Merge branch 'main' into tools/bcftools

.github/CODEOWNERS

@@ -1,13 +1,32 @@
 # See documentation here:
-# https://blog.github.com/2017-07-06-introducing-code-owners/
+# https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/creating-a-repository-on-github/about-code-owners
 
-tools/art/*                      @hexylena
-tools/circos/*                   @hexylena @shiltemann
-tools/jbrowse/*                  @hexylena @abretaud
-tools/blastxml_to_gapped_gff3/*  @hexylena
-tools/gff3_rebase/*              @hexylena
-tools/jq/*                       @hexylena
-tools/hmmer3/*                   @hexylena
-tools/progressivemauve/*         @hexylena
-tools/ncbi_entrez_eutils/*       @hexylena
-tools/mothur/*                   @shiltemann
+/tool_collections/snpeff/               @nsoranzo
+/tools/abyss/                           @nsoranzo
+/tools/ampvis2/                         @bernt-matthias
+/tools/art/                             @hexylena
+/tools/bcftools/                        @nsoranzo
+/tools/blastxml_to_gapped_gff3/         @hexylena
+/tools/cdhit/                           @nsoranzo
+/tools/circos/                          @hexylena @shiltemann
+/tools/collection_element_identifiers/  @nsoranzo
+/tools/column_maker/                    @nsoranzo
+/tools/dada2/                           @bernt-matthias
+/tools/emboss_5/                        @nsoranzo
+/tools/gff3_rebase/                     @hexylena
+/tools/hmmer3/                          @hexylena @nsoranzo
+/tools/jbrowse/                         @hexylena @abretaud
+/tools/jq/                              @hexylena
+/tools/minia/                           @nsoranzo
+/tools/mitos/                           @bernt-matthias
+/tools/mothur/                          @shiltemann
+/tools/ncbi_entrez_eutils/              @hexylena
+/tools/progressivemauve/                @hexylena
+/tools/prokka/                          @nsoranzo
+/tools/raxml/                           @nsoranzo
+/tools/revoluzer/                         @bernt-matthias
+/tools/scater/                          @nsoranzo
+/tools/seurat/                          @nsoranzo
+/tools/sickle/                          @nsoranzo
+/tools/stringtie/                       @nsoranzo
+/tools/ucsc_tools/                      @nsoranzo

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,6 @@
 FOR CONTRIBUTOR:
-* [ ] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo.
-* [ ] - License permits unrestricted use (educational + commercial)
-* [ ] - This PR adds a new tool or tool collection
-* [ ] - This PR updates an existing tool or tool collection
-* [ ] - This PR does something else (explain below)
+* [ ] I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo.
+* [ ] License permits unrestricted use (educational + commercial)
+* [ ] This PR adds a new tool or tool collection
+* [ ] This PR updates an existing tool or tool collection
+* [ ] This PR does something else (explain below)

.github/styler.R

@@ -0,0 +1,36 @@
+#!/usr/bin/env Rscript
+
+library("argparse")
+library("styler")
+
+parser <- ArgumentParser(description = "Call styler")
+parser$add_argument("dir",
+    metavar = "DIR", type = "character",
+    help = "File to parse"
+)
+parser$add_argument("--dry",
+    choices = c("off", "on"), default = "on"
+)
+args <- parser$parse_args()
+
+file_info <- file.info(args$dir)
+is_directory <- file_info$isdir
+
+if (is_directory) {
+    captured_output <- capture.output({
+        result <- style_dir(args$dir, indent_by = 4, dry = args$dry, recursive = TRUE)
+    })
+} else {
+    captured_output <- capture.output({
+        result <- style_file(args$dir, indent_by = 4, dry = args$dry)
+    })
+}
+
+n <- nrow(subset(result, changed == TRUE))
+if (n > 0) {
+    if (args$dry == "off") {
+        print(paste("Changed", n, "files"))
+    } else {
+        stop(paste("Linting failed for", n, "files"))
+    }
+}

.github/workflows/ci.yaml

@@ -7,12 +7,12 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_21.05
+  GALAXY_BRANCH: release_24.0
   MAX_CHUNKS: 40
 jobs:
   setup:
     name: Setup cache and determine changed repositories
-    if: github.repository_owner == 'galaxyproject'
+    if: ${{ github.repository_owner == 'galaxyproject' }}
     runs-on: ubuntu-latest
     outputs:
       galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
@@ -23,11 +23,11 @@ jobs:
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -37,17 +37,17 @@ jobs:
       id: get-fork-branch
       run: |
         TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
-        echo "::set-output name=fork::${TMP:-$GALAXY_FORK}"
+        echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT
         TMP="${{ github.event.client_payload.slash_command.args.named.branch }}"
-        echo "::set-output name=branch::${TMP:-$GALAXY_BRANCH}"
+        echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
-      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)"
-    - uses: actions/setup-python@v1
+      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -56,7 +56,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -74,6 +74,42 @@ jobs:
       run: |
         echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
 
+  lint:
+    name: Check for missing containers
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Planemo lint
+      uses: galaxyproject/planemo-ci-action@v1
+      id: lint
+      with:
+        mode: lint
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        tool-list: ${{ needs.setup.outputs.tool-list }}
+        additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion
+    - uses: actions/upload-artifact@v4
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
   test:
     name: Test tools
     # This job runs on Linux
@@ -84,7 +120,7 @@ jobs:
       fail-fast: false
       matrix:
         chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
-        python-version: ['3.7']
+        python-version: ['3.11']
     services:
       postgres:
         image: postgres:11
@@ -97,18 +133,23 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v2
+      id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
     - name: Planemo test
       uses: galaxyproject/planemo-ci-action@v1
       id: test
@@ -119,7 +160,10 @@ jobs:
         galaxy-branch: ${{ needs.setup.outputs.branch }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
-    - uses: actions/upload-artifact@v2
+        galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
+        # Limit each test to 15 minutes
+        test_timeout: 900
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -134,18 +178,18 @@ jobs:
     needs: [setup, test]
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -156,18 +200,19 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
     - name: Create URL to the run output
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
       id: vars
-      run: echo "::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
+      run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}