From 99e251cced8b4d579e852ff913c12ac3126f6f6d Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Fri, 29 Mar 2024 13:39:10 +0100
Subject: [PATCH] Add code coverage analysis by Codecov (#92)

---
 .github/workflows/pytest.yml | 18 ++++++++++++++++--
 .gitignore                   |  4 ++--
 README.md                    |  3 ++-
 environment.yml              |  3 ++-
 environment_ace.yml          |  3 ++-
 environment_mace.yml         |  3 ++-
 pyproject.toml               |  3 +++
 7 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 92100d12..08386128 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -38,7 +38,14 @@ jobs:
       run: ./install_gap.sh
 
     - name: Test basic install
-      run: pytest
+      run: pytest --cov
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+          flags: python-${{ matrix.python-version }}
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: duartegroup/mlp-train
 
 
   test-mace:
@@ -70,4 +77,11 @@ jobs:
       run: ./install_mace.sh
 
     - name: Test MACE install
-      run: pytest
+      run: pytest --cov
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+          flags: python-${{ matrix.python-version }}-mace
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: duartegroup/mlp-train
diff --git a/.gitignore b/.gitignore
index 4ba3241d..42e886fd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,5 +5,5 @@ dist/
 *DS_store
 **/__pycache__/
 **/__MACOSX/
-.coverage
-.pytest_cache
\ No newline at end of file
+.coverage*
+.pytest_cache
diff --git a/README.md b/README.md
index 60a20ecf..31b2aca7 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
-[![Test with pytest](https://github.com/duartegroup/mlp-train/actions/workflows/pytest.yml/badge.svg?event=push)](https://github.com/duartegroup/mlp-train/actions/workflows/pytest.yml)
+[![pytest CI](https://github.com/duartegroup/mlp-train/actions/workflows/pytest.yml/badge.svg?event=push)](https://github.com/duartegroup/mlp-train/actions/workflows/pytest.yml)
+[![codecov](https://codecov.io/gh/duartegroup/mlp-train/branch/main/graph/badge.svg)](https://codecov.io/gh/duartegroup/mlp-train)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg)](https://opensource.org/licenses/mit)
diff --git a/environment.yml b/environment.yml
index c1b37a44..ca43fd1d 100644
--- a/environment.yml
+++ b/environment.yml
@@ -14,7 +14,8 @@ dependencies:
   - dscribe=2.0
   - matplotlib-base
   - numpy
-  - pytest
+  - pytest=8
+  - pytest-cov=5
   - py-plumed
   - scipy
   - xtb
diff --git a/environment_ace.yml b/environment_ace.yml
index e6ff624e..992c3383 100644
--- a/environment_ace.yml
+++ b/environment_ace.yml
@@ -14,7 +14,8 @@ dependencies:
   - dscribe=2.0
   - matplotlib-base
   - numpy
-  - pytest
+  - pytest=8
+  - pytest-cov=5
   - py-plumed
   - scipy
   - xtb
diff --git a/environment_mace.yml b/environment_mace.yml
index aaac7b78..515fc635 100644
--- a/environment_mace.yml
+++ b/environment_mace.yml
@@ -15,7 +15,8 @@ dependencies:
   - dscribe=2.0
   - matplotlib-base
   - numpy
-  - pytest
+  - pytest=8
+  - pytest-cov=5
   - py-plumed
   - scipy
   - xtb
diff --git a/pyproject.toml b/pyproject.toml
index 02b85a3a..00591d84 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,3 +21,6 @@ line-length = 79
 
 [tool.ruff.format]
 quote-style = "single"
+
+[tool.pytest.ini_options]
+addopts = "--cov-report term --cov-report xml"