Merge pull request #51 from KoslickiLab/codecov

Codecov

.github/workflows/runTest.yml

@@ -17,12 +17,21 @@ jobs:
     - name: run YACHT
       run: python run_YACHT.py --json gtdb_ani_thresh_0.95_config.json --sample_file 'tests/testdata/sample.sig.zip' --significance 0.99 --min_coverage_list 1 0.6 0.2 0.1
     - name: test-unit
-      run: pytest tests/test_unit.py
+      run: pytest tests/test_unit.py --cov=./  --cov-report xml:covunit.xml
     - name: test-utils
-      run: pytest tests/test_utils.py
+      run: pytest tests/test_utils.py --cov=./  --cov-report xml:covutils.xml
     - name: test-workflow
-      run: pytest tests/test_workflow.py
+      run: pytest tests/test_workflow.py --cov=./  --cov-report xml:covworkflow.xml
     - name: integration-tests
-      run: pytest -vv tests/integration_tests.py
+      run: pytest -vv tests/integration_tests.py --cov=./  --cov-report xml:covntegration.xml
     - name: unit-tests
-      run: pytest -vv tests/unittests.py
+      run: pytest -vv tests/unittests.py --cov=./  --cov-report xml:covunittests.xml
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        files: ./covunit.xml,./covutils.xml,./covworkflow.xml,./covntegration.xml,./covunittests.xml
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+    - name: Badge Action
+      uses: emibcn/[email protected]
+

README.md

@@ -1,4 +1,5 @@
 # YACHT
+[![codecov](https://codecov.io/gh/KoslickiLab/YACHT/graph/badge.svg?token=AZD6LBFR5P)](https://codecov.io/gh/KoslickiLab/YACHT)
 
 YACHT is a mathematically rigorous hypothesis test for the presence or absence of organisms in a metagenomic sample, based on average nucleotide identity (ANI).
 

env/yacht_env.yml

@@ -11,12 +11,14 @@ dependencies:
   - numpy
   - pandas
   - scikit-learn
+  - codecov
   - pytest
+  - pytest-cov
   - loguru
   - maturin>=1,<2
   - tqdm
   - biom-format
   - pytaxonkit
   - pip:
     - openpyxl
-    - git+https://github.com/sourmash-bio/[email protected]
+    - git+https://github.com/sourmash-bio/[email protected]