Merge pull request #8 from misialq/ci-improvements

MAINT: CI updates

Author: misialq

.coveragerc

@@ -1,4 +1,5 @@
 [run]
+source=q2_moshpit
 branch = True
 omit =
     */tests*
@@ -7,6 +8,7 @@ omit =
     versioneer.py
 
 [report]
+fail_under = 90
 omit =
     */tests*
     */__init__.py

.github/workflows/ci.yml

@@ -29,8 +29,32 @@ jobs:
         pip install -q flake8
         flake8
 
-  build-and-test:
+  coverage:
     needs: lint
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: q2-shotgun-test
+        mamba-version: "*"
+        channels: conda-forge
+    - name: Run tests with coverage
+      run: |
+        mamba install -c https://packages.qiime2.org/qiime2/2022.4/tested -c conda-forge -c bioconda -c defaults -y --file requirements.txt
+        make dev
+        qiime dev refresh-cache
+        make test-cov
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        fail_ci_if_error: true
+
+  build-and-test:
+    needs: coverage
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
@@ -46,6 +70,5 @@ jobs:
       with:
         package-name: q2-moshpit
         additional-tests: pytest --pyargs q2_moshpit
-        # TODO: update this to `release` when tagging release
-        build-target: staged
+        build-target: dev
         library-token: ${{ secrets.LIBRARY_TOKEN }}

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021, QIIME 2 development team.
+Copyright (c) 2022, QIIME 2 development team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

Makefile

@@ -12,12 +12,14 @@ test: all
 	py.test
 
 test-cov: all
-	py.test --cov=q2_fondue
+	coverage run -m pytest
+	coverage xml
 
 install: all
 	$(PYTHON) setup.py install
 
 dev: all
+	pip install coverage
 	pip install -e .
 
 clean: distclean

ci/recipe/meta.yaml

@@ -19,6 +19,8 @@ requirements:
 
   run:
     - qiime2 {{ release }}.*
+    - q2-types-genomics {{ release }}.*
+    - q2templates {{ release }}.*
 
 test:
   imports:

ci/recipe/test_build.sh

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_moshpit/__init__.py

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

q2_moshpit/plugin_setup.py

@@ -0,0 +1,4 @@
+q2-types
+q2-types-genomics
+q2cli
+q2templates

requirements.txt

@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #