Merge pull request #404 from ComputationalCryoEM/issue_243

Add parallel coverage job to GitHub Actions.

Author: garrettwrong

.codecov.yml

@@ -0,0 +1,2 @@
+ignore:
+  - "*/tests/*”

.github/workflows/workflow.yml

@@ -34,8 +34,8 @@ jobs:
         include:
           # Re-include 3.6-stable with additional tox tasks.
           - python-version: 3.6
-            # Note since the environments are fresh, we don't need invoke `clean`.
-            pyenv: stable,docs,coveralls,report
+            pyenv: stable,docs
+
 
     steps:
     - uses: actions/checkout@v1
@@ -49,6 +49,9 @@ jobs:
         pip install tox tox-gh-actions
     - name: Test with tox
       run: tox --skip-missing-interpreters false -e py${{ matrix.python-version }}-${{ matrix.pyenv }}
+    - name: Upload Coverage to CodeCov
+      uses: codecov/codecov-action@v1
+
 
   docs:
     if: github.ref == 'refs/heads/master'

README.md

@@ -2,7 +2,7 @@
 
 [![Azure Build Status](https://dev.azure.com/ComputationalCryoEM/Aspire-Python/_apis/build/status/ComputationalCryoEM.ASPIRE-Python?branchName=master)](https://dev.azure.com/ComputationalCryoEM/Aspire-Python/_build/latest?definitionId=3&branchName=master)
 [![Github Actions Status](https://github.com/ComputationalCryoEM/ASPIRE-Python/actions/workflows/workflow.yml/badge.svg)](https://github.com/ComputationalCryoEM/ASPIRE-Python/actions/workflows/workflow.yml)
-[![Coverage Status](https://coveralls.io/repos/github/ComputationalCryoEM/ASPIRE-Python/badge.svg?branch=master)](https://coveralls.io/github/ComputationalCryoEM/ASPIRE-Python?branch=master)
+[![codecov](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python/branch/master/graph/badge.svg?token=3XFC4VONX0)](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python)
 
 # ASPIRE - Algorithms for Single Particle Reconstruction - v0.6.3
 

tox.ini

@@ -5,8 +5,6 @@ envlist =
     check
     docs
     py{3.6,3.7,3.8,3.9}-{stable,dev}
-    coveralls
-    report
 minversion = 3.8.0
 
 [testenv]
@@ -19,7 +17,8 @@ commands =
     python -V
     pip freeze
     python -c "import numpy; numpy.show_config()"
-    pytest --cov=aspire {posargs}
+    # --cov should generate `Coverage` data
+    pytest --cov=aspire --cov-report=xml {posargs}
 
 [testenv:py{3.6,3.7,3.8,3.9}-dev]
 whitelist_externals=
@@ -36,7 +35,8 @@ commands =
     python -V
     pip freeze
     python -c "import numpy; numpy.show_config()"
-    pytest --cov=aspire {posargs}
+    # --cov should generate `Coverage` data
+    pytest --cov=aspire --cov-report=xml {posargs}
 
 [testenv:docs]
 changedir = docs
@@ -76,25 +76,6 @@ commands =
     python setup.py sdist
     twine check dist/*.*
 
-[testenv:coveralls]
-deps =
-    coveralls
-skip_install = true
-commands =
-    - coveralls []
-
-[testenv:clean]
-commands = coverage erase
-skip_install = true
-deps = coverage
-
-[testenv:report]
-deps = coverage
-skip_install = true
-commands =
-    coverage report
-    coverage html
-
 [flake8]
 # The following for recomended for use with Black
 max-line-length = 88
@@ -126,3 +107,6 @@ python =
     3.7: py3.7
     3.8: py3.8
     3.9: py3.9
+
+[coverage:run]
+relative_files = True