updates from testing

bioconda · Apr 4, 2024 · a51acce · a51acce
1 parent 1b177cc
commit a51acce
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diff --git a/.github/check-for-additional-platforms.sh b/.github/check-for-additional-platforms.sh
@@ -0,0 +1,47 @@
+#!/bin/bash
+
+# Check to see if any changed recipes have specified the key
+# extra:additional-platforms, and if so, if they match the platform of the
+# currently-running machine.
+
+# arguments
+git_range=$1
+job_name=$2
+
+# Download ARM version of yq
+yq_platform=$(uname)
+yq_arch=$(uname -m)
+[[ $yq_arch = "aarch64" ]] && yq_arch="arm64"
+mkdir -p ${HOME}/bin
+wget https://github.com/mikefarah/yq/releases/latest/download/yq_${yq_platform}_${yq_arch} -O ${HOME}/bin/yq
+chmod +x ${HOME}/bin/yq
+
+# Find recipes changed from this merge
+files=`git diff --name-only --diff-filter AMR ${git_range} | grep -E 'meta.yaml$' `
+build=0
+
+for file in $files; do
+    echo $file
+    # To create a properly-formatted yaml that yq can parse, comment out jinja2
+    # variable setting with {% %} and remove variable use with {{ }}.
+    additional_platforms=$(cat $file \
+    | sed -E 's/(.*)\{%(.*)%\}(.*)/# \1\2\3/g' \
+    | tr -d '{{' | tr -d '}}' \
+    | ${HOME}/bin/yq '.extra.additional-platforms[]')
+    # Check if any additional platforms match this job
+    for additional_platform in $additional_platforms; do
+    if [ "${GITHUB_JOB}" = "${job_name}-${additional_platform}" ]
+    then
+        echo "Found at least one recipe for ${job_name}-${additional_platform}"
+        build=1
+        break
+    fi
+    done
+done
+
+# If no changed recipes apply to this platform, skip remaining steps
+if [[ build -lt 1 ]]
+then
+    echo "No recipes using this platform, skipping rest of job."
+    echo "skip_build=true" >> $GITHUB_OUTPUT
+fi
diff --git a/.github/workflows/PR-arm.yml b/.github/workflows/PR-arm.yml
@@ -6,8 +6,8 @@ concurrency:
   group: build-${{ github.event.pull_request.number || github.head_ref }}
   cancel-in-progress: true
 jobs:
-  build-osx-arm:
-    name: osx-arm64 Tests
+  build_and_test-osx-arm64:
+    name: build_and_test-osx-arm64
     runs-on: macOS-14 # M1
     strategy:
       fail-fast: true
@@ -17,39 +17,29 @@ jobs:
         with:
           fetch-depth: 0
 
-      # TODO: bail if there's no osx-arm64 recipes
-      # - run:
-      #     name: Check for Additional Platforms
-      #     command: ./.circleci/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test"
+      # bail if there's no osx-arm64 recipes
+      - name: Check for Additional Platforms
+        id: additional_platforms
+        run: ./.github/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test"
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
 
       - name: Fetch conda install script
+        if: steps.additional_platforms.outputs.skip_build != 'true'
         run: |
           wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
 
-      - name: Restore cache
-        id: cache
-        uses: actions/cache@v4
-        with:
-          path: /opt/mambaforge
-          key: ${{ runner.os }}--master--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}
-
       - name: Set up bioconda-utils
-        if: steps.cache.outputs.cache-hit != 'true'
+        if: steps.additional_platforms.outputs.skip_build != '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
+        if: steps.additional_platforms.outputs.skip_build != 'true'
         run: bash configure-conda.sh
 
       - name: Build and Test
+        if: steps.additional_platforms.outputs.skip_build != 'true'
         env:
           # Mimic circleci
           OSTYPE: "darwin"
@@ -78,6 +68,7 @@ jobs:
             --git-range origin/"$GITHUB_BASE_REF" HEAD
 
       - name: Prepare artifacts
+        if: steps.additional_platforms.outputs.skip_build != 'true'
         run: |
               (
               rm -rf /tmp/artifacts
@@ -90,6 +81,7 @@ jobs:
               ) || true
 
       - name: Archive packages
+        if: steps.additional_platforms.outputs.skip_build != 'true'
         uses: actions/upload-artifact@v4
         with:
           name: osx-arm64-packages

diff --git a/.github/workflows/master-arm.yml b/.github/workflows/master-arm.yml
@@ -1,12 +1,12 @@
-name: Upload
+name: Upload (osx-arm64)
 on:
   push:
     branches:
-      - target-for-arm-osx
-jobs:
+      - master
 
-  build-upload-osx-arm:
-    name: osx-arm64 Upload
+jobs:
+  build_and_upload-osx-arm64:
+    name: build_and_upload-osx-arm64
     if: github.repository == 'bioconda/bioconda-recipes'
     runs-on: macOS-14 # M1
     strategy:
@@ -17,39 +17,30 @@ jobs:
         with:
           fetch-depth: 0
 
-      # TODO: bail if there's no osx-arm64 recipes
-      # - run:
-      #     name: Check for Additional Platforms
-      #     command: ./.circleci/check-for-additional-platforms.sh "${CIRCLE_SHA1}~1 ${CIRCLE_SHA1}" "build_and_upload"
+      # bail if there's no osx-arm64 recipes
+      - name: Check for Additional Platforms
+        id: additional_platforms
+        run: ./.github/check-for-additional-platforms.sh "${GITHUB_SHA}~1 ${GITHUB_SHA}" "build_and_upload"
 
       - name: set path
-        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
+        run: |
+          echo "/opt/mambaforge/bin" >> $GITHUB_PATH
 
       - name: Fetch conda install script
+        if: steps.additional_platforms.outputs.skip_build != 'true'
         run: |
           wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
 
-      - name: Restore cache
-        id: cache
-        uses: actions/cache@v4
-        with:
-          path: /opt/mambaforge
-          key: ${{ runner.os }}--master--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}
-
       - name: Set up bioconda-utils
-        if: steps.cache.outputs.cache-hit != 'true'
+        if: steps.additional_platforms.outputs.skip_build != '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
+        if: steps.additional_platforms.outputs.skip_build != 'true'
         run: bash configure-conda.sh
 
       - name: Build and Upload
+        if: steps.additional_platforms.outputs.skip_build != 'true'
         env:
           QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
           QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
@@ -74,6 +65,4 @@ jobs:
             --repo bioconda/bioconda-recipes \
             --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
             --fallback build \
-            --artifact-source github-actions \
-            --dry-run
-          # TODO: remove dry-run after testing
+            --artifact-source github-actions