From 5abcfcb0507dd9a92a292004284b6c5b633d594a Mon Sep 17 00:00:00 2001 From: lecorguille Date: Mon, 31 May 2021 14:47:50 +0200 Subject: [PATCH 1/3] CI : enable github action --- .github/PULL_REQUEST_TEMPLATE.md | 6 + .github/workflows/pr.yaml | 437 +++++++++++++++++++++++++++++++ .travis.yml | 22 -- 3 files changed, 443 insertions(+), 22 deletions(-) create mode 100644 .github/PULL_REQUEST_TEMPLATE.md create mode 100644 .github/workflows/pr.yaml delete mode 100644 .travis.yml diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..cbc909c --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +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) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml new file mode 100644 index 0000000..c5fca4c --- /dev/null +++ b/.github/workflows/pr.yaml @@ -0,0 +1,437 @@ +name: Galaxy Tool Linting and Tests for push and PR +on: [push, pull_request] +env: + GALAXY_REPO: https://github.com/galaxyproject/galaxy + GALAXY_RELEASE: release_20.09 + MAX_CHUNKS: 4 +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 }} + commit_range: ${{ steps.get-commit-range.outputs.commit_range }} + nchunks: ${{ steps.get-chunks.outputs.nchunks }} + chunk_list: ${{ steps.get-chunks.outputs.chunk_list }} + 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: ${{ github.event.after }}' + - name: Determine latest commit in the Galaxy repo + id: get-galaxy-sha + run: echo "::set-output name=galaxy_head_sha::$(git ls-remote ${{ env.GALAXY_REPO }} refs/heads/${{ env.GALAXY_RELEASE }} | cut -f1)" + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Cache .cache/pip + uses: actions/cache@v2 + id: cache-pip + with: + path: ~/.cache/pip + key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }} + - name: Cache .planemo + uses: actions/cache@v2 + id: cache-planemo + with: + path: ~/.planemo + key: planemo_cache_py_${{ 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 Planemo and flake8 + run: pip install planemo flake8 flake8-import-order + - name: Fake a Planemo run to update cache + if: steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' + run: | + touch tool.xml + PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE + - uses: actions/checkout@v2 + with: + fetch-depth: 0 + # The range of commits to check for changes is: + # - `origin/master...` for all events happening on a feature branch + # - for events on the master branch we compare against the sha before the event + # (note that this does not work for feature branch events since we want all + # commits on the feature branch and not just the commits of the last event) + # - for pull requests we compare against the 1st ancestor, given the current + # HEAD is the merge between the PR branch and the base branch + - name: Set commit range (push to the feature branch) + if: github.ref != 'refs/heads/master' && github.event_name == 'push' + run: | + git fetch origin master + echo "COMMIT_RANGE=origin/master..." >> $GITHUB_ENV + - name: Set commit range (push to the master branch, e.g. merge) + if: github.ref == 'refs/heads/master' && github.event_name == 'push' + run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV + - name: Set commit range (pull request) + if: github.event_name == 'pull_request' + run: echo "COMMIT_RANGE=HEAD~.." >> $GITHUB_ENV + - id: get-commit-range + run: echo "::set-output name=commit_range::$COMMIT_RANGE" + - name: Planemo ci_find_repos for the commit range + run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --exclude_from .tt_skip --output repository_list.txt + - name: Show repository list + run: cat repository_list.txt + - uses: actions/upload-artifact@v2 + with: + name: Workflow artifacts + path: repository_list.txt + - name: Planemo ci_find_tools for the repository list + run: | + touch tool_list.txt + if [ -s repository_list.txt ]; then + planemo ci_find_tools --output tool_list.txt $(cat repository_list.txt) + fi + - name: Show tool list + run: cat tool_list.txt + - name: Compute chunks + id: get-chunks + run: | + nchunks=$(wc -l < tool_list.txt) + if [ "$nchunks" -gt "$MAX_CHUNKS" ]; then + nchunks=$MAX_CHUNKS + elif [ "$nchunks" -eq 0 ]; then + nchunks=1 + fi + echo "::set-output name=nchunks::$nchunks" + echo "::set-output name=chunk_list::[$(seq -s ", " 0 $(($nchunks - 1)))]" + - name: Show chunks + run: | + echo 'Using ${{ steps.get-chunks.outputs.nchunks }} chunks (${{ steps.get-chunks.outputs.chunk_list }})' + + # Planemo lint the changed repositories + lint: + name: Lint tools + needs: setup + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: [3.7] + steps: + # checkout the repository + # and use it as the current working directory + - uses: actions/checkout@v2 + with: + fetch-depth: 0 + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - uses: actions/download-artifact@v2 + with: + name: Workflow artifacts + path: ../workflow_artifacts/ + - name: Cache .cache/pip + uses: actions/cache@v2 + id: cache-pip + with: + path: ~/.cache/pip + key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }} + - name: Install Planemo + run: pip install planemo + - name: Planemo lint + run: | + set -e + while read -r DIR; do + planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; + done < ../workflow_artifacts/repository_list.txt + - name: Planemo ci_find_tools for the commit range + run: planemo ci_find_tools --changed_in_commit_range ${{ needs.setup.outputs.commit_range }} --exclude packages --exclude deprecated --exclude_from .tt_skip --output tool_list.txt + - name: Check if each changed tool is in the list of changed repositories + run: | + set -e + while read -r TOOL; do + # Check if any changed repo dir is a substring of $TOOL + if ! echo $TOOL | grep -qf ../workflow_artifacts/repository_list.txt; then + echo "Tool $TOOL not in changed repositories list: .shed.yml file missing" >&2 + exit 1 + fi + done < tool_list.txt + + # flake8 of Python scripts in the changed repositories + flake8: + name: Lint Python scripts + needs: setup + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: [3.7] + steps: + # checkout the repository to master + # and use it as the current working directory + - uses: actions/checkout@v2 + with: + fetch-depth: 1 + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - uses: actions/download-artifact@v2 + with: + name: Workflow artifacts + path: ../workflow_artifacts/ + - name: Cache .cache/pip + uses: actions/cache@v2 + id: cache-pip + with: + path: ~/.cache/pip + key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }} + - name: Install flake8 + run: pip install flake8 flake8-import-order + - name: Flake8 + run: | + if [ -s ../workflow_artifacts/repository_list.txt ]; then + flake8 $(cat ../workflow_artifacts/repository_list.txt) + fi + + lintr: + name: Lint R scripts + needs: setup + runs-on: ubuntu-latest + strategy: + matrix: + r-version: [4.0.1] + steps: + # checkout the repository to master + # and use it as the current working directory + - uses: actions/checkout@v2 + with: + fetch-depth: 1 + - uses: actions/download-artifact@v2 + with: + name: Workflow artifacts + path: ../workflow_artifacts/ + - uses: r-lib/actions/setup-r@master + with: + r-version: ${{ matrix.r-version }} + - name: Cache R packages + uses: actions/cache@v2 + with: + path: ${{ env.R_LIBS_USER }} + key: r_cache_${{ 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: lintr + run: | + library(lintr) + linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, + object_name_linter = NULL, object_usage_linter=NULL) + con <- file("../workflow_artifacts/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), stderr()) + } + } + } + quit(status = status) + shell: Rscript {0} + + # Planemo test the changed repositories, each chunk creates an artifact + # containing HTML and JSON reports for the executed tests + test: + name: Test tools + # This job runs on Linux + runs-on: ubuntu-latest + needs: setup + strategy: + fail-fast: false + matrix: + chunk: ${{ fromJson(needs.setup.outputs.chunk_list) }} + python-version: [3.7] + services: + postgres: + image: postgres:11 + env: + POSTGRES_USER: postgres + POSTGRES_PASSWORD: postgres + POSTGRES_DB: postgres + ports: + - 5432:5432 + steps: + # checkout the repository + # and use it as the current working directory + - uses: actions/checkout@v2 + with: + fetch-depth: 1 + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - uses: actions/download-artifact@v2 + with: + name: Workflow artifacts + path: ../workflow_artifacts/ + - name: Cache .cache/pip + uses: actions/cache@v2 + id: cache-pip + with: + path: ~/.cache/pip + key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }} + - name: Cache .planemo + uses: actions/cache@v2 + id: cache-planemo + with: + path: ~/.planemo + key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }} + - name: Install Planemo + run: pip install planemo + - name: Planemo ci_find_tools for the repository list, chunked + run: | + touch tool_list_chunk.txt + if [ -s ../workflow_artifacts/repository_list.txt ]; then + planemo ci_find_tools --chunk_count ${{ needs.setup.outputs.nchunks }} --chunk ${{ matrix.chunk }} --group_tools --output tool_list_chunk.txt $(cat ../workflow_artifacts/repository_list.txt) + fi + - name: Show tool list chunk + run: cat tool_list_chunk.txt + - name: Planemo test tools + run: | + mkdir json_output + while read -r TOOL_GROUP; do + # Check if any of the lines in .tt_biocontainer_skip is a substring of $TOOL_GROUP + if echo $TOOL_GROUP | grep -qf .tt_biocontainer_skip; then + PLANEMO_OPTIONS="" + else + PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init" + fi + json=$(mktemp -u -p json_output --suff .json) + PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json "$json" $TOOL_GROUP || true + docker system prune --all --force --volumes || true + done < tool_list_chunk.txt + if [ ! -s tool_list_chunk.txt ]; then + echo '{"tests":[]}' > "$(mktemp -u -p json_output --suff .json)" + fi + - name: Merge tool_test_output.json files + run: planemo merge_test_reports json_output/*.json tool_test_output.json + - name: Create tool_test_output.html + run: planemo test_reports tool_test_output.json --test_output tool_test_output.html + - name: Copy artifacts into place + run: | + mkdir upload + mv tool_test_output.json tool_test_output.html upload/ + - uses: actions/upload-artifact@v2 + 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] + strategy: + matrix: + python-version: [3.7] + # This job runs on Linux + runs-on: ubuntu-latest + steps: + - uses: actions/download-artifact@v2 + with: + path: artifacts + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Cache .cache/pip + uses: actions/cache@v2 + id: cache-pip + with: + path: ~/.cache/pip + key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }} + - name: Install Planemo + run: pip install planemo + - name: Install jq + run: sudo apt-get install jq + - name: Combine outputs + run: find artifacts/ -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} + + - name: Create tool_test_output.html + run: planemo test_reports tool_test_output.json --test_output tool_test_output.html + - name: Copy artifacts into place + run: | + mkdir upload + mv tool_test_output.json tool_test_output.html upload/ + - uses: actions/upload-artifact@v2 + with: + name: 'All tool test results' + path: upload + - name: Check status of combined outputs + run: | + if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then + echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details." + exit 1 + fi + + # deploy the tools to the toolsheds (first TTS for testing) + deploy: + name: Deploy + needs: [setup, lint, flake8, lintr, combine_outputs] + strategy: + matrix: + python-version: [3.7] + runs-on: ubuntu-latest + if: github.ref == 'refs/heads/master' && github.repository_owner == 'abims-sbr' + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: 1 + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - uses: actions/download-artifact@v2 + with: + name: Workflow artifacts + path: ../workflow_artifacts/ + - name: Cache .cache/pip + uses: actions/cache@v2 + id: cache-pip + with: + path: ~/.cache/pip + key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }} + - name: Install Planemo + run: pip install planemo + - name: Deploy on testtoolshed + env: + SHED_KEY: ${{ secrets.TTS_API_KEY }} + run: | + while read -r DIR; do + planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1; + done < ../workflow_artifacts/repository_list.txt + continue-on-error: true + - name: Deploy on toolshed + env: + SHED_KEY: ${{ secrets.TS_API_KEY }} + run: | + while read -r DIR; do + planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1; + done < ../workflow_artifacts/repository_list.txt diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index ccf408b..0000000 --- a/.travis.yml +++ /dev/null @@ -1,22 +0,0 @@ -# This is a special configuration file to run tests on Travis-CI via -# GitHub notifications when changes are committed. -# -# See http://travis-ci.org/ for details -language: python - -before_install: - - sudo apt-get install -y python-virtualenv - - virtualenv planemo-venv - - . planemo-venv/bin/activate - - pip install planemo - -script: - - travis_wait 20 - - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/01_Filter_Assemblies > /dev/null 2>&1 - - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/02_Pairwise > /dev/null 2>&1 - - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/03_POGs - - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/03b_Orthogroups_Tool > /dev/null 2>&1 - - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/04_BlastAlign > /dev/null 2>&1 - - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/05_CDS_search - - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/06_ConcatPhyl - - planemo test --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy_wrappers/07_MutCount From 8d28981f8692d2b830051462b3cc8e5d93c10999 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Tue, 5 Oct 2021 16:44:56 +0200 Subject: [PATCH 2/3] Update pr.yaml CI - update target galaxy to 21.05 --- .github/workflows/pr.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index c5fca4c..ff17786 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -2,7 +2,7 @@ name: Galaxy Tool Linting and Tests for push and PR on: [push, pull_request] env: GALAXY_REPO: https://github.com/galaxyproject/galaxy - GALAXY_RELEASE: release_20.09 + GALAXY_RELEASE: release_21.05 MAX_CHUNKS: 4 jobs: # the setup job does two things: From a16c0bf557ec205018d24db56a94891d3325719a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Wed, 27 Oct 2021 17:16:30 +0200 Subject: [PATCH 3/3] Create .tt_skip --- .tt_skip | 1 + 1 file changed, 1 insertion(+) create mode 100644 .tt_skip diff --git a/.tt_skip b/.tt_skip new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/.tt_skip @@ -0,0 +1 @@ +