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test PR for #53384 #53405

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test PR for #53384 #53405

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8dd96b2
ci: optimize fetch-depth in github actions
nh13 Jan 22, 2025
3924729
Update PR.yml
nh13 Jan 22, 2025
d51a162
Update build-failures.yml
nh13 Jan 22, 2025
949bd85
debug
nh13 Jan 22, 2025
5fce797
one more
nh13 Jan 22, 2025
2cc8bd1
Update snakemake-executor-plugin-slurm to 0.14.3
BiocondaBot Jan 22, 2025
8e7af7b
update action
nh13 Jan 22, 2025
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61 changes: 43 additions & 18 deletions .github/workflows/PR.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,21 @@ jobs:
max-parallel: 13
steps:
- uses: actions/checkout@v4

- name: Set GITHUB_BASE_REF if not already set
id: github_base_ref
run: |
if [ -z "$GITHUB_BASE_REF" ] ; then
export GITHUB_BASE_REF="master"
export GITHUB_BASE_REF="${GITHUB_BASE_REF}" >> $GITHUB_ENV
fi
echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT

- name: Fetch commits through the merge base
uses: fulcrumgenomics/fetch-through-merge-base@v1
with:
fetch-depth: 0
base-ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
head-ref: ${{ github.sha }}

- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
Expand Down Expand Up @@ -45,10 +58,6 @@ jobs:
conda config --show-sources
python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")'
echo '============'
if [ -z "$GITHUB_BASE_REF" ] ; then
export GITHUB_BASE_REF="master"
fi
git fetch origin "$GITHUB_BASE_REF"
bioconda-utils lint --loglevel debug --full-report --git-range origin/"$GITHUB_BASE_REF" HEAD
conda clean -y --all

Expand All @@ -61,8 +70,22 @@ jobs:
needs: lint
steps:
- uses: actions/checkout@v4

- name: Set GITHUB_BASE_REF if not already set
id: github_base_ref
run: |
if [ -z "$GITHUB_BASE_REF" ] ; then
export GITHUB_BASE_REF="master"
export GITHUB_BASE_REF="${GITHUB_BASE_REF}" >> $GITHUB_ENV
fi
echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT

- name: Fetch commits through the merge base
uses: fulcrumgenomics/fetch-through-merge-base@v1
with:
fetch-depth: 0
base-ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
head-ref: ${{ github.sha }}


- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
Expand Down Expand Up @@ -95,10 +118,6 @@ jobs:
eval "$(conda shell.bash hook)"
conda activate bioconda
source common.sh
if [ -z "$GITHUB_BASE_REF" ] ; then
export GITHUB_BASE_REF="master"
fi
git fetch origin "$GITHUB_BASE_REF"

bioconda-utils build recipes config.yml \
--docker --mulled-test \
Expand Down Expand Up @@ -148,8 +167,21 @@ jobs:
needs: build-linux
steps:
- uses: actions/checkout@v4

- name: Set GITHUB_BASE_REF if not already set
id: github_base_ref
run: |
if [ -z "$GITHUB_BASE_REF" ] ; then
export GITHUB_BASE_REF="master"
export GITHUB_BASE_REF="${GITHUB_BASE_REF}" >> $GITHUB_ENV
fi
echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT

- name: Fetch commits through the merge base
uses: fulcrumgenomics/fetch-through-merge-base@v1
with:
fetch-depth: 0
base-ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
head-ref: ${{ github.sha }}

- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
Expand Down Expand Up @@ -183,11 +215,6 @@ jobs:
rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2
done

if [ -z "$GITHUB_BASE_REF" ] ; then
export GITHUB_BASE_REF="master"
fi
git fetch origin "$GITHUB_BASE_REF"

bioconda-utils build recipes config.yml \
--git-range origin/"$GITHUB_BASE_REF" HEAD

Expand Down Expand Up @@ -220,8 +247,6 @@ jobs:
# needs: build-linux
# steps:
# - uses: actions/checkout@v4
# with:
# fetch-depth: 0

# # bail if there's no osx-arm64 recipes
# - name: Check for Additional Platforms
Expand Down
19 changes: 14 additions & 5 deletions .github/workflows/build-failures.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,21 @@ jobs:
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v4

- name: Set GITHUB_BASE_REF if not already set
id: github_base_ref
run: |
if [ -z "$GITHUB_BASE_REF" ] ; then
export GITHUB_BASE_REF="master"
export GITHUB_BASE_REF="${GITHUB_BASE_REF}" >> $GITHUB_ENV
fi
echo github_base_ref="${GITHUB_BASE_REF}" >> $GITHUB_OUTPUT

- name: Fetch commits through the merge base
uses: fulcrumgenomics/fetch-through-merge-base@v1
with:
fetch-depth: 0
base-ref: ${{ steps.github_base_ref.outputs.github_base_ref }}
head-ref: ${{ github.sha }}

- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
Expand Down Expand Up @@ -60,10 +73,6 @@ jobs:
echo "Automatically updated (nightly) list of build failures that currently block builds from the listed recipes. Please help with fixing them!" >> $md
bioconda-utils list-build-failures recipes --output-format markdown --link-prefix https://github.com/bioconda/bioconda-recipes/blob/master >> $md
else
if [ -z "$GITHUB_BASE_REF" ] ; then
export GITHUB_BASE_REF="master"
fi
git fetch origin "$GITHUB_BASE_REF"
md="build-failures/build-failures-${branch}.md"
echo "# Build failures on \`${branch}\`" > $md
echo "Automatically updated list of build failures that currently block builds from the listed recipes on the \`${branch}\` branch." >> $md
Expand Down
9 changes: 6 additions & 3 deletions .github/workflows/master.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,10 @@ jobs:
fail-fast: false
max-parallel: 13
steps:
# Fetch the last two commits for the --git-range argument to bioconda-utils
- uses: actions/checkout@v4
with:
fetch-depth: 0
fetch-depth: 2

- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
Expand Down Expand Up @@ -59,9 +60,10 @@ jobs:
fail-fast: false
max-parallel: 4
steps:
# Fetch the last two commits for the --git-range argument to bioconda-utils
- uses: actions/checkout@v4
with:
fetch-depth: 0
fetch-depth: 2

- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
Expand Down Expand Up @@ -111,9 +113,10 @@ jobs:
# fail-fast: false
# max-parallel: 4
# steps:
# # Fetch the last two commits for the --git-range argument to bioconda-utils
# - uses: actions/checkout@v4
# with:
# fetch-depth: 0
# fetch-depth: 2

# # bail if there's no osx-arm64 recipes
# - name: Check for Additional Platforms
Expand Down
2 changes: 0 additions & 2 deletions .github/workflows/nightly.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,6 @@ jobs:
max-parallel: 4
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0

- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
Expand Down
4 changes: 2 additions & 2 deletions recipes/snakemake-executor-plugin-slurm/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
{% set name = "snakemake-executor-plugin-slurm" %}
{% set version = "0.14.2" %}
{% set version = "0.14.3" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz
sha256: c9a3266b7a53a9f32bcf995a5c59e35235703398abf8ca5393eed124723f1ed5
sha256: b1846d147fe6a2bf4f47aa35bc65ee99942f83aba7a9d41faf097bdbf5460807

build:
noarch: python
Expand Down
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