Calculate unit test coverage (#61)

jan-janssen · web-flow · commit 279c991b8274 · 2025-09-20T10:35:36.000+02:00
* Update pyiron_atomistics to 0.7.18

* Calculate unit test coverage

* Add coverage to readme
diff --git a/.ci_support/environment-pyiron-atomistics-0-6-20.yml b/.ci_support/environment-pyiron-atomistics-0-6-20.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.6.20
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-6-21.yml b/.ci_support/environment-pyiron-atomistics-0-6-21.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.6.21
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-6-22.yml b/.ci_support/environment-pyiron-atomistics-0-6-22.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.6.22
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-6-23.yml b/.ci_support/environment-pyiron-atomistics-0-6-23.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.6.23
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-6-24.yml b/.ci_support/environment-pyiron-atomistics-0-6-24.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.6.24
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-6-25.yml b/.ci_support/environment-pyiron-atomistics-0-6-25.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.6.25
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-0.yml b/.ci_support/environment-pyiron-atomistics-0-7-0.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.0
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-1.yml b/.ci_support/environment-pyiron-atomistics-0-7-1.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.1
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-10.yml b/.ci_support/environment-pyiron-atomistics-0-7-10.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.10
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-11.yml b/.ci_support/environment-pyiron-atomistics-0-7-11.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.11
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-12.yml b/.ci_support/environment-pyiron-atomistics-0-7-12.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.12
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-13.yml b/.ci_support/environment-pyiron-atomistics-0-7-13.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.13
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-14.yml b/.ci_support/environment-pyiron-atomistics-0-7-14.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.14
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-15.yml b/.ci_support/environment-pyiron-atomistics-0-7-15.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.15
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-16.yml b/.ci_support/environment-pyiron-atomistics-0-7-16.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.16
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-17.yml b/.ci_support/environment-pyiron-atomistics-0-7-17.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.17
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-18.yml b/.ci_support/environment-pyiron-atomistics-0-7-18.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.18
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-2.yml b/.ci_support/environment-pyiron-atomistics-0-7-2.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.2
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-3.yml b/.ci_support/environment-pyiron-atomistics-0-7-3.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.3
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-4.yml b/.ci_support/environment-pyiron-atomistics-0-7-4.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.4
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-5.yml b/.ci_support/environment-pyiron-atomistics-0-7-5.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.5
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-6.yml b/.ci_support/environment-pyiron-atomistics-0-7-6.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.6
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-7.yml b/.ci_support/environment-pyiron-atomistics-0-7-7.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.7
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-8.yml b/.ci_support/environment-pyiron-atomistics-0-7-8.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.8
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.ci_support/environment-pyiron-atomistics-0-7-9.yml b/.ci_support/environment-pyiron-atomistics-0-7-9.yml
@@ -1,8 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- jupyter
-- papermill
+- coverage
 - pyiron-data =0.0.30
 - pyiron_atomistics =0.7.9
 - lammps =2024.02.07=*_openmpi_*
diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml
@@ -113,7 +113,14 @@ jobs:
       run: |
         pip install versioneer[toml]==0.29
         pip install . --no-deps --no-build-isolation
-        python -m unittest discover tests
+        coverage run
+        coverage report
+        coverage xml
+    - name: Upload coverage reports to Codecov
+      if: matrix.environment-file == '.ci_support/environment-pyiron-atomistics-0-7-18.yml'
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
 
   autobot:
     needs: [minimal, pyiron_atomistics_tests]
diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 # Dataclasses for pyiron
 [![Pipeline](https://github.com/pyiron/pyiron_dataclasses/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/pyiron_dataclasses/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/pyiron_dataclasses/graph/badge.svg?token=83H0OO0AFC)](https://codecov.io/gh/pyiron/pyiron_dataclasses)
 
 The `pyiron_dataclasses` module provides a series of [dataclasses](https://docs.python.org/3/library/dataclasses.html) 
 for the `pyiron` workflow framework. It can load HDF5 files created by `pyiron_atomistics` and read the content stored 
diff --git a/pyproject.toml b/pyproject.toml
@@ -51,3 +51,7 @@ style = "pep440-pre"
 versionfile_source = "pyiron_dataclasses/_version.py"
 parentdir_prefix = "pyiron_dataclasses"
 tag_prefix = "pyiron_dataclasses-"
+
+[tool.coverage.run]
+omit = ["pyiron_dataclasses/_version.py", "tests/*"]
+command_line = "-m unittest discover tests"
