diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 173e3be2..0a8c645f 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: 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 + GALAXY_FORK: galaxyproject + GALAXY_BRANCH: release_24.1 MAX_CHUNKS: 40 jobs: setup: @@ -96,25 +96,6 @@ 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/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util - python -m pip install git+https://git@github.com/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util -# -# --------------------------------------------------------- -# - name: Planemo lint uses: galaxyproject/planemo-ci-action@v1 id: lint @@ -169,28 +150,6 @@ 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/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util - python -m pip install git+https://git@github.com/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util - python -m pip install pillow tifffile -# -# --------------------------------------------------------- -# - name: Planemo test uses: galaxyproject/planemo-ci-action@v1 id: test diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 8c119537..bf006b98 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -16,8 +16,8 @@ on: - 'docs/**' - '*' env: - 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 + GALAXY_FORK: galaxyproject + GALAXY_BRANCH: release_24.1 MAX_CHUNKS: 4 MAX_FILE_SIZE: 1M concurrency: @@ -133,18 +133,7 @@ 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/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util - python -m pip install --no-dependencies git+https://git@github.com/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util -# -# --------------------------------------------------------- -# + - name: Planemo lint uses: galaxyproject/planemo-ci-action@v1 id: lint @@ -304,19 +293,6 @@ 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/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util - python -m pip install --no-dependencies git+https://git@github.com/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util - python -m pip install pillow tifffile -# -# --------------------------------------------------------- -# - name: Planemo test uses: galaxyproject/planemo-ci-action@v1 id: test diff --git a/tools/image_info/image_info.xml b/tools/image_info/image_info.xml index a18444ce..da3ea02d 100644 --- a/tools/image_info/image_info.xml +++ b/tools/image_info/image_info.xml @@ -1,5 +1,9 @@ - + with Bioformats + + 5.7.1 + 1 + operation_3443 @@ -7,7 +11,7 @@ python-bioformats - bftools + bftools