From 4ce5211ed91f5a4c8092e7be2a0d95e23380034e Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Mon, 18 Mar 2024 16:01:47 +0100 Subject: [PATCH] Add image verification support to CI (#117) * Update pr.yaml * Update * Update pr.yaml * Add `pip install pillow` * Temporarilly fix CI * Update pr.yaml * Update ci.yaml * Add test tool from `/test/functional/tools/image_diff.xml` * Update pr.yaml * Add .shed.yml * Add missing test files * Switch CI to galaxy fork `kostrykin/galaxy` branch `galaxy-image-analysis` This is a temporary change to enable the features from: - https://github.com/galaxyproject/galaxy/pull/17556 - https://github.com/galaxyproject/galaxy/pull/17581 * Remove `test` tool --- .github/workflows/ci.yaml | 45 +++++++++++++++++++++++++++++++++++++-- .github/workflows/pr.yaml | 29 +++++++++++++++++++++++-- 2 files changed, 70 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 95babe7d..a2968b45 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -6,8 +6,8 @@ on: repository_dispatch: types: [run-all-tool-tests-command] env: - GALAXY_FORK: galaxyproject - GALAXY_BRANCH: release_23.2 + GALAXY_FORK: kostrykin # Temporary change to enable the features from https://github.com/galaxyproject/galaxy/pull/17556 and https://github.com/galaxyproject/galaxy/pull/17581 + GALAXY_BRANCH: galaxy-image-analysis # Temporary change to enable the features from https://github.com/galaxyproject/galaxy/pull/17556 and https://github.com/galaxyproject/galaxy/pull/17581 MAX_CHUNKS: 40 jobs: setup: @@ -96,6 +96,25 @@ jobs: with: path: ~/.cache/pip key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} +# +# --------------------------------------------------------- +# This is a temporary addition to enable the features from +# - https://github.com/galaxyproject/galaxy/pull/17556 +# - https://github.com/galaxyproject/galaxy/pull/17581 +# + - name: Planemo setup + uses: galaxyproject/planemo-ci-action@v1 + with: + mode: setup + repository-list: ${{ needs.setup.outputs.repository-list }} + tool-list: ${{ needs.setup.outputs.tool-list }} + additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata + - run: | + python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util + python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util +# +# --------------------------------------------------------- +# - name: Planemo lint uses: galaxyproject/planemo-ci-action@v1 id: lint @@ -150,6 +169,28 @@ jobs: id: cpu-cores - name: Clean dotnet folder for space run: rm -Rf /usr/share/dotnet +# +# --------------------------------------------------------- +# This is a temporary addition to enable the features from +# - https://github.com/galaxyproject/galaxy/pull/17556 +# - https://github.com/galaxyproject/galaxy/pull/17581 +# + - name: Planemo setup + uses: galaxyproject/planemo-ci-action@v1 + with: + mode: setup + repository-list: ${{ needs.setup.outputs.repository-list }} + galaxy-fork: ${{ needs.setup.outputs.fork }} + galaxy-branch: ${{ needs.setup.outputs.branch }} + chunk: ${{ matrix.chunk }} + chunk-count: ${{ needs.setup.outputs.chunk-count }} + - run: | + python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util + python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util + python -m pip install pillow +# +# --------------------------------------------------------- +# - name: Planemo test uses: galaxyproject/planemo-ci-action@v1 id: test diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 2fa59905..fc0d696e 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -16,8 +16,8 @@ on: - 'docs/**' - '*' env: - GALAXY_FORK: galaxyproject - GALAXY_BRANCH: release_23.2 + GALAXY_FORK: kostrykin # Temporary change to enable the features from https://github.com/galaxyproject/galaxy/pull/17556 and https://github.com/galaxyproject/galaxy/pull/17581 + GALAXY_BRANCH: galaxy-image-analysis # Temporary change to enable the features from https://github.com/galaxyproject/galaxy/pull/17556 and https://github.com/galaxyproject/galaxy/pull/17581 MAX_CHUNKS: 4 MAX_FILE_SIZE: 1M concurrency: @@ -133,6 +133,18 @@ jobs: if: ${{ github.event_name != 'pull_request' }} run: | echo "FAIL_LEVEL=error" >> "$GITHUB_ENV" +# +# --------------------------------------------------------- +# This is a temporary addition to enable the features from +# - https://github.com/galaxyproject/galaxy/pull/17556 +# - https://github.com/galaxyproject/galaxy/pull/17581 +# + - run: | + python -m pip install --no-dependencies git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util + python -m pip install --no-dependencies git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util +# +# --------------------------------------------------------- +# - name: Planemo lint uses: galaxyproject/planemo-ci-action@v1 id: lint @@ -292,6 +304,19 @@ jobs: id: cpu-cores - name: Clean dotnet folder for space run: rm -Rf /usr/share/dotnet +# +# --------------------------------------------------------- +# This is a temporary addition to enable the features from +# - https://github.com/galaxyproject/galaxy/pull/17556 +# - https://github.com/galaxyproject/galaxy/pull/17581 +# + - run: | + python -m pip install --no-dependencies git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util + python -m pip install --no-dependencies git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util + python -m pip install pillow +# +# --------------------------------------------------------- +# - name: Planemo test uses: galaxyproject/planemo-ci-action@v1 id: test