Merge branch 'master' into aarch64-odgi

.circleci/config.yml

@@ -2,10 +2,10 @@
 version: 2.1
 
 executors:
-  # osx-arm64:
-  #   macos:
-  #     xcode: 14.2.0 # indicate your selected version of Xcode
-  #   resource_class: macos.m1.large.gen1
+  osx-arm64:
+    macos:
+      xcode: 15.4.0
+    resource_class: macos.m1.medium.gen1
   linux-aarch64:
     machine:
       image: ubuntu-2204:current
@@ -22,7 +22,13 @@ jobs: # a basic unit of work in a run
 
       - run:
           name: Check for Additional Platforms
-          command: ./.circleci/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test"
+          command: |
+            result=$(./scripts/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" "${CIRCLE_JOB}")
+            if [[ ${result} != "build" ]]
+            then
+                echo "No recipes using this platform, skipping rest of job."
+                circleci-agent step halt
+            fi
 
       - run:
           name: Fetch bioconda install script
@@ -47,14 +53,29 @@ jobs: # a basic unit of work in a run
       - run:
           name: Build and test
           command: |
-            . common.sh
-            source /opt/mambaforge/etc/profile.d/conda.sh
-            source /opt/mambaforge/etc/profile.d/mamba.sh
-            mamba activate bioconda
-            bioconda-utils build recipes config.yml \
-                --lint --docker --mulled-test \
-                --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \
-                --git-range origin/master HEAD
+            set -xe
+            eval "$(conda shell.bash hook)"
+            conda activate bioconda
+            source common.sh
+
+            # Sets up OSX SDK
+            if [[ $(uname) = "Darwin" ]]; then
+              if [[ "${OSX_SDK_DIR:-}" == "" ]]; then
+                  OSX_SDK_DIR="$(xcode-select -p)/Platforms/MacOSX.platform/Developer/SDKs"
+              fi
+              sudo chmod o+rwx ${OSX_SDK_DIR}
+              run_conda_forge_build_setup
+            fi
+
+            if command -V docker >/dev/null; then
+              bioconda-utils build recipes config.yml \
+                  --lint --docker --mulled-test \
+                  --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \
+                  --git-range origin/master HEAD
+            else
+              bioconda-utils build recipes config.yml \
+                  --lint --git-range origin/master HEAD
+            fi
 
       - run:
           name: Prepare artifacts
@@ -63,7 +84,7 @@ jobs: # a basic unit of work in a run
             mkdir -p /tmp/artifacts/packages
             cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0
             find -name .cache | xargs rm -rf || true
-            for n in index.html channeldata.json linux-aarch64 linux-64 osx-64 noarch; do
+            for n in index.html channeldata.json linux-aarch64 linux-64 osx-64 osx-arm64 noarch; do
               cp -rv $n /tmp/artifacts/packages || true
             done
             if command -V docker >/dev/null; then
@@ -93,7 +114,13 @@ jobs: # a basic unit of work in a run
 
       - run:
           name: Check for Additional Platforms
-          command: ./.circleci/check-for-additional-platforms.sh "${CIRCLE_SHA1}~1 ${CIRCLE_SHA1}" "build_and_upload"
+          command: |
+            result=$(./scripts/check-for-additional-platforms.sh "${CIRCLE_SHA1}~1 ${CIRCLE_SHA1}" "build_and_upload" "${CIRCLE_JOB}")
+            if [[ ${result} != "build" ]]
+            then
+                echo "No recipes using this platform, skipping rest of job."
+                circleci-agent step halt
+            fi
 
       - run:
           name: Fetch bioconda install script
@@ -118,9 +145,20 @@ jobs: # a basic unit of work in a run
       - run:
           name: Build and push
           command: |
-            source /opt/mambaforge/etc/profile.d/conda.sh
-            source /opt/mambaforge/etc/profile.d/mamba.sh
-            mamba activate bioconda
+            set -xe
+            eval "$(conda shell.bash hook)"
+            conda activate bioconda
+            source common.sh
+
+            # Sets up OSX SDK
+            if [[ $(uname) = "Darwin" ]]; then
+              if [[ "${OSX_SDK_DIR:-}" == "" ]]; then
+                  OSX_SDK_DIR="$(xcode-select -p)/Platforms/MacOSX.platform/Developer/SDKs"
+              fi
+              sudo chmod o+rwx ${OSX_SDK_DIR}
+              run_conda_forge_build_setup
+            fi
+
             bioconda-utils handle-merged-pr recipes config.yml \
               --repo bioconda/bioconda-recipes \
               --git-range ${CIRCLE_SHA1}~1 ${CIRCLE_SHA1} \
@@ -184,10 +222,10 @@ jobs: # a basic unit of work in a run
           name: Build and upload
           command: |
             set -e
-            . common.sh
-            source /opt/mambaforge/etc/profile.d/conda.sh
-            source /opt/mambaforge/etc/profile.d/mamba.sh
-            mamba activate bioconda
+            eval "$(conda shell.bash hook)"
+            conda activate bioconda
+            source common.sh
+
             echo '============'
             conda info --all
             conda config --show-sources
@@ -201,6 +239,52 @@ jobs: # a basic unit of work in a run
               --skiplist-leafs
             conda clean -y --all
 
+  nightly_build:
+    parameters:
+      os:
+        type: executor
+    executor: << parameters.os >>
+    steps:
+      - add_ssh_keys:
+          fingerprints:
+            - 1e:85:74:42:35:5f:c5:a2:35:c2:ec:b7:80:c0:7c:40
+
+      - checkout
+
+      - run:
+          name: Fetch bioconda install script
+          command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh
+
+      - run:
+          name: Install bioconda-utils
+          command: |
+            sudo mkdir -p /opt/
+            sudo chmod o+rwx /opt
+            bash install-and-set-up-conda.sh
+
+      - run:
+          name: Setup PATH
+          command:
+            echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV"
+
+      - run:
+          name: Configure conda
+          command: bash configure-conda.sh
+
+      # For now, do not upload ARM images to biocontainers: --mulled-upload-target biocontainers
+      - run:
+          name: Build and push leftover packages
+          command: |
+            set -e
+            eval "$(conda shell.bash hook)"
+            conda activate bioconda
+            source common.sh
+
+            # build and push all leftover packages
+            bioconda-utils build recipes config.yml \
+                --docker --mulled-test  --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \
+                --anaconda-upload \
+                --prelint --exclude bioconda-repodata-patches
 
 workflows:
   build and test (ARM):
@@ -214,7 +298,7 @@ workflows:
           matrix:
             parameters:
               os:
-                #- osx-arm64
+                - osx-arm64
                 - linux-aarch64
 
   build and upload (ARM):
@@ -226,10 +310,9 @@ workflows:
           matrix:
             parameters:
               os:
-                #- osx-arm64
+                - osx-arm64
                 - linux-aarch64
 
-
   Bulk branch (ARM):
     jobs:
       - bulk_build:
@@ -239,6 +322,24 @@ workflows:
           matrix:
             parameters:
               os: 
-                #- osx-arm64
+                # - osx-arm64 Bulk is on GitHub Actions
                 - linux-aarch64
               runner: [0, 1, 2, 3, 4, 5]
+
+  Nightly (ARM):
+    triggers:
+      - schedule:
+          cron: "0 0 * * *"
+          filters:
+            branches:
+              only: master
+    jobs:
+      - nightly_build:
+          filters:
+            branches:
+              only: master
+          matrix:
+            parameters:
+              os:
+                # - osx-arm64 Nightly is on GitHub Actions
+                - linux-aarch64

.github/workflows/Bulk.yml

@@ -62,7 +62,7 @@ jobs:
           conda clean -y --all
 
   build-osx:
-    name: Bulk OSX Builds
+    name: Bulk OSX-64 Builds
     if: "contains(github.event.head_commit.message, '[ci run]')"
     runs-on: macos-13
     strategy:
@@ -121,3 +121,65 @@ jobs:
             --lint --anaconda-upload --record-build-failures --skiplist-leafs \
             --exclude bioconda-repodata-patches
           conda clean -y --all
+
+  build-osx-arm:
+    name: Bulk OSX-ARM64 Builds
+    if: "contains(github.event.head_commit.message, '[ci run]')"
+    runs-on: macOS-14 # M1
+    strategy:
+      fail-fast: false
+      max-parallel: 1 # GHA free plan allows 5 concurrent Mac runners total, we still need most on osx-64.
+      matrix:
+        runner: [0]
+    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 BiocondaBot@users.noreply.github.com
+
+      - 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: Set up bioconda-utils
+        run: bash install-and-set-up-conda.sh
+
+      - 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: ${{ secrets.QUAY_OAUTH_TOKEN }}
+          # Mimic circleci
+          OSTYPE: "darwin"
+          CI: "true"
+        run: |
+          set -xe
+          eval "$(conda shell.bash hook)"
+          conda activate bioconda
+
+          source common.sh
+          # Sets up OSX SDK
+          run_conda_forge_build_setup
+
+          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 1 \
+            --lint --anaconda-upload --record-build-failures --skiplist-leafs \
+            --exclude bioconda-repodata-patches
+          conda clean -y --all

.github/workflows/CommentResponder.yml

@@ -1,27 +1,14 @@
 name: CommentResponder
 on:
-  status:
-  check_suite:
-    types:
-    - completed
   issue_comment:
     types:
     - created
 
-# Re-enable when the bot has been updated to handle azure
-#      (
-#        github.event_name == 'check_suite' &&
-#        github.event.check_suite.conclusion == 'success'
-#      ) ||
 jobs:
   comment:
     runs-on: ubuntu-latest
     name: bioconda-bot comment
     if: >-
-      (
-        github.event_name == 'status' &&
-        github.event.state == 'success'
-      ) ||
       (
         github.event_name == 'issue_comment' &&
         github.event.issue.pull_request &&