Merge branch 'master' into bulk

.circleci/config.yml

@@ -0,0 +1,345 @@
+# .circleci/config.yml
+version: 2.1
+
+executors:
+  osx-arm64:
+    macos:
+      xcode: 15.4.0
+    resource_class: macos.m1.medium.gen1
+  linux-aarch64:
+    machine:
+      image: ubuntu-2204:current
+    resource_class: arm.medium
+
+jobs: # a basic unit of work in a run
+  build_and_test:
+    parameters:
+      os:
+        type: executor
+    executor: << parameters.os >>
+    steps:
+      - checkout
+
+      - run:
+          name: Check for Additional Platforms
+          command: |
+            result=$(./scripts/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" "${CIRCLE_JOB}")
+            if [[ ${result} != "build" ]]
+            then
+                echo "No recipes using this platform, skipping rest of job."
+                circleci-agent step halt
+            fi
+
+      - run:
+          name: Fetch bioconda install script
+          command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
+
+      - run:
+          name: Install bioconda-utils
+          command: |
+            sudo mkdir -p /opt/
+            sudo chmod o+rwx /opt
+            bash install-and-set-up-conda.sh
+
+      - run:
+          name: Setup PATH
+          command:
+            echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV"
+
+      - run:
+          name: Configure conda
+          command: bash configure-conda.sh
+
+      - run:
+          name: Build and test
+          command: |
+            set -xe
+            eval "$(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
+          command: |
+            (
+            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 osx-arm64 noarch; do
+              cp -rv $n /tmp/artifacts/packages || true
+            done
+            if command -V docker >/dev/null; then
+              mkdir -p /tmp/artifacts/images
+              cd /tmp/artifacts/images
+              docker image ls --format='{{.Repository}}:{{.Tag}}' | \
+                { grep biocontainers || true ; } | \
+                xargs -n1 -P4 bash -c '
+                  test -n "${1+x}" || exit 0
+                  echo "Start compressing docker image ${1} ..."
+                  docker save "${1}" | gzip -c > "${1##*/}.tar.gz"
+                  echo "Finished compressing docker image ${1} ."
+                  ' --
+            fi
+            ) || true
+
+      - store_artifacts:
+          path: /tmp/artifacts
+
+  build_and_upload:
+    parameters:
+      os:
+        type: executor
+    executor: << parameters.os >>
+    steps:
+      - checkout
+
+      - run:
+          name: Check for Additional Platforms
+          command: |
+            result=$(./scripts/check-for-additional-platforms.sh "${CIRCLE_SHA1}~1 ${CIRCLE_SHA1}" "build_and_upload" "${CIRCLE_JOB}")
+            if [[ ${result} != "build" ]]
+            then
+                echo "No recipes using this platform, skipping rest of job."
+                circleci-agent step halt
+            fi
+
+      - run:
+          name: Fetch bioconda install script
+          command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
+
+      - run:
+          name: Install bioconda-utils
+          command: |
+            sudo mkdir -p /opt
+            sudo chmod o+rwx /opt
+            bash install-and-set-up-conda.sh
+
+      - run:
+          name: Setup PATH
+          command:
+            echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV"
+
+      - run:
+          name: Configure conda
+          command: bash configure-conda.sh
+
+      - run:
+          name: Build and push
+          command: |
+            set -xe
+            eval "$(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 ${CIRCLE_SHA1} \
+              --fallback build \
+              --artifact-source circleci
+
+  bulk_build:
+    parameters:
+      os:
+        type: executor
+      runner:
+        type: integer
+    executor: << parameters.os >>
+    steps:
+      - add_ssh_keys:
+          fingerprints:
+            - 1e:85:74:42:35:5f:c5:a2:35:c2:ec:b7:80:c0:7c:40
+
+      - checkout
+
+      - run:
+          name: Check for [ci run]
+          command: |
+            commit_message="$(git log --format=oneline -n 1 $CIRCLE_SHA1)"
+            if [[ $commit_message  =~ "[ci run]" ]]; then
+              echo "[ci run] found, continuing."
+            else
+              echo "[ci run] not found, exiting."
+              circleci-agent step halt
+            fi
+
+      - run:
+          name: set git user
+          command: |
+            git config user.name BiocondaBot
+            git config user.email [email protected]
+            git branch --set-upstream-to=origin/$CIRCLE_BRANCH $CIRCLE_BRANCH
+
+      - run:
+          name: Fetch bioconda install script
+          command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh
+
+      - run:
+          name: Install bioconda-utils
+          command: |
+            sudo mkdir -p /opt/
+            sudo chmod o+rwx /opt
+            bash install-and-set-up-conda.sh
+
+      - run:
+          name: Setup PATH
+          command:
+            echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV"
+
+      - run:
+          name: Configure conda
+          command: bash configure-conda.sh
+
+      # For now, do not upload ARM images to biocontainers: --mulled-upload-target biocontainers
+      - run:
+          name: Build and upload
+          command: |
+            set -e
+            eval "$(conda shell.bash hook)"
+            conda activate bioconda
+            source common.sh
+
+            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 << parameters.runner >> --n-workers 6 \
+              --docker --mulled-test --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \
+              --anaconda-upload \
+              --record-build-failures \
+              --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):
+    jobs:
+      - build_and_test:
+          filters:
+            branches:
+              ignore:
+                - master
+                - bulk
+          matrix:
+            parameters:
+              os:
+                - osx-arm64
+                - linux-aarch64
+
+  build and upload (ARM):
+    jobs:
+      - build_and_upload:
+          filters:
+            branches:
+              only: master
+          matrix:
+            parameters:
+              os:
+                - osx-arm64
+                - linux-aarch64
+
+  Bulk branch (ARM):
+    jobs:
+      - bulk_build:
+          filters:
+            branches:
+              only: bulk
+          matrix:
+            parameters:
+              os: 
+                # - 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