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Update ip_imageinfo, update CI to release_24.1 #124

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Merged
kostrykin merged 4 commits into from
Jul 11, 2024
Merged

Update ip_imageinfo, update CI to release_24.1 #124

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367166c
bump ip_imageinfo
bernt-matthias Jul 11, 2024
97c1c92
update CI
bernt-matthias Jul 11, 2024
11ddc66
use recent profile
bernt-matthias Jul 11, 2024
6bc8575
remove all temporary code
bernt-matthias Jul 11, 2024
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45 changes: 2 additions & 43 deletions .github/workflows/ci.yaml
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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: 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:
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
30 changes: 3 additions & 27 deletions .github/workflows/pr.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
8 changes: 6 additions & 2 deletions tools/image_info/image_info.xml
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Original file line number Diff line number Diff line change
@@ -1,13 +1,17 @@
<tool id="ip_imageinfo" name="Show image info" version="5.7.1">
<tool id="ip_imageinfo" name="Show image info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
<description>with Bioformats</description>
<macros>
<token name="@TOOL_VERSION@">5.7.1</token>
<token name="@VERSION_SUFFIX@">1</token>
</macros>
<edam_operations>
<edam_operation>operation_3443</edam_operation>
</edam_operations>
<xrefs>
<xref type="biii">python-bioformats</xref>
</xrefs>
<requirements>
<requirement type="package" version="5.7.1">bftools</requirement>
<requirement type="package" version="@TOOL_VERSION@">bftools</requirement>
</requirements>
<command>
<![CDATA[
Expand Down