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Add image verification support to CI #117

Merged
merged 13 commits into from
Mar 18, 2024
Merged

Add image verification support to CI #117

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646f8c1
Update pr.yaml
kostrykin Mar 15, 2024
c76e797
Update
kostrykin Mar 15, 2024
192fe4e
Update pr.yaml
kostrykin Mar 15, 2024
9587d71
Add `pip install pillow`
kostrykin Mar 15, 2024
1665b0b
Temporarilly fix CI
kostrykin Mar 15, 2024
d17b08c
Update pr.yaml
kostrykin Mar 16, 2024
efdf1a5
Update ci.yaml
kostrykin Mar 16, 2024
7154d16
Add test tool from `/test/functional/tools/image_diff.xml`
kostrykin Mar 16, 2024
6a4ac41
Update pr.yaml
kostrykin Mar 16, 2024
33b73f4
Add .shed.yml
kostrykin Mar 16, 2024
d7b2ed3
Add missing test files
kostrykin Mar 16, 2024
dba0717
Switch CI to galaxy fork `kostrykin/galaxy` branch `galaxy-image-anal…
kostrykin Mar 18, 2024
1f45a4c
Remove `test` tool
kostrykin Mar 18, 2024
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45 changes: 43 additions & 2 deletions .github/workflows/ci.yaml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
python -m pip install git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
#
# ---------------------------------------------------------
#
- name: Planemo lint
uses: galaxyproject/planemo-ci-action@v1
id: lint
Expand Down Expand Up @@ -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://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
python -m pip install git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
python -m pip install pillow
#
# ---------------------------------------------------------
#
- name: Planemo test
uses: galaxyproject/planemo-ci-action@v1
id: test
Expand Down
29 changes: 27 additions & 2 deletions .github/workflows/pr.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
python -m pip install --no-dependencies git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
#
# ---------------------------------------------------------
#
- name: Planemo lint
uses: galaxyproject/planemo-ci-action@v1
id: lint
Expand Down Expand Up @@ -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://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
python -m pip install --no-dependencies git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
python -m pip install pillow
#
# ---------------------------------------------------------
#
- name: Planemo test
uses: galaxyproject/planemo-ci-action@v1
id: test
Expand Down