From b73c0aa8797de31e62329da44217e135641f99c9 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 23 Apr 2024 21:43:16 -0400 Subject: [PATCH 01/14] Add test using ModelMimic generated data --- test/MVK_template.json | 13 +++++++++ test/TSC_template.json | 33 ++++++++++++++++++++++ test/test_evv.py | 62 ++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 test/MVK_template.json create mode 100644 test/TSC_template.json create mode 100644 test/test_evv.py diff --git a/test/MVK_template.json b/test/MVK_template.json new file mode 100644 index 0000000..7c6461f --- /dev/null +++ b/test/MVK_template.json @@ -0,0 +1,13 @@ +{ + "MVK": { + "module": "MODULE_LOCATION", + "test-case": "Test", + "test-dir": "TEST_DIRECTORY", + "ref-case": "Baseline", + "ref-dir": "BASELINE_DIRECTORY", + "var-set": "default", + "ninst": 30, + "component": "eam", + "img-fmt": "png" + } +} \ No newline at end of file diff --git a/test/TSC_template.json b/test/TSC_template.json new file mode 100644 index 0000000..b149ffa --- /dev/null +++ b/test/TSC_template.json @@ -0,0 +1,33 @@ +{ + "TSC": { + "module": "MODULE_LOCATION", + "test-case": "Test", + "test-dir": "TEST_DIRECTORY", + "ref-case": "Baseline", + "ref-dir": "BASELINE_DIRECTORY", + "var-set": "default", + "time-slice": [ + 10, + 600 + ], + "inspect-times": [ + 300, + 450, + 600 + ], + "variables": [ + "T", + "Q", + "V", + "CLDLIQ", + "CLDICE", + "NUMLIQ", + "NUMICE", + "num_a1", + "num_a2", + "num_a3" + ], + "p-threshold": 0.005, + "component": "eam" + } +} \ No newline at end of file diff --git a/test/test_evv.py b/test/test_evv.py new file mode 100644 index 0000000..fb80976 --- /dev/null +++ b/test/test_evv.py @@ -0,0 +1,62 @@ +from pathlib import Path +import evv4esm +import evv4esm # pylint: disable=import-error +from evv4esm.__main__ import main as evv # pylint: disable=import-error +from modelmimic import mimic as mmc +from collections import namedtuple +import json + +evv_lib_dir = Path(evv4esm.__file__).parent.resolve() +mimic_lib_dir = Path(mmc.__file__).parent.resolve() +cl_args = namedtuple("Args", ["cfg"]) +evv_tests = {"TSC": "tsc.py", "MVK": "ks.py"} + + +def gen_data_run_evv(evv_test): + _args = cl_args( + cfg=Path(mimic_lib_dir, "config", f"{evv_test}.toml") + ) + # Generate data for all the tests (should be a pass b4b / pass non-b4b / fail) + out_dirs = mmc.main(_args) + + # Load the EVV4ESM configuration template + with open(f"{evv_test}_template.json", "r", encoding="utf-8") as _template: + evv_cfg_template = json.loads(_template.read()) + + evv_cfg = {} + for result_check in ["pass_b4b", "pass_nb4b", "fail"]: + _check_cfg = dict(evv_cfg_template[evv_test]) + _check_cfg["module"] = str(Path(evv_lib_dir, "extensions", evv_tests[evv_test])) + _check_cfg["test-dir"] = str(out_dirs[result_check]["test"].resolve()) + _check_cfg["ref-dir"] = str(out_dirs[result_check]["baseline"].resolve()) + evv_cfg[f"{evv_test}_{result_check}"] = _check_cfg + + json_file = Path(f"{evv_test}_test_conf.json") + with open(json_file, "w") as config_file: + json.dump(evv_cfg, config_file, indent=4) + + evv_out_dir = Path(f"{evv_test}_test_output") + evv(["-e", str(json_file), "-o", str(evv_out_dir)]) + + with open(Path(evv_out_dir, "index.json")) as evv_f: + evv_status = json.load(evv_f) + + status = {} + for evv_ele in evv_status["Page"]["elements"]: + if "Table" in evv_ele: + _index = evv_ele["Table"]["index"][0] + _status = evv_ele["Table"]["data"]["Test status"][0].lower() == "pass" + status[_index] = _status + for _index in status: + if "pass" in _index: + assert status[_index], f"{_index} SHOULD BE PASS IS FAIL" + else: + assert not status[_index], f"{_index} SHOULD BE FAIL IS PASS" + + +def test_evv_tsc(): + gen_data_run_evv("TSC") + + +def test_evv_mvk(): + gen_data_run_evv("MVK") \ No newline at end of file From 756fda6a6d8be2398de814f24fc2d9ef74c1c42a Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 08:47:28 -0500 Subject: [PATCH 02/14] Add dev requirements for automated testing --- setup.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9570572..d586d07 100644 --- a/setup.py +++ b/setup.py @@ -32,7 +32,6 @@ from setuptools import setup - here = os.path.abspath(os.path.dirname(__file__)) with open(os.path.join(here, "README.md"), "r") as f: long_desc = f.read() @@ -77,6 +76,9 @@ "pybtex", "statsmodels>=0.14.0", ], + extras_require={ + "dev": ["modelmimic", "black", "isort", "pytest", "pydoctor"], + }, packages=["evv4esm"], entry_points={"console_scripts": ["evv = evv4esm.__main__:main"]}, zip_safe=False, From 98d522648cedc48013f60df99634656f56369d67 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 10:28:03 -0500 Subject: [PATCH 03/14] Fix test so it can be called from top level dir --- test/test_evv.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/test/test_evv.py b/test/test_evv.py index fb80976..8cd5416 100644 --- a/test/test_evv.py +++ b/test/test_evv.py @@ -13,14 +13,14 @@ def gen_data_run_evv(evv_test): - _args = cl_args( - cfg=Path(mimic_lib_dir, "config", f"{evv_test}.toml") - ) + _args = cl_args(cfg=Path(mimic_lib_dir, "config", f"{evv_test}.toml")) # Generate data for all the tests (should be a pass b4b / pass non-b4b / fail) out_dirs = mmc.main(_args) # Load the EVV4ESM configuration template - with open(f"{evv_test}_template.json", "r", encoding="utf-8") as _template: + with open( + Path(evv_lib_dir.parent, "test", f"{evv_test}_template.json"), "r", encoding="utf-8" + ) as _template: evv_cfg_template = json.loads(_template.read()) evv_cfg = {} @@ -59,4 +59,4 @@ def test_evv_tsc(): def test_evv_mvk(): - gen_data_run_evv("MVK") \ No newline at end of file + gen_data_run_evv("MVK") From 12ecf2e945e005d53c308fe61919a9b068361ce1 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 10:31:10 -0500 Subject: [PATCH 04/14] Move old test configs --- test/{ => archive}/mvk_b4b_pc0101123.json | 0 test/{ => archive}/mvk_maint1.0_edison_v_cori-knl.json | 0 test/{ => archive}/mvk_zm045_pc0101123.json | 0 test/{ => archive}/pge_b4b_pc0101123.json | 0 test/{ => archive}/pge_zm045_pc0101123.json | 0 test/{ => archive}/tsc_b4b_pc0101123.json | 0 test/{ => archive}/tsc_zm045_pc0101123.json | 0 7 files changed, 0 insertions(+), 0 deletions(-) rename test/{ => archive}/mvk_b4b_pc0101123.json (100%) rename test/{ => archive}/mvk_maint1.0_edison_v_cori-knl.json (100%) rename test/{ => archive}/mvk_zm045_pc0101123.json (100%) rename test/{ => archive}/pge_b4b_pc0101123.json (100%) rename test/{ => archive}/pge_zm045_pc0101123.json (100%) rename test/{ => archive}/tsc_b4b_pc0101123.json (100%) rename test/{ => archive}/tsc_zm045_pc0101123.json (100%) diff --git a/test/mvk_b4b_pc0101123.json b/test/archive/mvk_b4b_pc0101123.json similarity index 100% rename from test/mvk_b4b_pc0101123.json rename to test/archive/mvk_b4b_pc0101123.json diff --git a/test/mvk_maint1.0_edison_v_cori-knl.json b/test/archive/mvk_maint1.0_edison_v_cori-knl.json similarity index 100% rename from test/mvk_maint1.0_edison_v_cori-knl.json rename to test/archive/mvk_maint1.0_edison_v_cori-knl.json diff --git a/test/mvk_zm045_pc0101123.json b/test/archive/mvk_zm045_pc0101123.json similarity index 100% rename from test/mvk_zm045_pc0101123.json rename to test/archive/mvk_zm045_pc0101123.json diff --git a/test/pge_b4b_pc0101123.json b/test/archive/pge_b4b_pc0101123.json similarity index 100% rename from test/pge_b4b_pc0101123.json rename to test/archive/pge_b4b_pc0101123.json diff --git a/test/pge_zm045_pc0101123.json b/test/archive/pge_zm045_pc0101123.json similarity index 100% rename from test/pge_zm045_pc0101123.json rename to test/archive/pge_zm045_pc0101123.json diff --git a/test/tsc_b4b_pc0101123.json b/test/archive/tsc_b4b_pc0101123.json similarity index 100% rename from test/tsc_b4b_pc0101123.json rename to test/archive/tsc_b4b_pc0101123.json diff --git a/test/tsc_zm045_pc0101123.json b/test/archive/tsc_zm045_pc0101123.json similarity index 100% rename from test/tsc_zm045_pc0101123.json rename to test/archive/tsc_zm045_pc0101123.json From 6bd08855105e718092746dbc053c6140ed93c389 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 10:31:31 -0500 Subject: [PATCH 05/14] Remove old test configs --- test/archive/mvk_b4b_pc0101123.json | 12 ------ .../mvk_maint1.0_edison_v_cori-knl.json | 12 ------ test/archive/mvk_zm045_pc0101123.json | 12 ------ test/archive/pge_b4b_pc0101123.json | 38 ------------------- test/archive/pge_zm045_pc0101123.json | 38 ------------------- test/archive/tsc_b4b_pc0101123.json | 13 ------- test/archive/tsc_zm045_pc0101123.json | 13 ------- 7 files changed, 138 deletions(-) delete mode 100644 test/archive/mvk_b4b_pc0101123.json delete mode 100644 test/archive/mvk_maint1.0_edison_v_cori-knl.json delete mode 100644 test/archive/mvk_zm045_pc0101123.json delete mode 100644 test/archive/pge_b4b_pc0101123.json delete mode 100644 test/archive/pge_zm045_pc0101123.json delete mode 100644 test/archive/tsc_b4b_pc0101123.json delete mode 100644 test/archive/tsc_zm045_pc0101123.json diff --git a/test/archive/mvk_b4b_pc0101123.json b/test/archive/mvk_b4b_pc0101123.json deleted file mode 100644 index 27937eb..0000000 --- a/test/archive/mvk_b4b_pc0101123.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "mvk_bit-for-bit": { - "module": "/home/fjk/Documents/Code/EVV/evv/evv4esm/extensions/ks.py", - "test-case": "Test", - "test-dir": "/home/fjk/Documents/Data/E3SM/MVK/MVK_PL.ne4_ne4.FC5AV1C-04P2.cori-knl_intel.C.20190814_083745_svs62y/run", - "ref-case": "Reference", - "ref-dir": "/home/fjk/Documents/Data/E3SM/baselines/MVK_PL.ne4_ne4.FC5AV1C-04P2.cori-knl_intel", - "var-set": "default", - "ninst": 20, - "critical": 13 - } -} \ No newline at end of file diff --git a/test/archive/mvk_maint1.0_edison_v_cori-knl.json b/test/archive/mvk_maint1.0_edison_v_cori-knl.json deleted file mode 100644 index d1f8293..0000000 --- a/test/archive/mvk_maint1.0_edison_v_cori-knl.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "mvk_test_local": { - "module": "/ccs/home/kennedy/EVV/evv4esm/evv4esm/extensions/ks.py", - "test-case": "cori-knl.maint-1.0.ne4.FC5AV1C-L", - "test-dir": "/lustre/atlas1/cli106/proj-shared/salil/archive/cori-knl.maint-1.0.ne4.FC5AV1C-L/run", - "ref-case": "edison.maint-1.0.ne4.FC5AV1C-L", - "ref-dir": "/lustre/atlas1/cli106/proj-shared/salil/archive/edison.maint-1.0.ne4.FC5AV1C-L/run", - "var-set": "default", - "ninst": 30, - "critical": 13 - } -} diff --git a/test/archive/mvk_zm045_pc0101123.json b/test/archive/mvk_zm045_pc0101123.json deleted file mode 100644 index 2a7003c..0000000 --- a/test/archive/mvk_zm045_pc0101123.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "mvk_zmconv_c0_ocn_045": { - "module": "/home/fjk/Documents/Code/EVV/evv/evv4esm/extensions/ks.py", - "test-case": "Test", - "test-dir": "/home/fjk/Documents/Data/E3SM/MVK/MVK_PL.ne4_ne4.FC5AV1C-04P2.cori-knl_intel.C.20190802_125642_6cyb6x/run", - "ref-case": "Reference", - "ref-dir": "/home/fjk/Documents/Data/E3SM/MVK/MVK_PL.ne4_ne4.FC5AV1C-04P2.cori-knl_intel.C.20190814_083745_svs62y/run", - "var-set": "default", - "ninst": 20, - "critical": 13 - } -} \ No newline at end of file diff --git a/test/archive/pge_b4b_pc0101123.json b/test/archive/pge_b4b_pc0101123.json deleted file mode 100644 index 3908b66..0000000 --- a/test/archive/pge_b4b_pc0101123.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "pge_bit-for-bit": { - "module": "/home/fjk/Documents/Code/EVV/evv/evv4esm/extensions/pg.py", - "test-name": "Test", - "test-case": "PGN_P1x1.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.20190808_131552_4uv1o0", - "test-dir": "/home/fjk/Documents/Data/E3SM/PGN/PGN_P1x1.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.20190808_131552_4uv1o0/run", - "ref-name": "Baseline", - "ref-dir": "/home/fjk/Documents/Data/E3SM/baselines/PGN_P1x1.ne4_ne4.FC5AV1C-L.cori-knl_intel", - "variables": ["topphysbc", - "chkenergyfix", - "dadadj", - "zm_convr", - "zm_conv_evap", - "momtran", - "zm_conv_tend", - "convect_shallow_off", - "convect_shallow", - "clubb_ice1", - "clubb_det", - "clubb_ice4", - "micro_mg", - "cldwat_mic", - "aero_model_wetdep_ma", - "convtran2", - "cam_radheat", - "chemistry", - "clubb_srf", - "rayleigh_friction", - "aero_model_drydep_ma", - "Grav_wave_drag"], - "perturbations": { - "woprt": 0.0, "posprt": 1.0e-14, "negprt": -1.0e-14}, - "pge-cld": "cam.h0.cloud.nc", - "ninit": 6, - "init-file-template": "SMS_Ly5.ne4_ne4.FC5AV1C-04P2.eos_intel.ne45y.{}.{}.0002-{:02d}-01-00000.nc", - "instance-file-template": "{}cam_{:04d}.h0.0001-01-01-00000{}.nc" - } -} \ No newline at end of file diff --git a/test/archive/pge_zm045_pc0101123.json b/test/archive/pge_zm045_pc0101123.json deleted file mode 100644 index b41c0c0..0000000 --- a/test/archive/pge_zm045_pc0101123.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "pge_zmconv_c0_ocn_045": { - "module": "/home/fjk/Documents/Code/EVV/evv/evv4esm/extensions/pg.py", - "test-name": "Test", - "test-case": "PGN_P1x1.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.20190801_154712_6vlllj", - "test-dir": "/home/fjk/Documents/Data/E3SM/PGN/PGN_P1x1.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.20190801_154712_6vlllj/run", - "ref-name": "Baseline", - "ref-dir": "/home/fjk/Documents/Data/E3SM/baselines/PGN_P1x1.ne4_ne4.FC5AV1C-L.cori-knl_intel", - "variables": ["topphysbc", - "chkenergyfix", - "dadadj", - "zm_convr", - "zm_conv_evap", - "momtran", - "zm_conv_tend", - "convect_shallow_off", - "convect_shallow", - "clubb_ice1", - "clubb_det", - "clubb_ice4", - "micro_mg", - "cldwat_mic", - "aero_model_wetdep_ma", - "convtran2", - "cam_radheat", - "chemistry", - "clubb_srf", - "rayleigh_friction", - "aero_model_drydep_ma", - "Grav_wave_drag"], - "perturbations": { - "woprt": 0.0, "posprt": 1.0e-14, "negprt": -1.0e-14}, - "pge-cld": "cam.h0.cloud.nc", - "ninit": 6, - "init-file-template": "SMS_Ly5.ne4_ne4.FC5AV1C-04P2.eos_intel.ne45y.{}.{}.0002-{:02d}-01-00000.nc", - "instance-file-template": "{}cam_{:04d}.h0.0001-01-01-00000{}.nc" - } -} \ No newline at end of file diff --git a/test/archive/tsc_b4b_pc0101123.json b/test/archive/tsc_b4b_pc0101123.json deleted file mode 100644 index ae286c4..0000000 --- a/test/archive/tsc_b4b_pc0101123.json +++ /dev/null @@ -1,13 +0,0 @@ -{ - "tsc_bit-for-bit": { - "module": "/home/fjk/Documents/Code/EVV/evv/evv4esm/extensions/tsc.py", - "test-case": "Test", - "test-dir": "/home/fjk/Documents/Data/E3SM/TSC/TSC.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.20190814_122931_ih9kks/run", - "ref-case": "Reference", - "ref-dir": "/home/fjk/Documents/Data/E3SM/baselines/TSC.ne4_ne4.FC5AV1C-L.cori-knl_intel", - "time-slice": [10, 600], - "inspect-times": [300, 450, 600], - "variables": ["T", "Q", "V", "CLDLIQ", "CLDICE", "NUMLIQ", "NUMICE", "num_a1", "num_a2", "num_a3"], - "p-threshold": 0.005 - } -} \ No newline at end of file diff --git a/test/archive/tsc_zm045_pc0101123.json b/test/archive/tsc_zm045_pc0101123.json deleted file mode 100644 index 58dc464..0000000 --- a/test/archive/tsc_zm045_pc0101123.json +++ /dev/null @@ -1,13 +0,0 @@ -{ - "tsc_zmconv_c0_ocn_045": { - "module": "/home/fjk/Documents/Code/EVV/evv/evv4esm/extensions/tsc.py", - "test-case": "Test", - "test-dir": "/home/fjk/Documents/Data/E3SM/TSC/TSC.ne4_ne4.FC5AV1C-L.cori-knl_intel.C.20190802_105217_a3t36f/run", - "ref-case": "Reference", - "ref-dir": "/home/fjk/Documents/Data/E3SM/TSC/TSC.ne4_ne4.FC5AV1C-L.cori-knl_intel.G.20190710_143749_i2r1c6/run", - "time-slice": [10, 600], - "inspect-times": [300, 450, 600], - "variables": ["T", "Q", "V", "CLDLIQ", "CLDICE", "NUMLIQ", "NUMICE", "num_a1", "num_a2", "num_a3"], - "p-threshold": 0.005 - } -} \ No newline at end of file From 32f86a58c1512534f90f446a6aee3ab5146ac3e9 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 10:32:21 -0500 Subject: [PATCH 06/14] Add workflow configs --- .github/workflows/python-package.yml | 34 ++++++++++++++++++++++++ .github/workflows/python-publish.yml | 39 ++++++++++++++++++++++++++++ .gitignore | 1 + 3 files changed, 74 insertions(+) create mode 100644 .github/workflows/python-package.yml create mode 100644 .github/workflows/python-publish.yml diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 0000000..7165cbb --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,34 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Python package + +on: + push: + branches: [ "master" ] + pull_request: + branches: [ "master" ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.10", "3.11", "3.12"] + + steps: + - uses: actions/checkout@v4 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python3 -m pip install --upgrade pip + python3 -m pip install pytest + python3 -m pip install -e .\[dev\] + - name: Test with pytest + run: | + pytest -vvv diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml new file mode 100644 index 0000000..15e93dd --- /dev/null +++ b/.github/workflows/python-publish.yml @@ -0,0 +1,39 @@ +# This workflow will upload a Python Package using Twine when a release is created +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Upload Python Package + +on: + release: + types: [published] + +permissions: + contents: read + +jobs: + deploy: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.x' + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install build + - name: Build package + run: python -m build + - name: Publish package + uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 + with: + user: __token__ + password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.gitignore b/.gitignore index 387079b..ea87352 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ test/*_test test/*_test_* +test/data #####=== Vim ===##### [._]*.s[a-w][a-z] From 09fe85c8c46dceb03d9dfa4a0d6453e308c02712 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 10:39:19 -0500 Subject: [PATCH 07/14] Fix pre-commit issues --- .git-blame-ignore-revs | 2 +- .gitignore | 1 - LICENSE | 1 - README.md | 2 +- evv4esm/__main__.py | 8 +++---- evv4esm/ensembles/e3sm.py | 6 ++--- evv4esm/ensembles/tools.py | 6 ++--- evv4esm/extensions/ks.bib | 1 - evv4esm/extensions/ks_vars.json | 2 +- evv4esm/extensions/kso.py | 9 ++++---- evv4esm/extensions/ocean_vars.json | 2 +- evv4esm/extensions/pg.bib | 2 +- evv4esm/extensions/pg.py | 26 ++++++++-------------- evv4esm/extensions/tsc.bib | 2 +- evv4esm/extensions/tsc.py | 15 ++++++------- evv4esm/resources/css/acknowledgments.css | 6 ++--- evv4esm/resources/css/captionjs.min.css | 2 +- evv4esm/resources/css/jquery-ui.min.css | 2 +- evv4esm/resources/css/livv.css | 8 +++---- evv4esm/resources/css/normalize.css | 2 +- evv4esm/resources/js/common.js | 15 ++++++------- evv4esm/resources/js/jquery-ui.min.js | 2 +- evv4esm/resources/js/jquery.caption.min.js | 2 +- evv4esm/resources/js/lightbox.min.js | 2 +- evv4esm/resources/js/lightbox.min.map | 2 +- evv4esm/resources/validation.html | 2 +- evv4esm/utils.py | 4 +--- test/MVK_template.json | 2 +- test/TSC_template.json | 2 +- test/test_evv.py | 13 ++++++----- 30 files changed, 69 insertions(+), 82 deletions(-) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 6b706cf..99dce63 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -1 +1 @@ -0e03e4395fae0aa0b6ab475feb054e53135f2352 \ No newline at end of file +0e03e4395fae0aa0b6ab475feb054e53135f2352 diff --git a/.gitignore b/.gitignore index ea87352..ac2adf6 100644 --- a/.gitignore +++ b/.gitignore @@ -68,4 +68,3 @@ docs/_build/ # PyBuilder target/ - diff --git a/LICENSE b/LICENSE index 6d17b24..e81bc71 100644 --- a/LICENSE +++ b/LICENSE @@ -25,4 +25,3 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - diff --git a/README.md b/README.md index 051600a..6dead57 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,6 @@ Want to send us a private message? * github: @mkstratos * email: kelleherme [at] ornl.gov -**Joseph H. Kennedy** +**Joseph H. Kennedy** * github: @jhkennedy * email: kennedyjh [at] ornl.gov diff --git a/evv4esm/__main__.py b/evv4esm/__main__.py index 0ce3555..0ebf50d 100755 --- a/evv4esm/__main__.py +++ b/evv4esm/__main__.py @@ -28,15 +28,16 @@ # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +import argparse import os import sys import time -import argparse -import evv4esm import livvkit from livvkit.util import options +import evv4esm + def parse_args(args=None): parser = argparse.ArgumentParser( @@ -127,10 +128,9 @@ def main(cl_args=None): print(" Machine: " + livvkit.machine) print(" " + livvkit.comment) + from livvkit import elements, scheduler from livvkit.components import validation - from livvkit import scheduler from livvkit.util import functions - from livvkit import elements livvkit.pool_size = args.pool_size if args.extensions: diff --git a/evv4esm/ensembles/e3sm.py b/evv4esm/ensembles/e3sm.py index def85ad..33667a3 100644 --- a/evv4esm/ensembles/e3sm.py +++ b/evv4esm/ensembles/e3sm.py @@ -30,17 +30,15 @@ """E3SM specific ensemble functions.""" -import six - +import glob import os import re -import glob - from collections import OrderedDict from functools import partial import numpy as np import pandas as pd +import six from netCDF4 import Dataset diff --git a/evv4esm/ensembles/tools.py b/evv4esm/ensembles/tools.py index 63a1c5c..84a344f 100644 --- a/evv4esm/ensembles/tools.py +++ b/evv4esm/ensembles/tools.py @@ -30,12 +30,12 @@ """General tools for working with ensembles.""" import os + +import matplotlib.pyplot as plt import numpy as np import pandas as pd -import matplotlib.pyplot as plt -from matplotlib.gridspec import GridSpec -from evv4esm import pf_color_picker, light_pf_color_picker +from evv4esm import light_pf_color_picker, pf_color_picker def monthly_to_annual_avg(var_data, cal="ignore"): diff --git a/evv4esm/extensions/ks.bib b/evv4esm/extensions/ks.bib index bdc6d54..3921486 100644 --- a/evv4esm/extensions/ks.bib +++ b/evv4esm/extensions/ks.bib @@ -25,4 +25,3 @@ @article{MAHAJAN2019 eprint = {https://doi.org/10.1177/1094342019837341}, abstract = {We present a methodology for solution reproducibility for the Energy Exascale Earth System Model during its ongoing software infrastructure development to prepare for exascale computers. The nonlinear chaotic nature of climate system simulations precludes traditional model verification approaches since machine precision differences—resulting from code refactoring, changes in software environment, and so on—grow exponentially to a different weather state. Here, we leverage the nature of climate as a statistical description of the atmosphere in order to establish model reproducibility. We evaluate the degree to which two-sample equality of distribution tests can confidently detect the change in climate from minor tuning parameter changes on model output variables in order to establish the level of difference that indicates a new climate. To apply this (baselined test), we target a section of the model’s development cycle wherein no intentional science changes have been applied to its source code. We compare an ensemble of short simulations that were conducted using a verified model configuration against a new ensemble with the same configuration but with the latest software infrastructure (Common Infrastructure for Modeling the Earth, CIME5.0), compiler versions, and software libraries. We also compare these against ensemble simulations conducted using the original version of the software infrastructure (CIME4.0) of the earlier model configuration, but with the latest compilers and software libraries, to test the impact of new compilers and libraries in isolation from additional software infrastructure. The two-sample equality of distribution tests indicates that these ensembles indeed represent the same climate.} } - diff --git a/evv4esm/extensions/ks_vars.json b/evv4esm/extensions/ks_vars.json index 112ed90..9ed8ff3 100644 --- a/evv4esm/extensions/ks_vars.json +++ b/evv4esm/extensions/ks_vars.json @@ -157,4 +157,4 @@ "soa_a1_SRF", "soa_a2_2", "soa_a2_SRF"] -} \ No newline at end of file +} diff --git a/evv4esm/extensions/kso.py b/evv4esm/extensions/kso.py index 3f3b508..61846d3 100644 --- a/evv4esm/extensions/kso.py +++ b/evv4esm/extensions/kso.py @@ -52,16 +52,17 @@ import livvkit import numpy as np import pandas as pd -from evv4esm import EVVException, human_color_names -from evv4esm.ensembles import e3sm -from evv4esm.ensembles.tools import prob_plot -from evv4esm.utils import bib2html from livvkit import elements as el from livvkit.util import functions as fn from livvkit.util.LIVVDict import LIVVDict from scipy import stats from statsmodels.stats import multitest as smm +from evv4esm import EVVException, human_color_names +from evv4esm.ensembles import e3sm +from evv4esm.ensembles.tools import prob_plot +from evv4esm.utils import bib2html + def variable_set(name): var_sets = fn.read_json(os.path.join(os.path.dirname(__file__), "ocean_vars.json")) diff --git a/evv4esm/extensions/ocean_vars.json b/evv4esm/extensions/ocean_vars.json index 0277fc4..d442fa4 100644 --- a/evv4esm/extensions/ocean_vars.json +++ b/evv4esm/extensions/ocean_vars.json @@ -6,4 +6,4 @@ "velocityMeridional{}", "velocityZonal{}" ] -} \ No newline at end of file +} diff --git a/evv4esm/extensions/pg.bib b/evv4esm/extensions/pg.bib index 8c4a094..131e2fc 100644 --- a/evv4esm/extensions/pg.bib +++ b/evv4esm/extensions/pg.bib @@ -3,4 +3,4 @@ @article{SINGH2020 title = {A verification strategy for atmospheric model codes using initial condition perturbations}, journal = {Journal of Geophysical Research: Atmospheres}, year = {In prep.} -} \ No newline at end of file +} diff --git a/evv4esm/extensions/pg.py b/evv4esm/extensions/pg.py index c6b7ff5..84b1663 100644 --- a/evv4esm/extensions/pg.py +++ b/evv4esm/extensions/pg.py @@ -36,31 +36,23 @@ simulation for many initial conditions, with each initial condition subject to multiple perturbations. """ -import six - -import os -import math import argparse - -# import logging +import math +import os +from collections import OrderedDict from pathlib import Path - from pprint import pprint -from collections import OrderedDict +import livvkit +import matplotlib.patches as mpatches +import matplotlib.pyplot as plt import numpy as np import pandas as pd - -import matplotlib.pyplot as plt -import matplotlib.patches as mpatches - -from scipy import stats -from netCDF4 import Dataset - -import livvkit +import six from livvkit import elements as el from livvkit.util import functions as fn -from livvkit.util.LIVVDict import LIVVDict +from netCDF4 import Dataset +from scipy import stats from evv4esm.utils import bib2html diff --git a/evv4esm/extensions/tsc.bib b/evv4esm/extensions/tsc.bib index e0e5265..632708c 100644 --- a/evv4esm/extensions/tsc.bib +++ b/evv4esm/extensions/tsc.bib @@ -9,4 +9,4 @@ @Article{gmd-10-537-2017 PAGES = {537--552}, URL = {https://www.geosci-model-dev.net/10/537/2017/}, DOI = {10.5194/gmd-10-537-2017} -} \ No newline at end of file +} diff --git a/evv4esm/extensions/tsc.py b/evv4esm/extensions/tsc.py index 1e3a1b9..17ad111 100644 --- a/evv4esm/extensions/tsc.py +++ b/evv4esm/extensions/tsc.py @@ -52,24 +52,23 @@ import os from collections import OrderedDict from itertools import groupby -from pprint import pprint from pathlib import Path +from pprint import pprint +import livvkit +import matplotlib.pyplot as plt +import matplotlib.ticker as tkr import numpy as np import pandas as pd -import matplotlib.ticker as tkr -import matplotlib.pyplot as plt -from scipy import stats -from netCDF4 import Dataset - -import livvkit from livvkit import elements as el from livvkit.util import functions as fn from livvkit.util.LIVVDict import LIVVDict +from netCDF4 import Dataset +from scipy import stats +from evv4esm import human_color_names, light_pf_color_picker, pf_color_picker from evv4esm.ensembles import e3sm from evv4esm.utils import bib2html -from evv4esm import pf_color_picker, light_pf_color_picker, human_color_names def parse_args(args=None): diff --git a/evv4esm/resources/css/acknowledgments.css b/evv4esm/resources/css/acknowledgments.css index 426b5ef..76179a1 100644 --- a/evv4esm/resources/css/acknowledgments.css +++ b/evv4esm/resources/css/acknowledgments.css @@ -3,7 +3,7 @@ width: 80%; min-width: 800px; padding: 1em 0px 0.5em 0px; - border: 0px solid white; + border: 0px solid white; margin-left: auto; margin-right: auto; margin-bottom: 120px; @@ -25,7 +25,7 @@ } #acklogo { - margin-left: auto; + margin-left: auto; margin-right: auto; text-align: justify; } @@ -40,7 +40,7 @@ vertical-align: top; display: inline-block; } - + #logoORNL { padding-top: 30px; height: 75px; diff --git a/evv4esm/resources/css/captionjs.min.css b/evv4esm/resources/css/captionjs.min.css index 93ade03..3efbc19 100644 --- a/evv4esm/resources/css/captionjs.min.css +++ b/evv4esm/resources/css/captionjs.min.css @@ -1 +1 @@ -.captionjs{line-height:0}.captionjs figcaption{line-height:1;-ms-box-sizing:border-box;-o-box-sizing:border-box;box-sizing:border-box;width:100%}.captionjs.captionjs-animated,.captionjs.captionjs-hidden,.captionjs.captionjs-stacked{position:relative;overflow:hidden}.captionjs.captionjs-animated figcaption,.captionjs.captionjs-hidden figcaption,.captionjs.captionjs-stacked figcaption{position:absolute}.captionjs.captionjs-stacked figcaption{bottom:0}.captionjs.captionjs-animated figcaption{-webkit-transition:.25s bottom;transition:.25s bottom}.captionjs.captionjs-animated:hover figcaption{bottom:0!important}.captionjs.captionjs-hidden figcaption{-webkit-transition:.25s margin-bottom;transition:.25s margin-bottom}.captionjs.captionjs-hidden:hover figcaption{margin-bottom:0!important} \ No newline at end of file +.captionjs{line-height:0}.captionjs figcaption{line-height:1;-ms-box-sizing:border-box;-o-box-sizing:border-box;box-sizing:border-box;width:100%}.captionjs.captionjs-animated,.captionjs.captionjs-hidden,.captionjs.captionjs-stacked{position:relative;overflow:hidden}.captionjs.captionjs-animated figcaption,.captionjs.captionjs-hidden figcaption,.captionjs.captionjs-stacked figcaption{position:absolute}.captionjs.captionjs-stacked figcaption{bottom:0}.captionjs.captionjs-animated figcaption{-webkit-transition:.25s bottom;transition:.25s bottom}.captionjs.captionjs-animated:hover figcaption{bottom:0!important}.captionjs.captionjs-hidden figcaption{-webkit-transition:.25s margin-bottom;transition:.25s margin-bottom}.captionjs.captionjs-hidden:hover figcaption{margin-bottom:0!important} diff --git a/evv4esm/resources/css/jquery-ui.min.css b/evv4esm/resources/css/jquery-ui.min.css index 331ab37..115f472 100644 --- a/evv4esm/resources/css/jquery-ui.min.css +++ b/evv4esm/resources/css/jquery-ui.min.css @@ -4,4 +4,4 @@ * To view and modify this theme, visit 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-224px}.ui-icon-grip-solid-vertical{background-position:-32px -224px}.ui-icon-grip-solid-horizontal{background-position:-48px -224px}.ui-icon-gripsmall-diagonal-se{background-position:-64px -224px}.ui-icon-grip-diagonal-se{background-position:-80px -224px}.ui-corner-all,.ui-corner-top,.ui-corner-left,.ui-corner-tl{border-top-left-radius:3px}.ui-corner-all,.ui-corner-top,.ui-corner-right,.ui-corner-tr{border-top-right-radius:3px}.ui-corner-all,.ui-corner-bottom,.ui-corner-left,.ui-corner-bl{border-bottom-left-radius:3px}.ui-corner-all,.ui-corner-bottom,.ui-corner-right,.ui-corner-br{border-bottom-right-radius:3px}.ui-widget-overlay{background:#aaa;opacity:.3;filter:Alpha(Opacity=30)}.ui-widget-shadow{margin:0 0 0 0;padding:5px;background:#666;opacity:.3;filter:Alpha(Opacity=30);border-radius:8px} diff --git a/evv4esm/resources/css/livv.css b/evv4esm/resources/css/livv.css index fc2f76e..92b38c9 100644 --- a/evv4esm/resources/css/livv.css +++ b/evv4esm/resources/css/livv.css @@ -58,10 +58,10 @@ a { } #header-icon { - float: left; - padding: 12px; + float: left; + padding: 12px; padding-left: 15px; - width: 70px; + width: 70px; } #header-home { @@ -149,7 +149,7 @@ td { } /****************************************************************************** - Element Styling + Element Styling ******************************************************************************/ .error {} diff --git a/evv4esm/resources/css/normalize.css b/evv4esm/resources/css/normalize.css index b0c1902..192eb9c 100644 --- a/evv4esm/resources/css/normalize.css +++ b/evv4esm/resources/css/normalize.css @@ -346,4 +346,4 @@ template { [hidden] { display: none; -} \ No newline at end of file +} diff --git a/evv4esm/resources/js/common.js b/evv4esm/resources/js/common.js index 3c4a4b6..46d02e4 100644 --- a/evv4esm/resources/js/common.js +++ b/evv4esm/resources/js/common.js @@ -1,21 +1,21 @@ /* / Copyright (c) 2015-2023, UT-BATTELLE, LLC / All rights reserved. -/ +/ / Redistribution and use in source and binary forms, with or without / modification, are permitted provided that the following conditions are met: -/ +/ / 1. Redistributions of source code must retain the above copyright notice, this / list of conditions and the following disclaimer. -/ +/ / 2. Redistributions in binary form must reproduce the above copyright notice, / this list of conditions and the following disclaimer in the documentation / and/or other materials provided with the distribution. -/ +/ / 3. Neither the name of the copyright holder nor the names of its contributors / may be used to endorse or promote products derived from this software without / specific prior written permission. -/ +/ / THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND / ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED / WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE @@ -65,7 +65,7 @@ $(window).load(function () { /** - * Draws the navigation sidebar by looking at the index.json data and appends the + * Draws the navigation sidebar by looking at the index.json data and appends the * list of resultant pages to the nav div. */ function drawNav() { @@ -90,7 +90,7 @@ function drawNav() { /** - * Draws content to the page by looking at the name of the page and loading the + * Draws content to the page by looking at the name of the page and loading the * appropriate dataset. */ function drawContent() { @@ -123,4 +123,3 @@ function loadJSON(path) { }); return data; } - diff --git a/evv4esm/resources/js/jquery-ui.min.js b/evv4esm/resources/js/jquery-ui.min.js index 5824d12..0245f83 100644 --- a/evv4esm/resources/js/jquery-ui.min.js +++ b/evv4esm/resources/js/jquery-ui.min.js @@ -10,4 +10,4 @@ return e.datepicker._get(n,"constrainInput")?(i=e.datepicker._possibleChars(e.da if(t.keyCode===e.ui.keyCode.TAB&&!t.isDefaultPrevented()){var i=this.uiDialog.find(":tabbable"),s=i.filter(":first"),n=i.filter(":last");t.target!==n[0]&&t.target!==this.uiDialog[0]||t.shiftKey?t.target!==s[0]&&t.target!==this.uiDialog[0]||!t.shiftKey||(this._delay(function(){n.focus()}),t.preventDefault()):(this._delay(function(){s.focus()}),t.preventDefault())}},mousedown:function(e){this._moveToTop(e)&&this._focusTabbable()}}),this.element.find("[aria-describedby]").length||this.uiDialog.attr({"aria-describedby":this.element.uniqueId().attr("id")})},_createTitlebar:function(){var t;this.uiDialogTitlebar=e("
").addClass("ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix").prependTo(this.uiDialog),this._on(this.uiDialogTitlebar,{mousedown:function(t){e(t.target).closest(".ui-dialog-titlebar-close")||this.uiDialog.focus()}}),this.uiDialogTitlebarClose=e("").button({label:this.options.closeText,icons:{primary:"ui-icon-closethick"},text:!1}).addClass("ui-dialog-titlebar-close").appendTo(this.uiDialogTitlebar),this._on(this.uiDialogTitlebarClose,{click:function(e){e.preventDefault(),this.close(e)}}),t=e("").uniqueId().addClass("ui-dialog-title").prependTo(this.uiDialogTitlebar),this._title(t),this.uiDialog.attr({"aria-labelledby":t.attr("id")})},_title:function(e){this.options.title||e.html(" "),e.text(this.options.title)},_createButtonPane:function(){this.uiDialogButtonPane=e("
").addClass("ui-dialog-buttonpane ui-widget-content ui-helper-clearfix"),this.uiButtonSet=e("
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diff --git a/evv4esm/resources/validation.html b/evv4esm/resources/validation.html index e734dca..743cc19 100644 --- a/evv4esm/resources/validation.html +++ b/evv4esm/resources/validation.html @@ -65,4 +65,4 @@

- \ No newline at end of file + diff --git a/evv4esm/utils.py b/evv4esm/utils.py index 072c25a..cb6dc2e 100644 --- a/evv4esm/utils.py +++ b/evv4esm/utils.py @@ -1,10 +1,8 @@ # coding=utf-8 -import six - import pybtex.database import pybtex.io - +import six from pybtex.backends.html import Backend as BaseBackend from pybtex.style.formatting.plain import Style as PlainStyle diff --git a/test/MVK_template.json b/test/MVK_template.json index 7c6461f..b2adcd7 100644 --- a/test/MVK_template.json +++ b/test/MVK_template.json @@ -10,4 +10,4 @@ "component": "eam", "img-fmt": "png" } -} \ No newline at end of file +} diff --git a/test/TSC_template.json b/test/TSC_template.json index b149ffa..c0292d1 100644 --- a/test/TSC_template.json +++ b/test/TSC_template.json @@ -30,4 +30,4 @@ "p-threshold": 0.005, "component": "eam" } -} \ No newline at end of file +} diff --git a/test/test_evv.py b/test/test_evv.py index 8cd5416..65499aa 100644 --- a/test/test_evv.py +++ b/test/test_evv.py @@ -1,10 +1,11 @@ +import json +from collections import namedtuple from pathlib import Path -import evv4esm + +from modelmimic import mimic as mmc + import evv4esm # pylint: disable=import-error from evv4esm.__main__ import main as evv # pylint: disable=import-error -from modelmimic import mimic as mmc -from collections import namedtuple -import json evv_lib_dir = Path(evv4esm.__file__).parent.resolve() mimic_lib_dir = Path(mmc.__file__).parent.resolve() @@ -19,7 +20,9 @@ def gen_data_run_evv(evv_test): # Load the EVV4ESM configuration template with open( - Path(evv_lib_dir.parent, "test", f"{evv_test}_template.json"), "r", encoding="utf-8" + Path(evv_lib_dir.parent, "test", f"{evv_test}_template.json"), + "r", + encoding="utf-8", ) as _template: evv_cfg_template = json.loads(_template.read()) From d5cf20d3ef89d7c937dc4d7d11bb2285a3020b4b Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 10:40:05 -0500 Subject: [PATCH 08/14] Ignore blame for pre-commit fixes --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 99dce63..5fe82ac 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -1 +1,2 @@ 0e03e4395fae0aa0b6ab475feb054e53135f2352 +09fe85c8c46dceb03d9dfa4a0d6453e308c02712 From 1af29c68c0f249efc7429ef9f19e67f0cc09136a Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 11:05:18 -0500 Subject: [PATCH 09/14] Fix warnings for logo in pytest --- evv4esm/__main__.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/evv4esm/__main__.py b/evv4esm/__main__.py index 0ebf50d..48270a6 100755 --- a/evv4esm/__main__.py +++ b/evv4esm/__main__.py @@ -111,16 +111,16 @@ def main(cl_args=None): cl_args = sys.argv[1:] args = parse_args(cl_args) - print("--------------------------------------------------------------------") - print(" ______ __ __ __ __ ") - print(" | ____| \ \ / / \ \ / / ") - print(" | |__ \ \ / / \ \ / / ") - print(" | __| \ \/ / \ \/ / ") - print(" | |____ \ / \ / ") - print(" |______| \/ \/ ") - print(" ") - print(" Extended Verification and Validation for Earth System Models ") - print("--------------------------------------------------------------------") + print(r"--------------------------------------------------------------------") + print(r" ______ __ __ __ __ ") + print(r" | ____| \ \ / / \ \ / / ") + print(r" | |__ \ \ / / \ \ / / ") + print(r" | __| \ \/ / \ \/ / ") + print(r" | |____ \ / \ / ") + print(r" |______| \/ \/ ") + print(r" ") + print(r" Extended Verification and Validation for Earth System Models ") + print(r"--------------------------------------------------------------------") print("") print(" Current run: " + livvkit.timestamp) print(" User: " + livvkit.user) From d923a6c6e96b63902da86ce04518580389428277 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 11:14:14 -0500 Subject: [PATCH 10/14] Switch setup.py to pyproject.toml for package setup --- pyproject.toml | 94 ++++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 85 --------------------------------------------- 2 files changed, 94 insertions(+), 85 deletions(-) create mode 100644 pyproject.toml delete mode 100644 setup.py diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..3409c97 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,94 @@ +# coding=utf-8 +# Copyright (c) 2018-2024 UT-BATTELLE, LLC +# All rights reserved. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: +# +# 1. Redistributions of source code must retain the above copyright notice, this +# list of conditions and the following disclaimer. +# +# 2. Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation +# and/or other materials provided with the distribution. +# +# 3. Neither the name of the copyright holder nor the names of its contributors +# may be used to endorse or promote products derived from this software without +# specific prior written permission. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +[build-system] +requires = ["setuptools>=61.0", "setuptools_scm[toml]>=6.2"] +build-backend = "setuptools.build_meta" + +[project] +authors = [ + { name = "Michael Kelleher", email = "kelleherme@ornl.gov" }, + { name = "Joseph H. Kennedy", email = "kennedyjh@ornl.gov" }, +] +name = "evv4esm" +requires-python = ">=3.6" +description = "Extended verification and validation for earth system models" +readme = { file = "README.md", content-type = "text/markdown" } +license = { text = "BSD-3-Clause" } +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "Topic :: Scientific/Engineering", + "Topic :: Software Development :: Testing", + "License :: OSI Approved :: BSD License", + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", +] +dependencies = [ + "six", + "numpy", + "scipy", + "pandas>=2.1.0", + "livvkit>=3.0.1", + "netCDF4", + "matplotlib", + "pybtex", + "statsmodels>=0.14.0", +] +dynamic = ["version"] + +[project.optional-dependencies] +dev = ["modelmimic", "ruff", "black", "isort", "pytest"] + +[project.scripts] +evv = "evv4esm.__main__:main" + +[project.urls] +Homepage = "https://github.com/LIVVkit/evv4esm" + +[tool.setuptools.dynamic] +version = { attr = "evv4esm.__version__" } + +[tool.pydoctor] +project-name = "evv4esm" +make-html = true +html-output = "./docs" +docformat = "numpy" +intersphinx = "https://docs.python.org/3/objects.inv" +theme = "readthedocs" +privacy = ["PRIVATE:**.__*__", "PUBLIC:**.__init__"] +add-package = ["./evv4esm"] diff --git a/setup.py b/setup.py deleted file mode 100644 index d586d07..0000000 --- a/setup.py +++ /dev/null @@ -1,85 +0,0 @@ -# coding=utf-8 -# Copyright (c) 2018-2022 UT-BATTELLE, LLC -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without -# modification, are permitted provided that the following conditions are met: -# -# 1. Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# -# 2. Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation -# and/or other materials provided with the distribution. -# -# 3. Neither the name of the copyright holder nor the names of its contributors -# may be used to endorse or promote products derived from this software without -# specific prior written permission. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND -# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -import os -import re - -from setuptools import setup - -here = os.path.abspath(os.path.dirname(__file__)) -with open(os.path.join(here, "README.md"), "r") as f: - long_desc = f.read() -with open(os.path.join(here, "evv4esm", "__init__.py")) as f: - init_file = f.read() - -setup( - name="evv4esm", - version=re.search(r"{}\s*=\s*[(]([^)]*)[)]".format("__version_info__"), init_file) - .group(1) - .replace(", ", "."), - description="Extended verification and validation for earth system models", - long_description=long_desc, - long_description_content_type="text/markdown", - url="https://github.com/LIVVkit/evv4esm", - author="Joseph H. Kennedy", - author_email="kennedyjh@ornl.gov", - maintainer="Michael Kelleher", - maintainer_email="kelleherme@ornl.gov", - license="BSD", - include_package_data=True, - classifiers=[ - "Development Status :: 5 - Production/Stable", - "Intended Audience :: Science/Research", - "Topic :: Scientific/Engineering", - "Topic :: Software Development :: Testing", - "License :: OSI Approved :: BSD License", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - ], - install_requires=[ - "six", - "numpy", - "scipy", - "pandas>=2.1.0", - "livvkit>=3.0.1", - "netCDF4", - "matplotlib", - "pybtex", - "statsmodels>=0.14.0", - ], - extras_require={ - "dev": ["modelmimic", "black", "isort", "pytest", "pydoctor"], - }, - packages=["evv4esm"], - entry_points={"console_scripts": ["evv = evv4esm.__main__:main"]}, - zip_safe=False, -) From a4162f683a0a2a34c2a7c818bc26a0b7d566b011 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 11:16:47 -0500 Subject: [PATCH 11/14] Add pre-commit action and config --- .github/workflows/pre-commit.yml | 27 +++++++++++++++++++++++++++ .pre-commit-config.yaml | 21 +++++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 .github/workflows/pre-commit.yml create mode 100644 .pre-commit-config.yaml diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml new file mode 100644 index 0000000..13e3376 --- /dev/null +++ b/.github/workflows/pre-commit.yml @@ -0,0 +1,27 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Pre-Commit + +on: + push: + branches: [ "master" ] + pull_request: + branches: [ "master" ] + +jobs: + + pre-commit: + runs-on: ubuntu-latest + timeout-minutes: 2 + steps: + - name: Checkout code + uses: actions/checkout@v4 + - name: Set up python + uses: actions/setup-python@v5 + with: + python-version: 3.11 + - name: Runs pre-commit + run: | + pip install pre-commit + pre-commit run -a diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..3798bcf --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,21 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.0.1 + hooks: + - id: end-of-file-fixer + - id: trailing-whitespace + - id: check-toml + - repo: https://github.com/psf/black + rev: 22.3.0 + hooks: + - id: black + - repo: https://github.com/pycqa/isort + rev: 5.13.2 + hooks: + - id: isort + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.3.7 + hooks: + # Run the linter. + - id: ruff From d6f6ca0596439b60df5aa278fb1100c58010f084 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 12:09:05 -0500 Subject: [PATCH 12/14] Update required version numbers --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3409c97..07af393 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. [build-system] -requires = ["setuptools>=61.0", "setuptools_scm[toml]>=6.2"] +requires = ["setuptools>=64", "setuptools_scm[toml]>=8"] build-backend = "setuptools.build_meta" [project] @@ -66,7 +66,7 @@ dependencies = [ "livvkit>=3.0.1", "netCDF4", "matplotlib", - "pybtex", + "pybtex>=0.24.0", "statsmodels>=0.14.0", ] dynamic = ["version"] From 51c3fef39707a0e55c4b979f58f382accdae246f Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 13:20:13 -0500 Subject: [PATCH 13/14] Add setuptools to reqs, fixes failure in Py>=3.12 --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 07af393..870bd80 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -59,6 +59,7 @@ classifiers = [ "Programming Language :: Python :: 3.12", ] dependencies = [ + "setuptools", "six", "numpy", "scipy", From 49cf200dca35fa17f02d812d62ca065bf67f1802 Mon Sep 17 00:00:00 2001 From: Michael Kelleher Date: Tue, 14 May 2024 13:25:20 -0500 Subject: [PATCH 14/14] Add Py3.9 to test matrix --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 7165cbb..43501f3 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -16,7 +16,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v4