CI: add new workflows

.github/workflows/ci.yaml

@@ -0,0 +1,88 @@
+name: Test
+on:
+  pull_request:
+    branches: ["main"]
+  push:
+    branches: ["main"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    outputs:
+      latest-dev-tag: ${{ steps.fetch_latest_tags.outputs.latest-dev-tag }}
+      latest-stable-tag: ${{ steps.fetch_latest_tags.outputs.latest-stable-tag }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Checkout utilities
+        uses: actions/checkout@v4
+        with:
+          repository: bokulich-lab/utilities
+          path: utilities
+
+      - name: Install dependencies
+        run: python -m pip install requests
+
+      - name: Fetch latest tags
+        id: fetch-tags
+        run: |
+          latest_tags=$(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
+        run: |
+          bash utilities/ci/get-dependencies.sh ${{ vars.DISTRO }} ${{ steps.fetch-tags.outputs.latest-dev-tag }}
+          cat environment.yml
+
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: 3.8
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          activate-environment: conda-env
+          condarc-file: utilities/ci/condarc
+          # use-only-tar-bz2: true
+
+      - name: Get date
+        id: get-date
+        run: echo "today=$(/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 plugin
+        run: pip install .
+
+      - name: Install dev dependencies
+        run: pip install pytest coverage
+
+      - name: Run tests
+        run: 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/q2-ci.yaml

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+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
+      additional-reports-path: ./coverage.xml
+      additional-reports-name: coverage
+
+  coverage:
+    needs: [ci]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v3
+        name: 'Fetch coverage from builds'
+        with:
+          name: ${{ needs.ci.outputs.additional-reports-name }}
+          path: ${{ needs.ci.outputs.additional-reports-path }}
+
+      - uses: codecov/codecov-action@v4
+        name: 'Upload coverage'
+        with:
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}