diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml index 84fb230ad329f..274767126f86c 100644 --- a/.github/workflows/PR.yml +++ b/.github/workflows/PR.yml @@ -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" >> $GITHUB_PATH @@ -45,10 +58,6 @@ jobs: conda config --show-sources python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' echo '============' - if [ -z "$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 @@ -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" >> $GITHUB_PATH @@ -95,10 +118,6 @@ jobs: eval "$(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 \ @@ -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" >> $GITHUB_PATH @@ -183,11 +215,6 @@ jobs: rm -f /opt/mambaforge/envs/bioconda/conda-bld/$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/"$GITHUB_BASE_REF" HEAD @@ -220,8 +247,6 @@ jobs: # needs: build-linux # steps: # - uses: actions/checkout@v4 - # with: - # fetch-depth: 0 # # bail if there's no osx-arm64 recipes # - name: Check for Additional Platforms diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml index 49db9ce180f70..0c0654a02c1f2 100644 --- a/.github/workflows/build-failures.yml +++ b/.github/workflows/build-failures.yml @@ -17,8 +17,21 @@ jobs: runs-on: ubuntu-22.04 steps: - uses: actions/checkout@v4 + + - name: Set GITHUB_BASE_REF if not already set + id: github_base_ref + run: | + if [ -z "$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 @@ -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 diff --git a/.github/workflows/master.yml b/.github/workflows/master.yml index b2f84cdc4f187..a2d2f6fd2db1b 100644 --- a/.github/workflows/master.yml +++ b/.github/workflows/master.yml @@ -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 @@ -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 @@ -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 diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml index 850a5d83fc5ad..bbafe03269845 100644 --- a/.github/workflows/nightly.yml +++ b/.github/workflows/nightly.yml @@ -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 diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 171976c0ae9ef..020d76a469cb7 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.14.2" %} +{% set version = "0.14.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: c9a3266b7a53a9f32bcf995a5c59e35235703398abf8ca5393eed124723f1ed5 + sha256: b1846d147fe6a2bf4f47aa35bc65ee99942f83aba7a9d41faf097bdbf5460807 build: noarch: python