CI: add new workflows (#171)

.github/workflows/ci.yaml

@@ -0,0 +1,120 @@
+name: Test
+on:
+  pull_request:
+    branches: ["main"]
+  push:
+    branches: ["main"]
+env:
+    DISTRO: metagenome
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    outputs:
+      latest-dev-tag: ${{ steps.fetch_latest_tags.outputs.latest-dev-tag }}
+      latest-stable-tag: ${{ steps.fetch_latest_tags.outputs.latest-stable-tag }}
+      commit-msg: ${{ steps.get-commit-msg.outputs.commit-msg }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+            fetch-depth: 0
+
+      - name: Checkout utilities
+        uses: actions/checkout@v4
+        with:
+          repository: bokulich-lab/utilities
+          path: utilities
+
+      - name: Get last commit
+        id: get-commit-msg
+        run: |
+          echo "$(git log --pretty=%B -n 1 --skip 1)"
+          echo "commit-msg=$(git log --pretty=%B -n 1 --skip 1)" >> $GITHUB_OUTPUT
+
+      - name: Install dependencies
+        run: python -m pip install requests yq
+
+      - name: Fetch latest tags
+        id: fetch-tags
+        run: |
+          latest_tags=$(python utilities/ci/get-tags.py)
+          echo "$latest_tags" > tags.txt
+          echo "latest-dev-tag=$(grep 'latest-dev-tag' tags.txt | cut -d '=' -f 2)" >> $GITHUB_OUTPUT
+          echo "latest-stable-tag=$(grep 'latest-stable-tag' tags.txt | cut -d '=' -f 2)" >> $GITHUB_OUTPUT
+
+      - name: Create conda yaml
+        id: create-conda-yaml
+        run: |
+          bash utilities/ci/get-dependencies.sh "$DISTRO" ${{ steps.fetch-tags.outputs.latest-dev-tag }} utilities/ci/repositories.yaml
+          cat environment.yml >> $GITHUB_STEP_SUMMARY
+          echo "qiime-deps=$(tr '\n' ' ' < repo-urls.txt | xargs)" >> $GITHUB_OUTPUT
+
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: 3.8
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          activate-environment: conda-env
+          condarc-file: utilities/ci/condarc
+          # use-only-tar-bz2: true
+
+      - name: Get date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache conda env
+        uses: actions/cache@v3
+        with:
+          path: /usr/share/miniconda/envs
+          key:
+            conda-${{ runner.os }}--${{ runner.arch }}--${{
+            steps.get-date.outputs.today }}-${{
+            hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER
+            }}
+        env:
+          # Increase this value to reset cache if environment.yml has not changed
+          CACHE_NUMBER: 0
+        id: cache
+
+      - name: Update environment
+        run: mamba env update -n conda-env -f environment.yml
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Install dev versions of QIIME repos
+        run: mamba run -n conda-env pip install ${{ steps.create-conda-yaml.outputs.qiime-deps }}
+
+      - name: Update specific dependency, if requested
+        if: contains(${{ steps.get-commit-msg.outputs.commit-msg }}, '[add:')
+        run: |
+            commit_msg="${{ steps.get-commit-msg.outputs.commit-msg }}"
+            IFS=',' read -ra ADDR <<< "$commit_msg"
+            for i in "${ADDR[@]}"; do
+                pkg_name=$(echo "$i" | awk -F':' '/\[add/{print $2}')
+                commit_hash=$(echo "$i" | awk -F':' '/\[add/{print $3}' | awk -F']' '{print $1}')
+                if [[ $(yq '.repositories[].name' utilities/ci/repositories.yaml | grep -c $pkg_name) -eq 1 ]]; then
+                    pkg_url=$(yq ".repositories[] | select(.name == \"$pkg_name\") | .url" utilities/ci/repositories.yaml | tr -d '"')
+                    mamba run -n conda-env pip install "git+$pkg_url@$commit_hash"
+                fi
+            done
+
+      - name: Install plugin
+        run: |
+          mamba run -n conda-env pip install .
+          mamba run -n conda-env qiime dev refresh-cache
+
+      - name: Install dev dependencies
+        run: mamba run -n conda-env pip install pytest coverage parameterized
+
+      - name: Run tests
+        run: mamba run -n conda-env make test-cov
+
+      - uses: codecov/codecov-action@v4
+        name: Upload coverage report
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/ci-dev.yaml → .github/workflows/q2-ci.yaml

@@ -1,12 +1,20 @@
-name: CI
-on:
-  pull_request:
-    branches: ["main"]
-  push:
-    branches: ["main"]
+name: "QIIME2: build and test"
+on: issue_comment
 
 jobs:
+  react:
+    if: ${{ github.event.issue.pull_request && contains(github.event.comment.body, '/q2ci') }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: peter-evans/create-or-update-comment@v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          body: |
+            <br /> **Edit:** Running QIIME 2 CI...
+          reactions: "+1"
+
   ci:
+    if: ${{ github.event.issue.pull_request && contains(github.event.comment.body, '/q2ci') }}
     uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
     with:
       distro: metagenome

README.md

@@ -1,5 +1,6 @@
 # q2-moshpit
-![CI](https://github.com/bokulich-lab/q2-moshpit/actions/workflows/ci-dev.yaml/badge.svg)
+![CI](https://github.com/bokulich-lab/q2-moshpit/actions/workflows/ci.yaml/badge.svg)
+![QIIME CI](https://github.com/bokulich-lab/q2-moshpit/actions/workflows/q2-ci.yaml/badge.svg)
 [![codecov](https://codecov.io/gh/bokulich-lab/q2-moshpit/graph/badge.svg?token=PSCAYJUP01)](https://codecov.io/gh/bokulich-lab/q2-moshpit)
 
 **MO**dular **SH**otgun metagenome **P**ipelines with **I**ntegrated provenance **T**racking