Merge branch 'master' into jpfeuffer-patch-1

bioconda · Aug 9, 2023 · c8e0895 · c8e0895
2 parents 11f812c + aa08857
commit c8e0895
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diff --git a/.circleci/build-docs.sh b/.circleci/build-docs.sh
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,6 +1,10 @@
 # The autobump bot runs on CircleCI (rather than run on Azure Pipelines or
 # GitHub Actions) so that we avoid additional workload on those other services
 # which currently take care of PRs and bulk branch, respectively.
+#
+# Note that this runs the version of bioconda-utils configured in
+# bioconda-common/common.sh (via the installation script), rather than the
+# latest commit on the branch where this is running.
 
 version: 2
 
@@ -16,59 +20,52 @@ jobs:
       - checkout
 
       - run:
-          name: Download common definitions
-          command: curl -s https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh > .circleci/common.sh
+          name: Download bioconda install script
+          command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
 
       - run:
           name: set up env vars
-          command: echo "export PATH=$(pwd)/miniconda/bin:$PATH" >> "$BASH_ENV"
+          command: echo "export PATH=/opt/mambaforge/bin:$PATH" >> "$BASH_ENV"
+
+      - run:
+          name: Ensure cache has path to restore to
+          command: |
+            sudo mkdir -p /opt
+            sudo chown -R $USER /opt
 
       - restore_cache:
-          keys:
-            - bioconda-utils-{{
-              checksum ".circleci/common.sh" }}-{{
-              checksum ".circleci/config.yml" }}-{{
-              checksum "bioconda_utils/bioconda_utils-requirements.txt" }}
+          key: bioconda-utils-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum ".circleci/config.yml" }}-{{ checksum "common.sh" }}
 
       - run:
-          name: Setup dependencies
+          name: Install bioconda-utils
           command: |
-            if [ -d miniconda ]
-            then
-                echo "Restored from cache"
-                exit 0
+            source $BASH_ENV
+            if [ ! -e /opt/mambaforge ]; then
+              bash install-and-set-up-conda.sh
             fi
-            source .circleci/common.sh
-            git checkout ${BIOCONDA_UTILS_TAG}
-            curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VER}-Linux-x86_64.sh
-            bash miniconda.sh -b -p ./miniconda
-            conda config --system --add channels defaults
-            conda config --system --add channels bioconda
-            conda config --system --add channels conda-forge
-            conda install -y mamba
-            mamba install -y --file bioconda_utils/bioconda_utils-requirements.txt --file test-requirements.txt
-            conda clean -y --all
-            python setup.py install
 
       - save_cache:
-          key: bioconda-utils-{{
-             checksum ".circleci/common.sh" }}-{{
-             checksum ".circleci/config.yml" }}-{{
-             checksum "bioconda_utils/bioconda_utils-requirements.txt" }}
+          key: bioconda-utils-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum ".circleci/config.yml" }}-{{ checksum "common.sh" }}
           paths:
-            - miniconda
+            - /opt/mambaforge
 
-      - store_artifacts:
-          path: /tmp/artifacts
+      - run:
+          name: Configure conda
+          command: |
+            source $BASH_ENV
+            bash configure-conda.sh
 
       - run:
           name: Check recipes for new upstream releases
           command: |
+            source $BASH_ENV
             git clone [email protected]:bioconda/bioconda-recipes
             cd bioconda-recipes
             git config user.name "Autobump"
             git config user.email "[email protected]"
             mkdir -p /tmp/artifacts
+            eval "$(conda shell.bash hook)"
+            conda activate bioconda
             bioconda-utils autobump \
               --unparsed-urls /tmp/artifacts/unparsed_urls.txt \
               --failed-urls /tmp/artifacts/failed_urls.txt \
@@ -81,15 +78,18 @@ jobs:
               --commit-as BiocondaBot [email protected] \
               $AUTOBUMP_OPTS
 
+      - store_artifacts:
+          path: /tmp/artifacts
+
 workflows:
   version: 2
   bioconda-utils-autobump:
-     triggers:
-       - schedule:
-           cron: "0 * * * *"
-           filters:
+    triggers:
+      - schedule:
+          cron: "0 * * * *"
+          filters:
             branches:
-               only:
-                 - master
-     jobs:
-       - autobump
+              only:
+                - master
+    jobs:
+      - autobump
diff --git a/.github/quay-namespace-info.py b/.github/quay-namespace-info.py
@@ -40,6 +40,7 @@
     HEADERS = {'Content-Type': 'application/json'}
     QUAY_OAUTH_TOKEN = os.getenv('QUAY_OAUTH_TOKEN')
     if QUAY_OAUTH_TOKEN:
+        print(f'Quay Token found, using it for {args.namespace}')
         HEADERS['Authorization'] = f'Bearer {QUAY_OAUTH_TOKEN}'
 
     # Starting querying Quay
@@ -116,10 +117,10 @@
                 repo_status[repo]['is_public'] = "True (changed by script)"
                 # Again, be nice to Quay
                 time.sleep(0.3)
-                fh.write(f'Changed visibility of {args.namespace}/{repo} to public')
+                fh.write(f'Changed visibility of {args.namespace}/{repo} to public\n')
 
     # Print status
-    with open(f'{args.namespace}-status.tsv', 'w') as fh:
+    with open(f'{args.namespace}-status.txt', 'w') as fh:
         fh.write('namespace\tname\tis_public\n')
         for k,v in sorted(repo_status.items()):
             fh.write(f'{v["namespace"]}\t{v["name"]}\t{v["is_public"]}\n')
diff --git a/.github/workflows/GithubActionTests.yml b/.github/workflows/GithubActionTests.yml
@@ -1,6 +1,6 @@
 name: PR Tests
 on: [pull_request]
-concurrency: 
+concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
@@ -14,60 +14,105 @@ jobs:
           - not long_running_1 and not long_running_2
           - long_running_1
           - long_running_2
+
     steps:
-    - uses: actions/checkout@v1
-    - name: Setup
-      uses: bioconda/bioconda-actions/bioconda_utils_setup_conda/@master
-    - name: Install bioconda-utils
-      run: |
-        python setup.py install
-    - name: Build docker container
-      run: |
-        docker build -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest ./
-        docker history quay.io/bioconda/bioconda-utils-build-env-cos7:latest
-        docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info -a && conda list'
-        docker build -t quay.io/bioconda/bioconda-utils-test-env-cos7:latest -f ./Dockerfile.test ./
-    - name: Run tests '${{ matrix.py_test_marker }}'
-      run: |
-        if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
-            py.test --durations=0 test/ -v --log-level=DEBUG --tb=native -m '${{ matrix.py_test_marker }}'
-        else
-            echo "Skipping pytest - only docs modified"
-        fi
+      - uses: actions/checkout@v1
+
+      - name: set path
+        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
+
+      - name: Install bioconda-utils
+        run: |
+          export BIOCONDA_DISABLE_BUILD_PREP=1
+          wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
+          bash install-and-set-up-conda.sh
+          eval "$(conda shell.bash hook)"
+          mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+          conda activate bioconda
+          python setup.py install
+
+      - name: Build docker container
+        run: |
+          docker build -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest ./
+          docker history quay.io/bioconda/bioconda-utils-build-env-cos7:latest
+          docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info -a && conda list'
+          docker build -t quay.io/bioconda/bioconda-utils-test-env-cos7:latest -f ./Dockerfile.test ./
+
+      - name: Run tests '${{ matrix.py_test_marker }}'
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate bioconda
+          if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
+              py.test --durations=0 test/ -v --log-level=DEBUG --tb=native -m '${{ matrix.py_test_marker }}'
+          else
+              echo "Skipping pytest - only docs modified"
+          fi
   test-macosx:
     name: OSX tests
-    runs-on: macOS-latest
+    runs-on: macos-latest
     steps:
-    - uses: actions/checkout@v1
+      - uses: actions/checkout@v1
+
+      - name: set path
+        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
 
-    - name: set path
-      run: echo "${HOME}/miniconda/bin" >> $GITHUB_PATH
+      - name: Install bioconda-utils
+        run: |
+          export BIOCONDA_DISABLE_BUILD_PREP=1
+          wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
+          bash install-and-set-up-conda.sh
+          eval "$(conda shell.bash hook)"
+          mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+          conda activate bioconda
+          python setup.py install
 
-    - name: Install bioconda-utils
-      run: |
-        export BIOCONDA_PREP_MACOS_FOR_BUILDING=0
-        curl -L "https://raw.githubusercontent.com/bioconda/bioconda-common/master/macos-github-runner.sh" | bash
-        mamba install -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
-        python setup.py install
+      - name: Run tests
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate bioconda
+          if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
+              py.test --durations=0 test/ -v --log-level=DEBUG -k "not docker" --tb=native
+          else
+              echo "Skipping pytest - only docs modified"
+          fi
 
-    - name: Run tests
-      run: |
-        if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
-            py.test --durations=0 test/ -v --log-level=DEBUG -k "not docker" --tb=native
-        else
-            echo "Skipping pytest - only docs modified"
-        fi
   autobump-test:
     name: autobump test
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - name: Setup
-      uses: bioconda/bioconda-actions/bioconda_utils_setup_conda@master
-    - name: Install bioconda-utils
-      run: |
-        python setup.py install
-    - name: Test autobump
-      env:
-        AUTOBUMP_OPTS: --dry-run
-      uses: bioconda/bioconda-actions/bioconda_utils_autobump@master
+      - uses: actions/checkout@v1
+      - name: set path
+        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
+
+      - name: Install bioconda-utils
+        run: |
+          export BIOCONDA_DISABLE_BUILD_PREP=1
+          wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
+          bash install-and-set-up-conda.sh
+          eval "$(conda shell.bash hook)"
+          mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+          conda activate bioconda
+          python setup.py install
+
+      - name: Test autobump
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate bioconda
+          git clone --depth 1 https://github.com/bioconda/bioconda-recipes.git
+          cd bioconda-recipes
+          git config user.name Autobump
+          git config user.email [email protected]
+          mkdir /tmp/artifacts
+          bioconda-utils autobump \
+            --packages "a*" \
+            --unparsed-urls /tmp/artifacts/unparsed_urls.txt \
+            --failed-urls /tmp/artifacts/failed_urls.txt \
+            --recipe-status /tmp/artifacts/status.txt \
+            --create-pr \
+            --no-check-pinnings \
+            --no-check-pending-deps \
+            --no-follow-graph \
+            --exclude bioconductor-* \
+            --commit-as BiocondaBot [email protected] \
+            --max-updates 5 \
+            --dry-run