Update pr workflow

.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/pr.yaml

@@ -2,7 +2,6 @@ name: Galaxy Tool Linting and Tests for push and PR
 on:
   pull_request:
     paths-ignore:
-      - '.github/**'
       - 'deprecated/**'
       - 'docs/**'
       - '*'
@@ -11,13 +10,12 @@ on:
       - main
       - master
     paths-ignore:
-      - '.github/**'
       - 'deprecated/**'
       - 'docs/**'
       - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.1
+  GALAXY_BRANCH: release_24.1
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
@@ -45,7 +43,7 @@ jobs:
       commit-range: ${{ steps.discover.outputs.commit-range }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - name: Print github context properties
       run: |
@@ -59,17 +57,17 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -80,7 +78,7 @@ jobs:
       run: pip install wheel
     - name: Install flake8
       run: pip install flake8 flake8-import-order
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -111,38 +109,29 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
-
-    - name: Set fail level for pull request
-      if: ${{ github.event_name == 'pull_request' }}
-      run:
-        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
-    - name: Set fail level for merge
-      if: ${{ github.event_name != 'pull_request' }}
-      run:
-        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
-        fail-level: ${{ env.FAIL_LEVEL }}
+        fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -157,16 +146,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -175,7 +164,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -184,57 +173,37 @@ jobs:
   lintr:
     name: Lint R scripts
     needs: setup
-    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
+    if: ${{ needs.setup.outputs.repository-list != '' }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-20.04]
         r-version: ['release']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.r-version }}
     - name: Cache R packages
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
-    - name: Install non-R lintr dependencies
-      run: sudo apt-get install libcurl4-openssl-dev
-    - name: Install lintr
-      run: |
-        install.packages('remotes')
-        remotes::install_cran("lintr")
-      shell: Rscript {0}
-    - name: Save repositories to file
-      run: echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
+    - name: Install packages
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        packages: |
+          any::argparse 
+          any::styler
     - name: lintr
       run: |
-        library(lintr)
-        linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_name_linter = NULL)
-        con <- file("repository_list.txt", "r")
-        status <- 0
-        while (TRUE) {
-          repo <- readLines(con, n = 1)
-          if (length(repo) == 0) {
-             break
-          }
-          lnt <- lint_dir(repo, relative_path=T, linters=linters)
-          if (length(lnt) > 0) {
-            status <- 1
-            for (l in lnt) {
-              rel_path <- paste(repo, l$filename, sep="/")
-              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message, paste("(", l$line, ")")), stderr())
-              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message, paste("(", l$line, ")")), "rlint_report.txt", append=TRUE)
-            }
-          }
-        }
-        quit(status = status)
-      shell: Rscript {0}
-    - uses: actions/upload-artifact@v3
+        set -eo pipefail
+        echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
+        git status
+        git diff --exit-code | tee rlint_report.txt
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -246,7 +215,7 @@ jobs:
     if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Check file sizes
@@ -261,7 +230,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -278,7 +247,7 @@ 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
@@ -289,26 +258,26 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
         key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v1
+      uses: SimenB/github-actions-cpu-cores@v2
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -325,7 +294,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 1800
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -342,16 +311,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -362,10 +331,12 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+        markdown-report: true
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
     - name: Check outputs
       uses: galaxyproject/planemo-ci-action@v1
       id: check
@@ -386,16 +357,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -429,7 +400,7 @@ jobs:
       with:
         sha: ${{ github.event.after }}
     - name: Create comment
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         issue-number: ${{ steps.getpr.outputs.number }}