v5.8.6+galaxy0 #26
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| #!/usr/bin/env Rscript | ||
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| library("argparse") | ||
| library("styler") | ||
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| 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$parse_args() | ||
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| file_info <- file.info(args$dir) | ||
| is_directory <- file_info$isdir | ||
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| if (is_directory) { | ||
| captured_output <- capture.output({ | ||
| result <- style_dir(args$dir, indent_by = 4, dry = args$dry, recursive = TRUE) | ||
| }) | ||
| } else { | ||
| captured_output <- capture.output({ | ||
| result <- style_file(args$dir, indent_by = 4, dry = args$dry) | ||
| }) | ||
| } | ||
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| n <- nrow(subset(result, changed == TRUE)) | ||
| if (n > 0) { | ||
| if (args$dry == "off") { | ||
| print(paste("Changed", n, "files")) | ||
| } else { | ||
| stop(paste("Linting failed for", n, "files")) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -2,13 +2,13 @@ name: Galaxy Tool Linting and Tests for push and PR | |
| on: [push, pull_request] | ||
| env: | ||
| GALAXY_FORK: galaxyproject | ||
| GALAXY_BRANCH: release_24.1 | ||
| MAX_CHUNKS: 4 | ||
| MAX_FILE_SIZE: 1M | ||
| concurrency: | ||
| # group runs by PR, but keep runs on main separate | ||
| # because we do not want to cancel toolshed uploads | ||
| group: pr-${{ (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/main') && github.run_number || github.ref }} | ||
|
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| cancel-in-progress: true | ||
| jobs: | ||
| # the setup job does two things: | ||
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@@ -19,6 +19,7 @@ jobs: | |
| # - a file containing the list of changed repositories | ||
| # which are needed in subsequent steps. | ||
| setup: | ||
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| name: Setup cache and determine changed repositories | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
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@@ -30,7 +31,7 @@ jobs: | |
| commit-range: ${{ steps.discover.outputs.commit-range }} | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.11'] | ||
| steps: | ||
| - name: Print github context properties | ||
| run: | | ||
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@@ -96,7 +97,7 @@ jobs: | |
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: ['3.11'] | ||
| steps: | ||
| # checkout the repository | ||
| # and use it as the current working directory | ||
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@@ -134,7 +135,7 @@ jobs: | |
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: ['3.11'] | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| with: | ||
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@@ -166,52 +167,32 @@ jobs: | |
| strategy: | ||
| matrix: | ||
| os: [ubuntu-20.04] | ||
| r-version: ['release'] | ||
| steps: | ||
| - 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@v4 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: r_cache_${{ matrix.os }}_${{ matrix.r-version }} | ||
| - name: Install packages | ||
| uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| packages: | | ||
| any::argparse | ||
| any::styler | ||
| - name: lintr | ||
| run: | | ||
| set -eo pipefail | ||
| echo '${{ 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' | ||
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@@ -257,7 +238,7 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }} | ||
| python-version: ['3.11'] | ||
| services: | ||
| postgres: | ||
| image: postgres:11 | ||
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@@ -288,16 +269,28 @@ jobs: | |
| with: | ||
| path: ~/.planemo | ||
| key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | ||
| - name: Prepare specific job_conf for Sirius | ||
| uses: danielr1996/[email protected] | ||
| env: | ||
| USERNAME_SIRIUS: "${{ secrets.USERNAME_SIRIUS }}" | ||
| PASSWORD_SIRIUS: "${{ secrets.PASSWORD_SIRIUS }}" | ||
| with: | ||
| input: "${{ github.workspace }}/config/job_conf_planemo.xml" | ||
| output: "${{ github.workspace }}/config/job_conf_planemo_subst.xml" | ||
| - name: Planemo test | ||
| uses: galaxyproject/planemo-ci-action@v1 | ||
| id: test | ||
| env: | ||
| USERNAME_SIRIUS: "${{ secrets.USERNAME_SIRIUS }}" | ||
| PASSWORD_SIRIUS: "${{ secrets.PASSWORD_SIRIUS }}" | ||
| with: | ||
| mode: test | ||
| repository-list: ${{ needs.setup.outputs.repository-list }} | ||
| galaxy-fork: ${{ env.GALAXY_FORK }} | ||
| galaxy-branch: ${{ env.GALAXY_BRANCH }} | ||
| chunk: ${{ matrix.chunk }} | ||
| chunk-count: ${{ needs.setup.outputs.chunk-count }} | ||
| additional-planemo-options: --job_config_file "${{ github.workspace }}/config/job_conf_planemo_subst.xml" | ||
|
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| - uses: actions/upload-artifact@v2 | ||
| with: | ||
| name: 'Tool test output ${{ matrix.chunk }}' | ||
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@@ -307,63 +300,70 @@ jobs: | |
| # to `|| true`) and create a global test report as json and html which | ||
| # is provided as artifact | ||
| # - check if any tool test actually failed (by lookup in the combined json) | ||
| # and fail this step if this is the case | ||
| combine_outputs: | ||
| name: Combine chunked test results | ||
| needs: [setup, test] | ||
| if: ${{ always() && needs.setup.outputs.repository-list != '' }} | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ['3.11'] | ||
| steps: | ||
| - uses: actions/download-artifact@v4 | ||
| with: | ||
| path: artifacts | ||
| - 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: Combine outputs | ||
| uses: galaxyproject/planemo-ci-action@v1 | ||
| id: combine | ||
| with: | ||
| mode: combine | ||
| html-report: true | ||
| markdown-report: true | ||
| - uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: 'All tool test results' | ||
| path: upload | ||
| - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY | ||
| - name: Check outputs | ||
| uses: galaxyproject/planemo-ci-action@v1 | ||
| id: check | ||
| with: | ||
| mode: check | ||
| - name: Check if all test chunks succeeded | ||
| run: | | ||
| NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l) | ||
| if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then | ||
| exit 1 | ||
| fi | ||
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| # deploy the tools to the toolsheds (first TTS for testing) | ||
| deploy: | ||
| name: Deploy | ||
| needs: [setup, lint, combine_outputs] | ||
| if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }} | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| 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 | ||
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@@ -386,7 +386,7 @@ jobs: | |
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| determine-success: | ||
| name: Check workflow success | ||
| needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs] | ||
| if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
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@@ -402,6 +402,6 @@ jobs: | |
| - name: Indicate file size check status | ||
| if: ${{ needs.file_sizes.result != 'success' && needs.file_sizes.result != 'skipped' }} | ||
| run: exit 1 | ||
| - name: Check tool test status | ||
| if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }} | ||
| run: exit 1 | ||
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Those are IUC updates, correct? Maybe put them into a separate PR so we know what belongs to this PR?
(I assume you need to change CI for testing as well)