Re-add support for Coverage reports through codecov.io

.coveragerc

@@ -1,6 +1,5 @@
 [run]
 source = aiida
-omit = aiida/test*.py,aiida/*/test*.py,aiida/*/*/test*.py,aiida/*/*/*/test*.py,aiida/*/*/*/*/test*.py,aiida/*/*/*/*/*/test*.py,aiida/*/migrations/*.py,aiida/*/migrations/versions/*.py
 
 [html]
 directory = .ci/coverage/html

.github/workflows/ci.yml

@@ -138,6 +138,16 @@ jobs:
       run:
         .github/workflows/tests.sh
 
+    - name: Upload coverage report
+      if: matrix.python-version == 3.5
+      uses: codecov/codecov-action@v1.0.5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        name: aiida-pytests-py3.5-${{ matrix.backend }}
+        flags: ${{ matrix.backend }}
+        file: ./coverage.xml
+        fail_ci_if_error: false
+
   verdi:
 
     runs-on: ubuntu-latest

.github/workflows/tests.sh

@@ -3,16 +3,26 @@ set -ev
 
 # Make sure the folder containing the workchains is in the python path before the daemon is started
 export PYTHONPATH="${PYTHONPATH}:${GITHUB_WORKSPACE}/.ci"
-# show timings of tests
-export PYTEST_ADDOPTS=" --durations=0"
 
+# pytest options:
+# - report timings of tests
+# - pytest-cov configuration taken from top-level .coveragerc
+# - coverage is reported as XML and in terminal,
+#   including the numbers/ranges of lines which are not covered
+# - coverage results of multiple tests are collected
+# - coverage is reported on files in aiida/
+export PYTEST_ADDOPTS="${PYTEST_ADDOPTS} --durations=0 --cov-config=.coveragerc --cov-report xml --cov-report term-missing --cov-append --cov=aiida"
+
+# daemon tests
 verdi daemon start 4
 verdi -p test_${AIIDA_TEST_BACKEND} run .ci/test_daemon.py
 verdi daemon stop
 
-AIIDA_TEST_PROFILE=test_$AIIDA_TEST_BACKEND pytest tests
-AIIDA_TEST_PROFILE=test_$AIIDA_TEST_BACKEND pytest .ci/pytest
+# tests for the testing infrastructure
 pytest --noconftest .ci/test_test_manager.py
 pytest --noconftest .ci/test_profile_manager.py
+python .ci/test_plugin_testcase.py  # uses custom unittest test runner
+AIIDA_TEST_PROFILE=test_$AIIDA_TEST_BACKEND pytest .ci/pytest
 
-python .ci/test_plugin_testcase.py
+# main aiida-core tests
+AIIDA_TEST_PROFILE=test_$AIIDA_TEST_BACKEND pytest tests

README.md

@@ -6,7 +6,7 @@ AiiDA (www.aiida.net) is a workflow manager for computational science with a str
 |-----|----------------------------------------------------------------------------|
 |Latest release| [![PyPI version](https://badge.fury.io/py/aiida-core.svg)](https://badge.fury.io/py/aiida-core) [![conda-forge](https://img.shields.io/conda/vn/conda-forge/aiida-core.svg?style=flat)](https://anaconda.org/conda-forge/aiida-core) [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-core.svg)](https://pypi.python.org/pypi/aiida-core/) |
 |Getting help| [![Docs status](https://readthedocs.org/projects/aiida-core/badge)](http://aiida-core.readthedocs.io/) [![Google Group](https://img.shields.io/badge/-Google%20Group-lightgrey.svg)](https://groups.google.com/forum/#!forum/aiidausers)
-|Build status| [![Build Status](https://travis-ci.org/aiidateam/aiida-core.svg?branch=develop)](https://travis-ci.org/aiidateam/aiida-core) [![Coverage Status](https://coveralls.io/repos/github/aiidateam/aiida-core/badge.svg?branch=develop)](https://coveralls.io/github/aiidateam/aiida-core?branch=develop) |
+|Build status| [![Build Status](https://travis-ci.org/aiidateam/aiida-core.svg?branch=develop)](https://travis-ci.org/aiidateam/aiida-core) [![Coverage Status](https://codecov.io/gh/aiidateam/aiida-core/branch/develop/graph/badge.svg)](https://codecov.io/gh/aiidateam/aiida-core) |
 |Activity| [![PyPI-downloads](https://img.shields.io/pypi/dm/aiida-core.svg?style=flat)](https://pypistats.org/packages/aiida-core) [![Commit Activity](https://img.shields.io/github/commit-activity/m/aiidateam/aiida-core.svg)](https://github.com/aiidateam/aiida-core/pulse)
 |Community| [![Affiliated with NumFOCUS](https://img.shields.io/badge/NumFOCUS-affiliated%20project-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org/sponsored-projects/affiliated-projects) [![Twitter](https://img.shields.io/twitter/follow/aiidateam.svg?style=social&label=Follow)](https://twitter.com/aiidateam)
 

docs/requirements_for_rtd.txt

@@ -8,6 +8,7 @@ click-completion~=0.5.1
 click-config-file~=0.5.0
 click-spinner~=0.1.8
 click~=7.0
+coverage<5.0
 django~=2.2
 docutils==0.15.2
 ete3~=3.1
@@ -31,6 +32,7 @@ pygments~=2.5
 pymatgen>=2019.7.2
 pymysql~=0.9.3
 pyparsing~=2.4
+pytest-cov~=2.7
 pytest-timeout~=1.3
 pytest~=5.3
 python-dateutil~=2.8

setup.json

@@ -92,6 +92,8 @@
       "pgtest~=1.3,>=1.3.1",
       "pytest~=5.3",
       "pytest-timeout~=1.3",
+      "pytest-cov~=2.7",
+      "coverage<5.0",
       "sqlalchemy-diff~=0.1.3"
     ],
     "dev_precommit": [