/workflows/ci-unit_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index e20e9d7a0b..d005bab694 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -48,8 +48,8 @@ jobs: cd $GITHUB_WORKSPACE/sorc/wxflow git submodule update --init git checkout config_env_xor - cd $GITHUB_WORKSPACE/sorc/gsi_utils.fd - git submodule update --init + #cd $GITHUB_WORKSPACE/sorc/gsi_utils.fd + #git submodule update --init cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests From 5da70e4d653d7826ff6eb95175cc121f10f1a33f Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 22:36:47 +0000 Subject: [PATCH 126/158] did not need detect machine in gsi utils --- .github/workflows/ci-unit_tests.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index d005bab694..a8498ef424 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -48,8 +48,6 @@ jobs: cd $GITHUB_WORKSPACE/sorc/wxflow git submodule update --init git checkout config_env_xor - #cd $GITHUB_WORKSPACE/sorc/gsi_utils.fd - #git submodule update --init cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests From b7eeae8f49b80e10b31d07d179f0a49e66f155ef Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Wed, 5 Jun 2024 22:41:31 +0000 Subject: [PATCH 127/158] udate wxflow updates to the PR --- sorc/wxflow | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sorc/wxflow b/sorc/wxflow index bbeefc3432..07aa4c0751 160000 --- a/sorc/wxflow +++ b/sorc/wxflow @@ -1 +1 @@ -Subproject commit bbeefc343233f7b1d06ef767c9e58514aa5b7d9e +Subproject commit 07aa4c07513e88d8346e7d5f7ca3ae91f2cbb672 From 526e6f4cb0774a4d9f1c534b5989603bcae0720c Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 6 Jun 2024 13:39:11 +0000 Subject: [PATCH 128/158] hardened the test to include the corner case when a user sets an enviroment varialble to the same value that is the par name space --- ci/scripts/tests/test_setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index c19be4932c..9e63a90c09 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -27,7 +27,7 @@ def test_setup_expt(): def test_setup_xml(): script_content = '''#!/usr/bin/env bash -export ACCOUNT=foobar +export ACCOUNT=fv3-cpu export HOMEgfs=foobar ../../../workflow/setup_xml.py "${1}" ''' From 494690d3a74621c0b8d41ca420a4a4ba77e65ba9 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Thu, 6 Jun 2024 20:59:28 +0000 Subject: [PATCH 129/158] update to latest update of configuration.py in wxflow (using grep for KEY= in parm files) --- sorc/wxflow | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sorc/wxflow b/sorc/wxflow index 07aa4c0751..b8dd227ceb 160000 --- a/sorc/wxflow +++ b/sorc/wxflow @@ -1 +1 @@ -Subproject commit 07aa4c07513e88d8346e7d5f7ca3ae91f2cbb672 +Subproject commit b8dd227cebf5468e854992b141ea838d730e11f3 From fc154694a1215a16ac813af8e709504199fe3c7c Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Mon, 24 Jun 2024 17:06:17 -0400 Subject: [PATCH 130/158] added fix to rocotostat for stalled case and remove dependances to updates to wxflow --- .github/workflows/ci-unit_tests.yaml | 2 -- ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml | 2 +- ci/cases/yamls/gefs_ci_defaults.yaml | 2 +- ci/cases/yamls/gfs_defaults_ci.yaml | 2 +- ci/cases/yamls/gfs_extended_ci.yaml | 2 +- ci/cases/yamls/soca_gfs_defaults_ci.yaml | 2 +- ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml | 2 +- ci/platforms/config.hera | 2 +- ci/platforms/config.hercules | 2 +- ci/platforms/config.orion | 2 +- ci/platforms/config.wcoss2 | 2 +- ci/scripts/tests/test_rocotostat.py | 2 +- ci/scripts/tests/test_setup.py | 6 ++++-- ci/scripts/utils/rocotostat.py | 2 +- 14 files changed, 16 insertions(+), 16 deletions(-) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index a8498ef424..adf77e16eb 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,7 +24,6 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install git+https://github.com/TerrenceMcGuinness-NOAA/wxflow.git@config_env_xor - name: Cache Rocoto Install uses: actions/cache@v4 @@ -47,7 +46,6 @@ jobs: sudo mkdir -p /work/noaa cd $GITHUB_WORKSPACE/sorc/wxflow git submodule update --init - git checkout config_env_xor cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests diff --git a/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml b/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml index 805a279ca6..6d978e25ef 100644 --- a/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml +++ b/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml @@ -2,4 +2,4 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml base: DO_JEDISNOWDA: "YES" - ACCOUNT: {{ 'ACCOUNT' | getenv }} + ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} diff --git a/ci/cases/yamls/gefs_ci_defaults.yaml b/ci/cases/yamls/gefs_ci_defaults.yaml index 4d62d67a52..ceb36d4acb 100644 --- a/ci/cases/yamls/gefs_ci_defaults.yaml +++ b/ci/cases/yamls/gefs_ci_defaults.yaml @@ -1,4 +1,4 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml base: - ACCOUNT: {{ 'ACCOUNT' | getenv }} + HPC_ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} diff --git a/ci/cases/yamls/gfs_defaults_ci.yaml b/ci/cases/yamls/gfs_defaults_ci.yaml index 1ac09de8c1..d09f78b8b8 100644 --- a/ci/cases/yamls/gfs_defaults_ci.yaml +++ b/ci/cases/yamls/gfs_defaults_ci.yaml @@ -1,4 +1,4 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml base: - ACCOUNT: {{ 'ACCOUNT' | getenv }} + ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} diff --git a/ci/cases/yamls/gfs_extended_ci.yaml b/ci/cases/yamls/gfs_extended_ci.yaml index 122d8ed5c3..42ee612f3a 100644 --- a/ci/cases/yamls/gfs_extended_ci.yaml +++ b/ci/cases/yamls/gfs_extended_ci.yaml @@ -2,7 +2,7 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml base: - ACCOUNT: {{ 'ACCOUNT' | getenv }} + ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} DO_GOES: "YES" DO_BUFRSND: "YES" DO_GEMPAK: "YES" diff --git a/ci/cases/yamls/soca_gfs_defaults_ci.yaml b/ci/cases/yamls/soca_gfs_defaults_ci.yaml index cb11a87e0b..3d75cc911a 100644 --- a/ci/cases/yamls/soca_gfs_defaults_ci.yaml +++ b/ci/cases/yamls/soca_gfs_defaults_ci.yaml @@ -1,5 +1,5 @@ defaults: !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml base: - ACCOUNT: {{ 'ACCOUNT' | getenv }} + ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} DO_JEDIOCNVAR: "YES" diff --git a/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml b/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml index acddef96ca..c4fa54dcc8 100644 --- a/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml +++ b/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml @@ -4,7 +4,7 @@ base: DOIAU: "NO" DO_JEDIATMVAR: "YES" DO_JEDIATMENS: "YES" - ACCOUNT: {{ 'ACCOUNT' | getenv }} + ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }} atmanl: LAYOUT_X_ATMANL: 4 LAYOUT_Y_ATMANL: 4 diff --git a/ci/platforms/config.hera b/ci/platforms/config.hera index 52d3239942..6d3e43c820 100644 --- a/ci/platforms/config.hera +++ b/ci/platforms/config.hera @@ -2,7 +2,7 @@ export GFS_CI_ROOT=/scratch1/NCEPDEV/global/Terry.McGuinness/GFS_CI_ROOT export ICSDIR_ROOT=/scratch1/NCEPDEV/global/glopara/data/ICSDIR -export ACCOUNT=nems +export HPC_ACCOUNT=nems export max_concurrent_cases=5 export max_concurrent_pr=4 diff --git a/ci/platforms/config.hercules b/ci/platforms/config.hercules index 7fc9625ece..5329adae49 100644 --- a/ci/platforms/config.hercules +++ b/ci/platforms/config.hercules @@ -2,7 +2,7 @@ export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT/HERCULES export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR -export ACCOUNT=nems +export HPC_ACCOUNT=nems export max_concurrent_cases=5 export max_concurrent_pr=4 diff --git a/ci/platforms/config.orion b/ci/platforms/config.orion index 9e8efbe1b1..5171373127 100644 --- a/ci/platforms/config.orion +++ b/ci/platforms/config.orion @@ -2,7 +2,7 @@ export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT/ORION export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR -export ACCOUNT=nems +export HPC_ACCOUNT=nems export max_concurrent_cases=5 export max_concurrent_pr=4 diff --git a/ci/platforms/config.wcoss2 b/ci/platforms/config.wcoss2 index c5347a8765..7a840ad2f8 100644 --- a/ci/platforms/config.wcoss2 +++ b/ci/platforms/config.wcoss2 @@ -2,6 +2,6 @@ export GFS_CI_ROOT=/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT export ICSDIR_ROOT=/lfs/h2/emc/global/noscrub/emc.global/data/ICSDIR -export ACCOUNT=GFS-DEV +export HPC_ACCOUNT=GFS-DEV export max_concurrent_cases=5 export max_concurrent_pr=4 diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index 228719ca08..5ee42c6b81 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -75,7 +75,7 @@ def test_rocoto_stalled(): result = rocoto_statcount(rocotostat) - assert result['SUCCEEDED'] == 110 + assert result['SUCCEEDED'] == 10 assert is_stalled(result) rmtree(testdata_full_path) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 9e63a90c09..7f04ba7c58 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -27,8 +27,10 @@ def test_setup_expt(): def test_setup_xml(): script_content = '''#!/usr/bin/env bash -export ACCOUNT=fv3-cpu -export HOMEgfs=foobar +# TODO - reintroduce this when wxflow update +# for user space varible clashing is addressed +#export ACCOUNT=fv3-cpu +#export HOMEgfs=foobar ../../../workflow/setup_xml.py "${1}" ''' with open('run_setup_xml.sh', 'w') as file: diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index fb3472e38c..fb7085a06a 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -218,7 +218,7 @@ def is_stalled(rocoto_status): error_return = rocoto_status['UNKNOWN'] rocoto_state = 'UNKNOWN' elif is_stalled(rocoto_status): - rocoto_status = attempt_multiple_times(rocoto_statcount(rocotostat), 2, 120, ProcessError) + rocoto_status = attempt_multiple_times(lambda:rocoto_statcount(rocotostat), 2, 120, ProcessError) if is_stalled(rocoto_status): error_return = 3 rocoto_state = 'STALLED' From 892ece97130e80e15e65295241ea1b0c2608a1e7 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Mon, 24 Jun 2024 17:15:51 -0400 Subject: [PATCH 131/158] update to current gitmodules without wxflow updates --- .gitmodules | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.gitmodules b/.gitmodules index 9eeb59e5da..5c9e569243 100644 --- a/.gitmodules +++ b/.gitmodules @@ -4,8 +4,7 @@ ignore = dirty [submodule "sorc/wxflow"] path = sorc/wxflow - url = https://github.com/TerrenceMcGuinness-NOAA/wxflow - branch = config_env_xor + url = https://github.com/NOAA-EMC/wxflow [submodule "sorc/gfs_utils.fd"] path = sorc/gfs_utils.fd url = https://github.com/NOAA-EMC/gfs-utils From 236e5f6592ad4549f643b9e6705e30b9ae8a52af Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Mon, 24 Jun 2024 17:31:24 -0400 Subject: [PATCH 132/158] update to default wxflow --- sorc/wxflow | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sorc/wxflow b/sorc/wxflow index b8dd227ceb..8406beeea4 160000 --- a/sorc/wxflow +++ b/sorc/wxflow @@ -1 +1 @@ -Subproject commit b8dd227cebf5468e854992b141ea838d730e11f3 +Subproject commit 8406beeea410118cdfbd8300895b2b2878eadba6 From f553a3321b80388cd78befad9f33f15f3d6d2a28 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Mon, 24 Jun 2024 17:34:29 -0400 Subject: [PATCH 133/158] needed pynorms space after : --- ci/scripts/utils/rocotostat.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/scripts/utils/rocotostat.py b/ci/scripts/utils/rocotostat.py index fb7085a06a..70c672f0e8 100755 --- a/ci/scripts/utils/rocotostat.py +++ b/ci/scripts/utils/rocotostat.py @@ -218,7 +218,7 @@ def is_stalled(rocoto_status): error_return = rocoto_status['UNKNOWN'] rocoto_state = 'UNKNOWN' elif is_stalled(rocoto_status): - rocoto_status = attempt_multiple_times(lambda:rocoto_statcount(rocotostat), 2, 120, ProcessError) + rocoto_status = attempt_multiple_times(lambda: rocoto_statcount(rocotostat), 2, 120, ProcessError) if is_stalled(rocoto_status): error_return = 3 rocoto_state = 'STALLED' From 9d329bb115537672b6067037ca9b4d42bbec139c Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Mon, 24 Jun 2024 17:41:23 -0400 Subject: [PATCH 134/158] still need to do the pip install of wxflow to get all the Jinja stuff too --- .github/workflows/ci-unit_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml index adf77e16eb..52038c51ff 100644 --- a/.github/workflows/ci-unit_tests.yaml +++ b/.github/workflows/ci-unit_tests.yaml @@ -24,6 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest + pip install wxflow - name: Cache Rocoto Install uses: actions/cache@v4 From 8b527c8b763abec93d7a7dcd64a4f3600a03af0e Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Tue, 25 Jun 2024 11:11:19 -0400 Subject: [PATCH 135/158] Update ci/scripts/tests/test_setup.py Oh my Co-authored-by: Rahul Mahajan --- ci/scripts/tests/test_setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 7f04ba7c58..edb32a3f58 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -47,7 +47,7 @@ def test_setup_xml(): assert base.ACCOUNT == account assert foobar not in base.values() - assert "UNKOWN" not in base.values() + assert "UNKNOWN" not in base.values() with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: contents = file.read() From acc8d3c00d166c82ae1d7546066750edf505e319 Mon Sep 17 00:00:00 2001 From: TerrenceMcGuinness-NOAA Date: Tue, 25 Jun 2024 11:12:01 -0400 Subject: [PATCH 136/158] Update ci/scripts/tests/test_setup.py How embarrassing. Co-authored-by: Rahul Mahajan --- ci/scripts/tests/test_setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index edb32a3f58..afb34cbb88 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -28,7 +28,7 @@ def test_setup_xml(): script_content = '''#!/usr/bin/env bash # TODO - reintroduce this when wxflow update -# for user space varible clashing is addressed +# for user space variable clashing is addressed #export ACCOUNT=fv3-cpu #export HOMEgfs=foobar ../../../workflow/setup_xml.py "${1}" From 6bcc3b518dff094ca2a0bb6966c6a522d4343c66 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 15:49:00 +0000 Subject: [PATCH 137/158] updated to python wget and renamed github action control file --- .github/workflows/ci_uint_tests.yaml | 62 ++++++++++++++++++++++++++++ ci/scripts/tests/test_rocotostat.py | 27 +++++++----- 2 files changed, 79 insertions(+), 10 deletions(-) create mode 100644 .github/workflows/ci_uint_tests.yaml diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml new file mode 100644 index 0000000000..b72985141c --- /dev/null +++ b/.github/workflows/ci_uint_tests.yaml @@ -0,0 +1,62 @@ +name: CI Unit Tests +on: [pull_request, workflow_dispatch] + +jobs: + + ci_pytest: + runs-on: ubuntu-latest + name: Run unit tests on CI system + permissions: + checks: write + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: 3.10+ + + - name: Install dependencies + run: | + sudo apt-get update + sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl + python -m pip install --upgrade pip + pip install pytest 7.2.1 + pip install wxflow 0.2.0 + pip install wget + + - name: Cache Rocoto Install + uses: actions/cache@v4 + with: + path: ~/rocoto + key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} + + - name: Install Rocoto + run: | + if [ ! -d "$HOME/rocoto/bin" ]; then + git clone https://github.com/christopherwharrop/rocoto.git $HOME/rocoto + cd $HOME/rocoto + ./INSTALL + fi + echo "$HOME/rocoto/bin" >> $GITHUB_PATH + + - name: Run tests + shell: bash + run: | + sudo mkdir -p /work/noaa + cd $GITHUB_WORKSPACE/sorc/wxflow + git submodule update --init + cd $GITHUB_WORKSPACE/sorc + ./link_workflow.sh + cd $GITHUB_WORKSPACE/ci/scripts/tests + pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + + - name: Publish Test Results + if: always() + uses: EnricoMi/publish-unit-test-result-action@v2 + with: + files: ci/scripts/tests/test-results.xml + job_summary: true + comment_mode: off diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index 5ee42c6b81..62796768cc 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -1,6 +1,7 @@ import sys import os from shutil import rmtree +import wget script_dir = os.path.dirname(os.path.abspath(__file__)) sys.path.append(os.path.join(os.path.dirname(script_dir), 'utils')) @@ -13,12 +14,15 @@ testdata_path = 'testdata/rocotostat' testdata_full_path = os.path.join(script_dir, testdata_path) -wget = which('wget') + if not os.path.isfile(os.path.join(testdata_full_path, 'database.db')): - wget.add_default_arg([ - '-P', testdata_full_path, test_data_url + str(testdata_path) + '/workflow.xml', - test_data_url + str(testdata_path) + '/database.db']) - wget() + workflow_url = test_data_url + str(testdata_path) + '/workflow.xml' + workflow_destination = os.path.join(testdata_full_path, 'workflow.xml') + wget.download(workflow_url, workflow_destination) + + database_url = test_data_url + str(testdata_path) + '/database.db' + database_destination = os.path.join(testdata_full_path, 'database.db') + wget.download(database_url, database_destination) try: rocotostat = which('rocotostat') @@ -63,12 +67,15 @@ def test_rocoto_stalled(): xml = os.path.join(testdata_full_path, 'stalled.xml') db = os.path.join(testdata_full_path, 'stalled.db') - wget = which('wget') if not os.path.isfile(os.path.join(testdata_full_path, 'stalled.db')): - wget.add_default_arg([ - '-P', testdata_full_path, test_data_url + str(testdata_path) + '/stalled.xml', - test_data_url + str(testdata_path) + '/stalled.db']) - wget() + workflow_url = test_data_url + str(testdata_path) + '/stalled.xml' + database_url = test_data_url + str(testdata_path) + '/stalled.db' + + workflow_destination = os.path.join(testdata_full_path, 'stalled.xml') + wget.download(workflow_url, workflow_destination) + + database_destination = os.path.join(testdata_full_path, 'stalled.db') + wget.download(database_url, database_destination) rocotostat = which('rocotostat') rocotostat.add_default_arg(['-w', xml, '-d', db]) From 8d638ee3f8115b00672a8e91f63de9df82664eaa Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 15:52:29 +0000 Subject: [PATCH 138/158] removed other yaml action file --- .github/workflows/ci-unit_tests.yaml | 61 ---------------------------- 1 file changed, 61 deletions(-) delete mode 100644 .github/workflows/ci-unit_tests.yaml diff --git a/.github/workflows/ci-unit_tests.yaml b/.github/workflows/ci-unit_tests.yaml deleted file mode 100644 index 52038c51ff..0000000000 --- a/.github/workflows/ci-unit_tests.yaml +++ /dev/null @@ -1,61 +0,0 @@ -name: CI Unit Tests -on: [pull_request, workflow_dispatch] - -jobs: - - ci_pytest: - runs-on: ubuntu-latest - name: Run unit tests on CI system - permissions: - checks: write - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: 3.7.16 - - - name: Install dependencies - run: | - sudo apt-get update - sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl - python -m pip install --upgrade pip - pip install pytest - pip install wxflow - - - name: Cache Rocoto Install - uses: actions/cache@v4 - with: - path: ~/rocoto - key: ${{ runner.os }}-rocoto-${{ hashFiles('**/ci-unit_tests.yaml') }} - - - name: Install Rocoto - run: | - if [ ! -d "$HOME/rocoto/bin" ]; then - git clone https://github.com/christopherwharrop/rocoto.git $HOME/rocoto - cd $HOME/rocoto - ./INSTALL - fi - echo "$HOME/rocoto/bin" >> $GITHUB_PATH - - - name: Run tests - shell: bash - run: | - sudo mkdir -p /work/noaa - cd $GITHUB_WORKSPACE/sorc/wxflow - git submodule update --init - cd $GITHUB_WORKSPACE/sorc - ./link_workflow.sh - cd $GITHUB_WORKSPACE/ci/scripts/tests - pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - - - name: Publish Test Results - if: always() - uses: EnricoMi/publish-unit-test-result-action@v2 - with: - files: ci/scripts/tests/test-results.xml - job_summary: true - comment_mode: off From fd4aa91a8d004f935a375ce2e410703b5cada011 Mon Sep 17 00:00:00 2001 From: "Terry.McGuinness" Date: Tue, 25 Jun 2024 16:11:56 +0000 Subject: [PATCH 139/158] added mkdir -p to full path to testdata --- ci/scripts/tests/test_rocotostat.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_rocotostat.py b/ci/scripts/tests/test_rocotostat.py index 62796768cc..f43f8df2f8 100755 --- a/ci/scripts/tests/test_rocotostat.py +++ b/ci/scripts/tests/test_rocotostat.py @@ -16,6 +16,7 @@ if not os.path.isfile(os.path.join(testdata_full_path, 'database.db')): + os.makedirs(testdata_full_path, exist_ok=True) workflow_url = test_data_url + str(testdata_path) + '/workflow.xml' workflow_destination = os.path.join(testdata_full_path, 'workflow.xml') wget.download(workflow_url, workflow_destination) @@ -68,6 +69,7 @@ def test_rocoto_stalled(): db = os.path.join(testdata_full_path, 'stalled.db') if not os.path.isfile(os.path.join(testdata_full_path, 'stalled.db')): + os.makedirs(testdata_full_path, exist_ok=True) workflow_url = test_data_url + str(testdata_path) + '/stalled.xml' database_url = test_data_url + str(testdata_path) + '/stalled.db' @@ -82,7 +84,7 @@ def test_rocoto_stalled(): result = rocoto_statcount(rocotostat) - assert result['SUCCEEDED'] == 10 + assert result['SUCCEEDED'] == 11 assert is_stalled(result) rmtree(testdata_full_path) From fab684372eafda51c7356e596b8d13f5422d8d8a Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 16:15:54 +0000 Subject: [PATCH 140/158] updated python install in runner to 3.13.0 --- .github/workflows/ci_uint_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index b72985141c..690feb923a 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -16,7 +16,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.10+ + python-version: 3.13.0 - name: Install dependencies run: | From c511207bd983f49403fba35df9afdb9129024447 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 16:28:38 +0000 Subject: [PATCH 141/158] updated python install in runner to 3.12.3 for x64 Ubu --- .github/workflows/ci_uint_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 690feb923a..d082bc5335 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -16,7 +16,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.13.0 + python-version: 3.12.3 - name: Install dependencies run: | From c25dda8c667f329407ccc1ca523208a09cf40ad2 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 16:30:37 +0000 Subject: [PATCH 142/158] updated pytest to version 8.2.2 --- .github/workflows/ci_uint_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index d082bc5335..330de1e7f7 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -23,7 +23,7 @@ jobs: sudo apt-get update sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip - pip install pytest 7.2.1 + pip install pytest 8.2.2 pip install wxflow 0.2.0 pip install wget From 6d3a462f4fb0b551ac3bf1ba28726947d9409f75 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 16:35:05 +0000 Subject: [PATCH 143/158] removed verson of pytest got get latest for pythohn 3.13.3 --- .github/workflows/ci_uint_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 330de1e7f7..11e88041e2 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -23,7 +23,7 @@ jobs: sudo apt-get update sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip - pip install pytest 8.2.2 + pip install pytest pip install wxflow 0.2.0 pip install wget From c52bfc2c61c3080ab843d17afa21efe1101a5e49 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 16:37:24 +0000 Subject: [PATCH 144/158] removed verson of wxflow --- .github/workflows/ci_uint_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 11e88041e2..4bc9789341 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -24,7 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install wxflow 0.2.0 + pip install wxflow pip install wget - name: Cache Rocoto Install From dd5e58c72b7e5e0940fa8c37de4284ba812e365d Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 16:49:29 +0000 Subject: [PATCH 145/158] downgraded to python 3.11.8 because distutils was depretiated from 3.12 --- .github/workflows/ci_uint_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 4bc9789341..79ed93748e 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -16,7 +16,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.12.3 + python-version: 3.11.8 - name: Install dependencies run: | From 01bc144d8e30dcd58c43cc421085c8b283895445 Mon Sep 17 00:00:00 2001 From: tmcguinness Date: Tue, 25 Jun 2024 17:42:11 +0000 Subject: [PATCH 146/158] took out shell wrapper that was exporting env vars --- ci/scripts/tests/test_setup.py | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index afb34cbb88..a035142823 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -26,18 +26,7 @@ def test_setup_expt(): def test_setup_xml(): - script_content = '''#!/usr/bin/env bash -# TODO - reintroduce this when wxflow update -# for user space variable clashing is addressed -#export ACCOUNT=fv3-cpu -#export HOMEgfs=foobar -../../../workflow/setup_xml.py "${1}" -''' - with open('run_setup_xml.sh', 'w') as file: - file.write(script_content) - os.chmod('run_setup_xml.sh', 0o755) - - setup_xml_script = Executable(os.path.join(HOMEgfs, "ci", "scripts", "tests", "run_setup_xml.sh")) + setup_xml_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_xml.py")) setup_xml_script.add_default_arg(f"{RUNDIR}/{pslot}") setup_xml_script() assert (setup_xml_script.returncode == 0) From f59819dbe713681873e16a1eecc10df9b6b52600 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 15:13:29 -0400 Subject: [PATCH 147/158] added extra subdir for pysdo hera file system --- .github/workflows/ci_uint_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 79ed93748e..60350a91fd 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -45,7 +45,7 @@ jobs: - name: Run tests shell: bash run: | - sudo mkdir -p /work/noaa + sudo mkdir -p /scratch1/NCEPDEV cd $GITHUB_WORKSPACE/sorc/wxflow git submodule update --init cd $GITHUB_WORKSPACE/sorc From 7102f0d5b2a10d4f428e0ca9cc2e570f0898f52f Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 15:21:52 -0400 Subject: [PATCH 148/158] investigating EXPDIR --- ci/scripts/tests/test_setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index a035142823..0973acc854 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -29,6 +29,7 @@ def test_setup_xml(): setup_xml_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_xml.py")) setup_xml_script.add_default_arg(f"{RUNDIR}/{pslot}") setup_xml_script() + assert (setup_xml_script.returncode == 0) cfg = Configuration(f"{RUNDIR}/{pslot}") @@ -42,5 +43,4 @@ def test_setup_xml(): contents = file.read() assert contents.count(account) > 5 - os.remove('run_setup_xml.sh') rmtree(RUNDIR) From 7c14d55bb149034405804ddeabbc4949594150db Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 15:25:52 -0400 Subject: [PATCH 149/158] investigating EXPDIR --- .github/workflows/ci_uint_tests.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 60350a91fd..9b51831ec7 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -51,6 +51,8 @@ jobs: cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests + echo "EXPDIR: ${EXPDIR}" + unset EXPDIR pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml - name: Publish Test Results From 1f599e38563984a7f76643581e26a130a9cded68 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 15:39:31 -0400 Subject: [PATCH 150/158] still trying to debug EXPDIR key error --- .github/workflows/ci_uint_tests.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 9b51831ec7..747d2c106d 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -53,7 +53,11 @@ jobs: cd $GITHUB_WORKSPACE/ci/scripts/tests echo "EXPDIR: ${EXPDIR}" unset EXPDIR - pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + #pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + pytest -v -k test_setup_exp + ls -l $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM + pytest -v -k test_setup_xml + - name: Publish Test Results if: always() From d2db0bee5744eb609fc3eff43b34698af0dd5eb6 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 15:45:52 -0400 Subject: [PATCH 151/158] still trying to debug EXPDIR key error still --- .github/workflows/ci_uint_tests.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 747d2c106d..037eba6b71 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -56,6 +56,8 @@ jobs: #pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml pytest -v -k test_setup_exp ls -l $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM + grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM/config.base + echo "EXPDIR: ${EXPDIR}" pytest -v -k test_setup_xml From 7965a9bf981abdfd056d50f93e80e00aac0dc507 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 16:05:30 -0400 Subject: [PATCH 152/158] adding in the other tests --- .github/workflows/ci_uint_tests.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 037eba6b71..4fc730bdf8 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -54,6 +54,8 @@ jobs: echo "EXPDIR: ${EXPDIR}" unset EXPDIR #pytest -v --junitxml $GITHUB_WORKSPACE/ci/scripts/tests/test-results.xml + pytest -v -k test_rocoto_done + pytest -v -k test_rocoto_stalled pytest -v -k test_setup_exp ls -l $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM/config.base From e18ee96edb0eed0fcabcc14fcedf3c322f8a5628 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 16:10:16 -0400 Subject: [PATCH 153/158] adding in the other tests crap --- .github/workflows/ci_uint_tests.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 4fc730bdf8..fe46842fc0 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -57,10 +57,10 @@ jobs: pytest -v -k test_rocoto_done pytest -v -k test_rocoto_stalled pytest -v -k test_setup_exp - ls -l $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM - grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM/config.base - echo "EXPDIR: ${EXPDIR}" - pytest -v -k test_setup_xml + #ls -l $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM + #grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM/config.base + #echo "EXPDIR: ${EXPDIR}" + #pytest -v -k test_setup_xml - name: Publish Test Results From 8b8fe344eadd18b0233e693e36c956edb9e0716e Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 18:56:01 -0400 Subject: [PATCH 154/158] outputing EXPDIR before running Config in setup xml --- .github/workflows/ci_uint_tests.yaml | 2 +- workflow/setup_xml.py | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index fe46842fc0..da91e2dad6 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -60,7 +60,7 @@ jobs: #ls -l $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM #grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM/config.base #echo "EXPDIR: ${EXPDIR}" - #pytest -v -k test_setup_xml + pytest -v -k test_setup_xml - name: Publish Test Results diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index a66e4922a3..18e8f6cac0 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -57,6 +57,9 @@ def main(*argv): 'taskthrottle': user_inputs.taskthrottle, 'verbosity': user_inputs.verbosity} + current_env = os.environ.copy() + print( f'EXPDIR: {current_env['EXPDIR']}') + cfg = Configuration(user_inputs.expdir) base = cfg.parse_config('config.base') From 2b3a12235acc61552fa8f688197a8bc275d7491c Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 18:59:22 -0400 Subject: [PATCH 155/158] outputing EXPDIR before running Config in setup xml 2 --- workflow/setup_xml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index 18e8f6cac0..673463e529 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -58,7 +58,7 @@ def main(*argv): 'verbosity': user_inputs.verbosity} current_env = os.environ.copy() - print( f'EXPDIR: {current_env['EXPDIR']}') + print( f'EXPDIR: {current_env["EXPDIR"]}') cfg = Configuration(user_inputs.expdir) From f6d5dd65c4703076a7095af4909762c5ceb0c518 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 19:19:13 -0400 Subject: [PATCH 156/158] tring env unclaching wxflow repo to see if it is solving the EXPDIR problem with setup_xml --- .github/workflows/ci_uint_tests.yaml | 5 +---- workflow/setup_xml.py | 3 --- 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index da91e2dad6..80652d84ae 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -24,7 +24,7 @@ jobs: sudo apt-get install -y perl libxml-libxml-perl libxml-libxslt-perl libdatetime-perl python -m pip install --upgrade pip pip install pytest - pip install wxflow + pip install git+https://github.com/TerrenceMcGuinness-NOAA/wxflow.git@config_env_xor pip install wget - name: Cache Rocoto Install @@ -57,9 +57,6 @@ jobs: pytest -v -k test_rocoto_done pytest -v -k test_rocoto_stalled pytest -v -k test_setup_exp - #ls -l $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM - #grep EXPDIR $GITHUB_WORKSPACE/ci/scripts/tests/testdata/RUNDIR/C48_ATM/config.base - #echo "EXPDIR: ${EXPDIR}" pytest -v -k test_setup_xml diff --git a/workflow/setup_xml.py b/workflow/setup_xml.py index 673463e529..a66e4922a3 100755 --- a/workflow/setup_xml.py +++ b/workflow/setup_xml.py @@ -57,9 +57,6 @@ def main(*argv): 'taskthrottle': user_inputs.taskthrottle, 'verbosity': user_inputs.verbosity} - current_env = os.environ.copy() - print( f'EXPDIR: {current_env["EXPDIR"]}') - cfg = Configuration(user_inputs.expdir) base = cfg.parse_config('config.base') From 69b226eb794f289b5a854251a31e567feeee8325 Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Tue, 25 Jun 2024 19:47:11 -0400 Subject: [PATCH 157/158] try test with updated wxflow (if works then get to that fix) --- .github/workflows/ci_uint_tests.yaml | 1 + .gitmodules | 3 ++- sorc/wxflow | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci_uint_tests.yaml b/.github/workflows/ci_uint_tests.yaml index 80652d84ae..f0d2b0b69e 100644 --- a/.github/workflows/ci_uint_tests.yaml +++ b/.github/workflows/ci_uint_tests.yaml @@ -48,6 +48,7 @@ jobs: sudo mkdir -p /scratch1/NCEPDEV cd $GITHUB_WORKSPACE/sorc/wxflow git submodule update --init + git checkout config_env_xor cd $GITHUB_WORKSPACE/sorc ./link_workflow.sh cd $GITHUB_WORKSPACE/ci/scripts/tests diff --git a/.gitmodules b/.gitmodules index 5c9e569243..a3593b4804 100644 --- a/.gitmodules +++ b/.gitmodules @@ -4,7 +4,8 @@ ignore = dirty [submodule "sorc/wxflow"] path = sorc/wxflow - url = https://github.com/NOAA-EMC/wxflow + url = https://github.com/TerrenceMcGuinness-NOAA/wxflow.git + branch = config_env_xor [submodule "sorc/gfs_utils.fd"] path = sorc/gfs_utils.fd url = https://github.com/NOAA-EMC/gfs-utils diff --git a/sorc/wxflow b/sorc/wxflow index 8406beeea4..57af2f5f53 160000 --- a/sorc/wxflow +++ b/sorc/wxflow @@ -1 +1 @@ -Subproject commit 8406beeea410118cdfbd8300895b2b2878eadba6 +Subproject commit 57af2f5f53747cf60d6d366fd82dd6fbd0749df0 From 5300dc271eac92a177694c7220669fef37a0d85f Mon Sep 17 00:00:00 2001 From: Terry McGuinness Date: Wed, 26 Jun 2024 11:45:49 -0400 Subject: [PATCH 158/158] added corner case for checking expected fail for when name snapces are irreconcilable when set to same vaule in config file --- ci/scripts/tests/test_setup.py | 61 +++++++++++++++++++++++++++++++--- sorc/wxflow | 2 +- 2 files changed, 58 insertions(+), 5 deletions(-) diff --git a/ci/scripts/tests/test_setup.py b/ci/scripts/tests/test_setup.py index 0973acc854..88929de483 100755 --- a/ci/scripts/tests/test_setup.py +++ b/ci/scripts/tests/test_setup.py @@ -1,5 +1,6 @@ -from wxflow import Executable, Configuration +from wxflow import Executable, Configuration, ProcessError from shutil import rmtree +import pytest import os _here = os.path.dirname(__file__) @@ -26,10 +27,18 @@ def test_setup_expt(): def test_setup_xml(): - setup_xml_script = Executable(os.path.join(HOMEgfs, "workflow", "setup_xml.py")) + script_content = '''#!/usr/bin/env bash +export ACCOUNT=fooman +export HOMEgfs=foobar +../../../workflow/setup_xml.py "${1}" +''' + with open('run_setup_xml.sh', 'w') as file: + file.write(script_content) + os.chmod('run_setup_xml.sh', 0o755) + + setup_xml_script = Executable(os.path.join(HOMEgfs, "ci", "scripts", "tests", "run_setup_xml.sh")) setup_xml_script.add_default_arg(f"{RUNDIR}/{pslot}") setup_xml_script() - assert (setup_xml_script.returncode == 0) cfg = Configuration(f"{RUNDIR}/{pslot}") @@ -37,10 +46,54 @@ def test_setup_xml(): assert base.ACCOUNT == account assert foobar not in base.values() - assert "UNKNOWN" not in base.values() + assert "UNKOWN" not in base.values() with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: contents = file.read() assert contents.count(account) > 5 + os.remove('run_setup_xml.sh') rmtree(RUNDIR) + + +def test_setup_xml_fail_config_env_cornercase(): + script_content = '''#!/usr/bin/env bash +export ACCOUNT=fv3-cpu +export HOMEgfs=foobar +../../../workflow/setup_xml.py "${1}" +''' + with open('run_setup_xml.sh', 'w') as file: + file.write(script_content) + os.chmod('run_setup_xml.sh', 0o755) + + try: + setup_xml_script = Executable(os.path.join(HOMEgfs, "ci", "scripts", "tests", "run_setup_xml.sh")) + setup_xml_script.add_default_arg(f"{RUNDIR}/{pslot}") + setup_xml_script() + assert (setup_xml_script.returncode == 0) + + cfg = Configuration(f"{RUNDIR}/{pslot}") + base = cfg.parse_config('config.base') + assert base.ACCOUNT == account + + assert foobar not in base.values() + assert "UNKOWN" not in base.values() + + with open(f"{RUNDIR}/{pslot}/{pslot}.xml", 'r') as file: + contents = file.read() + assert contents.count(account) > 5 + + except ProcessError as e: + # We expect this fail becuse ACCOUNT=fv3-cpu in config.base and environment + pass + except Exception as e: + # If an exception occurs, pass the test with a custom message + pytest.fail(f"Expected exception occurred: {e}") + + finally: + # Cleanup code to ensure it runs regardless of test outcome + os.remove('run_setup_xml.sh') + try: + rmtree(RUNDIR) + except FileNotFoundError: + pass diff --git a/sorc/wxflow b/sorc/wxflow index 57af2f5f53..5382a0e8af 160000 --- a/sorc/wxflow +++ b/sorc/wxflow @@ -1 +1 @@ -Subproject commit 57af2f5f53747cf60d6d366fd82dd6fbd0749df0 +Subproject commit 5382a0e8afa26c9c036ffcc93113fef6d4d08e1a