genenotebook: give a few more seconds to startup #260
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| name: Galaxy Tool Linting and Tests for push and PR | |
| on: [push, pull_request] | |
| env: | |
| GALAXY_FORK: galaxyproject | |
| GALAXY_BRANCH: release_23.0 | |
| MAX_CHUNKS: 4 | |
| MAX_FILE_SIZE: 1M | |
| concurrency: | |
| # Group runs by PR, but keep runs on the default branch separate | |
| # because we do not want to cancel ToolShed uploads | |
| group: pr-${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && github.run_number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| # the setup job does two things: | |
| # 1. cache the pip cache and .planemo | |
| # 2. determine the list of changed repositories | |
| # it produces one artifact which contains | |
| # - a file with the latest SHA from the chosen branch of the Galaxy repo | |
| # - a file containing the list of changed repositories | |
| # which are needed in subsequent steps. | |
| setup: | |
| name: Setup cache and determine changed repositories | |
| runs-on: ubuntu-latest | |
| outputs: | |
| galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| repository-list: ${{ steps.discover.outputs.repository-list }} | |
| tool-list: ${{ steps.discover.outputs.tool-list }} | |
| chunk-count: ${{ steps.discover.outputs.chunk-count }} | |
| chunk-list: ${{ steps.discover.outputs.chunk-list }} | |
| commit-range: ${{ steps.discover.outputs.commit-range }} | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| steps: | |
| - name: Print github context properties | |
| run: | | |
| echo 'event: ${{ github.event_name }}' | |
| echo 'sha: ${{ github.sha }}' | |
| echo 'ref: ${{ github.ref }}' | |
| echo 'head_ref: ${{ github.head_ref }}' | |
| echo 'base_ref: ${{ github.base_ref }}' | |
| echo 'event.before: ${{ github.event.before }}' | |
| echo 'event.after: ${{ github.event.after }}' | |
| - name: Determine latest commit in the Galaxy repo | |
| id: get-galaxy-sha | |
| run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| - name: Cache .planemo | |
| uses: actions/cache@v3 | |
| id: cache-planemo | |
| with: | |
| path: ~/.planemo | |
| key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| # Install the `wheel` package so that when installing other packages which | |
| # are not available as wheels, pip will build a wheel for them, which can be cached. | |
| - name: Install wheel | |
| run: pip install wheel | |
| - name: Install flake8 | |
| run: pip install flake8 flake8-import-order | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: discover | |
| with: | |
| create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }} | |
| galaxy-fork: ${{ env.GALAXY_FORK }} | |
| galaxy-branch: ${{ env.GALAXY_BRANCH }} | |
| max-chunks: ${{ env.MAX_CHUNKS }} | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install GMOD python modules | |
| run: pip install tripal==3.2.1 biopython bcbio-gff chado==2.3.9 apollo==4.2.13 | |
| - name: Show commit range | |
| run: echo '${{ steps.discover.outputs.commit-range }}' | |
| - name: Show repository list | |
| run: echo '${{ steps.discover.outputs.repository-list }}' | |
| - name: Show tool list | |
| run: echo '${{ steps.discover.outputs.tool-list }}' | |
| - name: Show chunks | |
| run: | | |
| echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})' | |
| # Planemo lint the changed repositories | |
| lint: | |
| name: Lint tool-list | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.7'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ 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 }} | |
| - uses: actions/upload-artifact@v3 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'Tool linting output' | |
| path: lint_report.txt | |
| # flake8 of Python scripts in the changed repositories | |
| flake8: | |
| name: Lint Python scripts | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.7'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Install flake8 | |
| run: pip install flake8 flake8-import-order | |
| - name: Flake8 | |
| run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --ignore=E501,E117 --output-file pylint_report.txt --tee | |
| - uses: actions/upload-artifact@v3 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'Python linting output' | |
| path: pylint_report.txt | |
| lintr: | |
| name: Lint R scripts | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04] | |
| r-version: ['release'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| 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 | |
| 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: lintr | |
| run: | | |
| library(lintr) | |
| linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_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 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'R linting output' | |
| path: rlint_report.txt | |
| file_sizes: | |
| name: Check file sizes | |
| needs: setup | |
| if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Check file sizes | |
| run: | | |
| touch file_size_report.txt | |
| git diff --diff-filter=d --name-only ${{ needs.setup.outputs.commit-range }} > git.diff | |
| while read line; do | |
| find "$line" -type f -size +${{ env.MAX_FILE_SIZE }} >> file_size_report.txt | |
| done < git.diff | |
| if [[ -s file_size_report.txt ]]; then | |
| echo "Files larger than ${{ env.MAX_FILE_SIZE }} found" | |
| cat file_size_report.txt | |
| exit 1 | |
| fi | |
| - uses: actions/upload-artifact@v3 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'File size report' | |
| path: file_size_report.txt | |
| # Planemo test the changed repositories, each chunk creates an artifact | |
| # containing HTML and JSON reports for the executed tests | |
| test: | |
| name: Test tools | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }} | |
| python-version: ['3.8'] | |
| apollo: [0, 1] | |
| services: | |
| postgres: | |
| image: postgres:11 | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: postgres | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Cache .planemo | |
| uses: actions/cache@v3 | |
| id: cache-planemo | |
| with: | |
| path: ~/.planemo | |
| key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Get number of CPU cores | |
| uses: SimenB/github-actions-cpu-cores@v1 | |
| id: cpu-cores | |
| - name: Install GMOD python modules | |
| run: pip install tripal==3.2.1 biopython bcbio-gff chado==2.3.9 apollo==4.2.13 | |
| - name: Bootstrap Apollo | |
| if: ${{ contains(needs.setup.outputs.repository-list, 'tools/apollo') }} | |
| env: | |
| APOLLO_REMOTE: "${{ matrix.apollo }}" | |
| BLAT_ENABLED: "1" | |
| ARROW_GLOBAL_CONFIG_PATH: "${{ github.workspace }}/tools/apollo/test-data/arrow.yml" | |
| GALAXY_SHARED_DIR: "${{ github.workspace }}/apollo_shared_dir" | |
| run: ./bootstrap_apollo.sh | |
| - name: Prepare specific job_conf for Apollo tools | |
| if: ${{ contains(needs.setup.outputs.repository-list, 'tools/apollo') }} | |
| uses: danielr1996/[email protected] | |
| env: | |
| APOLLO_REMOTE: "${{ matrix.apollo }}" | |
| BLAT_ENABLED: "1" | |
| ARROW_GLOBAL_CONFIG_PATH: "${{ runner.workspace }}/galaxy-tools/tools/apollo/test-data/arrow.yml" | |
| GALAXY_SHARED_DIR: "${{ runner.workspace }}/galaxy-tools/apollo_shared_dir" | |
| DEFAULT_MOUNTS: "$defaults" | |
| with: | |
| input: "${{ github.workspace }}/job_conf_apollo.xml" | |
| output: "${{ github.workspace }}/job_conf_apollo_subst.xml" | |
| - name: Planemo test | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: test | |
| env: | |
| APOLLO_REMOTE: "${{ matrix.apollo }}" | |
| BLAT_ENABLED: "1" | |
| ARROW_GLOBAL_CONFIG_PATH: "${{ github.workspace }}/tools/apollo/test-data/arrow.yml" | |
| GALAXY_SHARED_DIR: "${{ github.workspace }}/apollo_shared_dir" | |
| 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 }} | |
| galaxy-slots: ${{ steps.cpu-cores.outputs.count }} | |
| # Limit each test to 15 minutes | |
| test_timeout: 900 | |
| additional-planemo-options: "${{ contains(needs.setup.outputs.repository-list, 'tools/apollo') && format('--job_config_file {0}/job_conf_apollo_subst.xml', github.workspace) || '' }}" | |
| - name: Show Apollo logs | |
| if: ${{ contains(needs.setup.outputs.repository-list, 'tools/apollo') }} | |
| run: docker logs apollo | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: 'Tool test output ${{ matrix.chunk }}' | |
| path: upload | |
| # - combine the results of the test chunks (which will never fail due | |
| # 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: ${{ needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| path: artifacts | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Install jq | |
| run: sudo apt-get install jq | |
| - name: Combine outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: combine | |
| with: | |
| mode: combine | |
| html-report: true | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - name: Check outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: check | |
| with: | |
| mode: check | |
| # deploy the tools to the toolsheds (first TTS for testing) | |
| deploy: | |
| name: Deploy | |
| needs: [setup, lint, flake8, lintr, combine_outputs] | |
| if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxy-genome-annotation' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Deploy on testtoolshed | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| with: | |
| mode: deploy | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| shed-target: testtoolshed | |
| shed-key: ${{ secrets.TTS_API_KEY }} | |
| continue-on-error: true | |
| - name: Deploy on toolshed | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| with: | |
| mode: deploy | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| shed-target: toolshed | |
| shed-key: ${{ secrets.TS_API_KEY }} | |
| 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: | |
| - name: Check tool lint status | |
| if: ${{ needs.lint.result != 'success' && needs.flake8.result != 'skipped' }} | |
| run: exit 1 | |
| - name: Indicate Python script lint status | |
| if: ${{ needs.flake8.result != 'success' && needs.flake8.result != 'skipped' }} | |
| run: exit 1 | |
| - name: Indicate R script lint status | |
| if: ${{ needs.lintr.result != 'success' && needs.lintr.result != 'skipped' }} | |
| run: exit 1 | |
| - 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 |