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Update bioconda_pr.yaml
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‎.github/workflows/bioconda_pr.yaml‎

Lines changed: 82 additions & 96 deletions
Original file line numberDiff line numberDiff line change
@@ -15,148 +15,134 @@ jobs:
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id: vars
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run: |
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set -e
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INIT_PATH=$(find . -type f -name '__init__.py' | head -n1)
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echo "📄 Found __init__.py at: $INIT_PATH"
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echo 'import ast' > get_version.py
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echo 'with open("'$INIT_PATH'") as f:' >> get_version.py
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echo ' tree = ast.parse(f.read())' >> get_version.py
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echo 'for node in ast.walk(tree):' >> get_version.py
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echo ' if isinstance(node, ast.Assign):' >> get_version.py
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echo ' if getattr(node.targets[0], "id", None) == "__version__":' >> get_version.py
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echo ' print(node.value.s)' >> get_version.py
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echo ' break' >> get_version.py
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VERSION=$(python3 get_version.py)
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python3 - <<EOF > .version.tmp
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import ast
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with open("$INIT_PATH") as f:
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tree = ast.parse(f.read())
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for node in ast.walk(tree):
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if isinstance(node, ast.Assign) and getattr(node.targets[0], "id", None) == "__version__":
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print(node.value.s)
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break
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EOF
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VERSION=$(cat .version.tmp)
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PACKAGE=$(basename $(dirname "$INIT_PATH"))
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if [ -z "$VERSION" ]; then
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echo "❌ __version__ not found in $INIT_PATH"
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cat "$INIT_PATH"
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echo "❌ __version__ not found"
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exit 1
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fi
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echo "📦 PACKAGE: $PACKAGE"
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echo "📌 VERSION: $VERSION"
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echo "VERSION=$VERSION" >> $GITHUB_ENV
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echo "PACKAGE=$PACKAGE" >> $GITHUB_ENV
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- name: Generate meta.yaml in recipes/${PACKAGE}
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- name: Generate meta.yaml in recipes/${{ env.PACKAGE }}
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run: |
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mkdir -p recipes/${PACKAGE}
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echo "{% set name = \"${PACKAGE}\" %}" > recipes/${PACKAGE}/meta.yaml
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echo "{% set version = \"${VERSION}\" %}" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "package:" >> recipes/${PACKAGE}/meta.yaml
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echo " name: \"{{ name|lower }}\"" >> recipes/${PACKAGE}/meta.yaml
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echo " version: \"{{ version }}\"" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "source:" >> recipes/${PACKAGE}/meta.yaml
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echo " url: https://github.com/kamome1201/${PACKAGE}/archive/refs/tags/v{{ version }}.tar.gz" >> recipes/${PACKAGE}/meta.yaml
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echo " sha256: \"TO_BE_REPLACED\"" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "build:" >> recipes/${PACKAGE}/meta.yaml
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echo " number: 0" >> recipes/${PACKAGE}/meta.yaml
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echo " noarch: python" >> recipes/${PACKAGE}/meta.yaml
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echo " script: \"{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps\"" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "requirements:" >> recipes/${PACKAGE}/meta.yaml
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echo " host:" >> recipes/${PACKAGE}/meta.yaml
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echo " - python >=3.8" >> recipes/${PACKAGE}/meta.yaml
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echo " - pip" >> recipes/${PACKAGE}/meta.yaml
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echo " - setuptools" >> recipes/${PACKAGE}/meta.yaml
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echo " - wheel" >> recipes/${PACKAGE}/meta.yaml
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echo " run:" >> recipes/${PACKAGE}/meta.yaml
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echo " - python >=3.8" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "test:" >> recipes/${PACKAGE}/meta.yaml
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echo " imports:" >> recipes/${PACKAGE}/meta.yaml
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echo " - ${PACKAGE}" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "about:" >> recipes/${PACKAGE}/meta.yaml
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echo " home: \"https://github.com/kfuku52/${PACKAGE}\"" >> recipes/${PACKAGE}/meta.yaml
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echo " license: \"BSD-3-Clause\"" >> recipes/${PACKAGE}/meta.yaml
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echo " license_file: \"LICENSE\"" >> recipes/${PACKAGE}/meta.yaml
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echo " summary: \"Short summary of what ${PACKAGE} does.\"" >> recipes/${PACKAGE}/meta.yaml
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cat <<EOF > recipes/${PACKAGE}/meta.yaml
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{% set name = "${PACKAGE}" %}
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{% set version = "${VERSION}" %}
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package:
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name: "{{ name|lower }}"
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version: "{{ version }}"
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source:
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url: https://github.com/kamome1201/${PACKAGE}/archive/refs/tags/v{{ version }}.tar.gz
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sha256: "TO_BE_REPLACED"
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build:
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number: 0
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noarch: python
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script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps"
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requirements:
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host:
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- python >=3.8
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- pip
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- setuptools
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- wheel
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run:
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- python >=3.8
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test:
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imports:
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- ${PACKAGE}
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about:
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home: "https://github.com/kfuku52/${PACKAGE}"
79+
license: "BSD-3-Clause"
80+
license_file: "LICENSE"
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summary: "Short summary of what ${PACKAGE} does."
82+
EOF
8383

8484
- name: Download source archive and compute SHA256
8585
run: |
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url="https://github.com/kamome1201/${PACKAGE}/archive/refs/tags/v${VERSION}.tar.gz"
8787
wget -O source.tar.gz "$url"
88-
sha256=$(sha256sum source.tar.gz | awk '{print $1}')
89-
echo "SHA256=$sha256" >> $GITHUB_ENV
88+
SHA256=$(sha256sum source.tar.gz | awk '{print $1}')
89+
echo "SHA256=$SHA256" >> $GITHUB_ENV
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9191
- name: Clone your fork of bioconda-recipes
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run: |
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git clone https://github.com/kamome1201/bioconda-recipes.git
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cd bioconda-recipes
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git remote add upstream https://github.com/bioconda/bioconda-recipes.git
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git fetch upstream
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git checkout -b add-${PACKAGE}-${VERSION} upstream/master
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- name: Create new branch
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run: |
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cd bioconda-recipes
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git checkout -b add-${PACKAGE}-${VERSION}
97+
git checkout -B add-${PACKAGE}-${VERSION} upstream/master
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- name: Copy recipe into bioconda-recipes
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run: |
106101
cp -r recipes/${PACKAGE} bioconda-recipes/recipes/
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108103
- name: Replace sha256 in meta.yaml
109104
run: |
110-
sed -i "s/sha256: .*/sha256: \"${SHA256}\"/" bioconda-recipes/recipes/${PACKAGE}/meta.yaml
105+
sed -i "s|sha256: .*|sha256: \"${SHA256}\"|" bioconda-recipes/recipes/${PACKAGE}/meta.yaml
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112107
- name: Create config.yml for bioconda-utils
113108
run: |
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echo "channels:" > bioconda-recipes/config.yml
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echo " - bioconda" >> bioconda-recipes/config.yml
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echo " - conda-forge" >> bioconda-recipes/config.yml
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echo " - defaults" >> bioconda-recipes/config.yml
109+
cat <<EOF > bioconda-recipes/config.yml
110+
channels:
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- bioconda
112+
- conda-forge
113+
- defaults
114+
EOF
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119116
- name: Check copied recipe contents
120117
run: |
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ls -R bioconda-recipes/recipes
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123-
- name: Check if recipe was copied correctly
124-
run: |
125-
if [ ! -d bioconda-recipes/recipes/${PACKAGE} ]; then
126-
echo "❌ Recipe folder not found!"
127-
ls -R bioconda-recipes/recipes
128-
exit 1
129-
fi
130-
118+
ls -R bioconda-recipes/recipes/${PACKAGE}
119+
131120
- name: Run lint + build + test with bioconda-utils (Docker)
132121
run: |
133122
ABS_PATH=$(realpath bioconda-recipes)
134123
docker run --rm -v $ABS_PATH:/bioconda-recipes \
135124
quay.io/bioconda/bioconda-utils-build-env \
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bash -c "cd /bioconda-recipes && bioconda-utils build recipes config.yml --packages ${PACKAGE} --loglevel info --docker --git-range master"
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- name: Show recipe and config path inside container
127+
- name: Commit and push
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run: |
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ls -R bioconda-recipes/recipes/${PACKAGE}
141-
cat bioconda-recipes/config.yml
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# - name: Commit and push
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# run: |
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# cd bioconda-recipes
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# git add recipes/${PACKAGE}
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# git commit -m "Update ${PACKAGE} recipe to v$VERSION"
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# git push origin add-${PACKAGE}-${VERSION}
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# - name: Create Pull Request
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# uses: peter-evans/create-pull-request@v5
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# with:
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# token: ${{ secrets.GH_PAT }}
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# title: "Update ${PACKAGE} recipe to v${{ env.VERSION }}"
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# commit-message: "Auto PR for Bioconda: ${PACKAGE} v${{ env.VERSION }}"
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# base: master
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# branch: add-${PACKAGE}-${{ env.VERSION }}
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# body: |
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# This PR was automatically generated by GitHub Actions.
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# - Package: ${{ env.PACKAGE }}
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# - Version: v${{ env.VERSION }}
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# - sha256: ${{ env.SHA256 }}
129+
cd bioconda-recipes
130+
git config user.name "github-actions"
131+
git config user.email "[email protected]"
132+
git add recipes/${PACKAGE}
133+
git commit -m "Add ${PACKAGE} v${VERSION} [auto-generated]"
134+
git push origin add-${PACKAGE}-${VERSION}
135+
136+
- name: Create Pull Request
137+
uses: peter-evans/create-pull-request@v5
138+
with:
139+
token: ${{ secrets.GH_PAT }}
140+
title: "Add ${PACKAGE} recipe v${{ env.VERSION }}"
141+
commit-message: "Auto PR: ${PACKAGE} v${{ env.VERSION }}"
142+
base: master
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branch: add-${PACKAGE}-${{ env.VERSION }}
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body: |
145+
This PR was automatically generated by GitHub Actions.
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- **Package**: ${{ env.PACKAGE }}
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- **Version**: v${{ env.VERSION }}
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- **SHA256**: ${{ env.SHA256 }}

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