Merge pull request #4 from danforthcenter/activate-coverage

.deepsource.toml

@@ -10,3 +10,7 @@ enabled = true
   runtime_version = "3.x.x"
   max_line_length = 127
   skip_doc_coverage = ["magic", "init", "class", "module"]
+
+[[analyzers]]
+name = "test-coverage"
+enabled = true

.github/workflows/continuous-integration.yml

@@ -43,11 +43,11 @@ jobs:
       run: |
         pip install .
         py.test --cov-report=xml --cov=plantcv tests/
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+    - name: Upload coverage to Deepsource
+      uses: deepsourcelabs/test-coverage-action@master
       with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
-        flags: unittests
-        env_vars: OS,PYTHON
-        fail_ci_if_error: true
+        key: python
+        coverage-file: coverage.xml
+        dsn: ${{ secrets.DEEPSOURCE_DSN }}
+      env:
+        DEEPSOURCE_DSN: ${{ secrets.DEEPSOURCE_DSN }}

README.md

@@ -2,11 +2,13 @@
 Geospatial add-on package to PlantCV
 
 [![builds](https://github.com/danforthcenter/plantcv-geospatial/actions/workflows/continuous-integration.yml/badge.svg?branch=main)](https://github.com/danforthcenter/plantcv-geospatial/actions/workflows/continuous-integration.yml)
-[![codecov](https://codecov.io/gh/danforthcenter/plantcv-geospatial/graph/badge.svg?token=M9TBGYVXJ9)](https://codecov.io/gh/danforthcenter/plantcv-geospatial)
+[![DeepSource](https://app.deepsource.com/gh/danforthcenter/plantcv-geospatial.svg/?label=code+coverage&show_trend=true&token=4ueUDDsEmz3YIs1UPNFPdk4r)](https://app.deepsource.com/gh/danforthcenter/plantcv-geospatial/)
 [![DeepSource](https://app.deepsource.com/gh/danforthcenter/plantcv-geospatial.svg/?label=active+issues&show_trend=true&token=4ueUDDsEmz3YIs1UPNFPdk4r)](https://app.deepsource.com/gh/danforthcenter/plantcv-geospatial/)
 
 ## Installation
 
+Developers should set up a PlantCV conda environment from source code as normal, then:
+
 ```bash
 cd plantcv-geospatial
 pip install -e .