MAINT: clean up CI tasks (#32)

.github/workflows/ci.yml

@@ -12,20 +12,18 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: set up python 3.6
+    - name: Set up python 3.8
       uses: actions/setup-python@v1
       with:
-        python-version: 3.6
+        python-version: 3.8
 
-    - name: install dependencies
-      run: python -m pip install --upgrade pip
-
-    - name: lint
+    - name: Install dependencies
       run: |
         pip install -q https://github.com/qiime2/q2lint/archive/master.zip
-        q2lint
         pip install -q flake8
-        flake8
+
+    - name: Lint
+      run: make lint
 
   build-and-test:
     needs: lint
@@ -39,10 +37,18 @@ jobs:
         # necessary for versioneer
         fetch-depth: 0
 
+    - name: Hack - template coverage output path
+      run: echo "COV=coverage xml -o $GITHUB_WORKSPACE/coverage.xml" >> $GITHUB_ENV
+
     # TODO: update this to @v1 when it lands
     - uses: qiime2/action-library-packaging@alpha1
       with:
         package-name: q2-types-genomics
-        additional-tests: pytest --pyargs q2_types_genomics
+        additional-tests: ${{ env.COV }}
         build-target: dev
         library-token: ${{ secrets.LIBRARY_TOKEN }}
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        fail_ci_if_error: true

Makefile

@@ -12,7 +12,8 @@ test: all
 	py.test
 
 test-cov: all
-	py.test --cov=q2_types_genomics
+	coverage run -m pytest
+	coverage xml
 
 install: all
 	$(PYTHON) setup.py install

ci/recipe/meta.yaml

@@ -1,7 +1,5 @@
-# revert to proper versioning when ready for the first release
 {% set data = load_setup_py_data() %}
-{% set version = '2022.4.0.dev0' %}
-{% set release = '2022.4' %}
+{% set version = data.get('version') or 'placehold' %}
 
 package:
   name: q2-types-genomics
@@ -22,13 +20,18 @@ requirements:
     - python {{ python }}
     - bowtie2
     - samtools
-    - q2-types {{ release }}.*
-    - qiime2 {{ release }}.*
+    - q2-types {{ qiime2_epoch }}.*
+    - qiime2 {{ qiime2_epoch }}.*
 
 test:
+  requires:
+    - coverage
+    - pytest-cov
   imports:
     - q2_types_genomics
     - qiime2.plugins.types_genomics
+  commands:
+    - pytest --cov q2_types_genomics --pyargs q2_types_genomics
 
 about:
   home: https://github.com/bokulich-lab/q2-types-genomics