Bulk: testing for failures

.circleci/config.yml

@@ -229,6 +229,7 @@ workflows:
               ignore:
                 - master
                 - bulk
+                - /bulk.*/
           matrix:
             parameters:
               os:

.github/workflows/Bulk.yml

@@ -2,87 +2,18 @@ name: Bulk branch
 on:
   push:
     branches:
-      - bulk
+      - bulk-osx-failures
 jobs:
-  build-linux:
-    name: Bulk Linux Builds
-    if: "contains(github.event.head_commit.message, '[ci run]')"
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      max-parallel: 6
-      matrix:
-        runner: [0, 1, 2, 3, 4, 5]
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          # checkout as BiocondaBot in order to have the permission to push fail logs
-          token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}}
-
-      - name: set git user
-        run: |
-          git config user.name BiocondaBot
-          git config user.email [email protected]
-
-      - name: set path
-        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
-
-      - name: Fetch conda install script
-        run: |
-          wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh
-
-      - name: Restore cache
-        id: cache
-        uses: actions/cache@v4
-        with:
-          path: /opt/mambaforge
-          key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}
-
-      - name: Set up bioconda-utils
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: bash install-and-set-up-conda.sh
-
-      # This script can be used to reconfigure conda to use the right channel setup.
-      # This has to be done after the cache is restored, because
-      # the channel setup is not cached as it resides in the home directory.
-      # We could use a system-wide (and therefore cached) channel setup,
-      # but mamba does not support that at the time of implementation
-      # (it ignores settings made with --system).
-      - name: Configure conda
-        run: bash configure-conda.sh
-
-      - name: Build and upload
-        env:
-          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-          INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
-          QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
-          # Mimic circleci
-          OSTYPE: "linux-gnu"
-          CI: "true"
-        run: |
-          set -e
-          eval "$(conda shell.bash hook)"
-          conda activate bioconda
-          echo '============'
-          conda info --all
-          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 '============'
-          bioconda-utils build recipes config.yml \
-            --worker-offset ${{ matrix.runner }} --n-workers 6 \
-            --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
-            --lint --record-build-failures --skiplist-leafs
-          conda clean -y --all
 
   build-osx:
     name: Bulk OSX Builds
     if: "contains(github.event.head_commit.message, '[ci run]')"
     runs-on: macos-13
     strategy:
       fail-fast: false
-      max-parallel: 4
+      max-parallel: 1
       matrix:
-        runner: [0, 1, 2, 3]
+        runner: [0] #, 1, 2, 3]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -99,7 +30,7 @@ jobs:
 
       - name: Fetch conda install script
         run: |
-          wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh
+          wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk-osx-failures/{common,install-and-set-up-conda,configure-conda}.sh
 
       - name: Restore cache
         id: cache
@@ -133,17 +64,15 @@ jobs:
           set -e
           eval "$(conda shell.bash hook)"
           conda activate bioconda
-
-          # The SDK isn't actually cached, so reinstall it
+          source common.sh
           run_conda_forge_build_setup
-
+          echo $MACOSX_DEPLOYMENT_TARGET
+          echo $MACOSX_SDK_VERSION
           echo '============'
           conda info --all
           conda config --show-sources
           conda activate bioconda
           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 '============'
-          bioconda-utils build recipes config.yml \
-            --worker-offset ${{ matrix.runner }} --n-workers 4 \
-            --lint --anaconda-upload --record-build-failures --skiplist-leafs
+          bioconda-utils build recipes config.yml --packages bowtie
           conda clean -y --all

recipes/bowtie/meta.yaml

@@ -12,7 +12,6 @@ source:
     - rename_version_to_version_txt.patch
 
 build:
-  skip: True  # [py<30]
   number: 8
   run_exports:
     - {{ pin_subpackage("bowtie", max_pin="x.x") }}