Add coverage (#17)

* Added coverage actions Improved README and pyproject.toml * Added coverage badge * Fixed actions
JosePizarro3 · Jun 10, 2024 · cb6e9d3 · cb6e9d3
1 parent 1a9d4dd
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diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
@@ -1,40 +1,61 @@
 name: install-and-test
 on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
 jobs:
   install-and-test:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install '.[dev]'
-    - name: mypy
-      run: |
-        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/pyssmf tests
-    - name: Test with pytest
-      run: |
-        python -m pytest -sv tests
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install dependencies
+        run: |
+          pip install uv
+          uv pip install '.[dev]' --system
+      - name: mypy
+        run: |
+          python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/pyssmf tests
+      - name: Build coverage file
+        run: |
+          pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src tests | tee pytest-coverage.txt
+      - name: Pytest coverage comment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml
+      - name: Submit to coveralls
+        continue-on-error: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          coveralls --service=github
   build-and-install:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Build the package
-      run: |
-        pip install --upgrade pip
-        pip install build
-        python -m build --sdist
-    - name: Install the package
-      run: |
-        pip install dist/*.tar.gz
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Build the package
+        run: |
+          pip install uv
+          uv pip install --upgrade pip --system
+          uv pip install build --system
+          python -m build --sdist
+      - name: Install the package
+        run: |
+          uv pip install dist/*.tar.gz --system
   ruff-linting:
       runs-on: ubuntu-latest
       steps:

diff --git a/README.md b/README.md
@@ -1,3 +1,5 @@
+[![Coverage Status](https://coveralls.io/repos/github/JosePizarro3/pySSMF/badge.svg?branch=develop)](https://coveralls.io/github/JosePizarro3/pySSMF?branch=develop)
+
 # pySSMF
 
 ## Installation steps
@@ -16,18 +18,51 @@ python3.9 -m venv .pyenv
 source .pyenv/bin/activate
 ```
 
+We recommend using `uv` for pip installing all packages:
+```sh
+pip install uv
+```
+
 Make sure to have pip upgraded to its latest version:
 ```sh
-pip install --upgrade pip
+uv pip install --upgrade pip
 ```
 
 Now, install the dependencies in editable mode (this is done by adding the flag `-e` and it is useful when debugging the code):
 ```sh
-pip install -e '.[dev]'
+uv pip install -e '.[dev]'
 ```
 
 The `[dev]` option will allow to install the optional-dependencies specified in the configuration `pyproject.toml` file.
 
+### Run the tests
+
+You can run local tests using the `pytest` package:
+
+```sh
+python -m pytest -sv tests
+```
+
+where the `-s` and `-v` options toggle the output verbosity.
+
+Our CI/CD pipeline produces a more comprehensive test report using `coverage` and `coveralls` packages. We suggest you to generate your own coverage reports locally by doing:
+
+```sh
+uv pip install coverage coveralls
+python -m pytest --cov=src  tests
+```
+
+### Run linting and auto-formatting
+
+We use [Ruff](https://docs.astral.sh/ruff/) for auto-formatting our Python modules. This package is included as part of the `[dev]` dependencies of the project, and can be run in the terminal:
+
+```sh
+ruff check .
+ruff format . --check
+```
+
+Ruff auto-formatting is also a part of the GitHub workflow actions. Make sure that before you make a Pull Request, `ruff format . --check` runs in your local without any errors otherwise the workflow action will fail.
+
 ### Using VSCode for debugging
 
 I recommend to use VSCode as your visual editor for debugging. The project comes with a `settings.json` file which already takes care of formatting everytime you save changes in a file (using [Ruff](https://docs.astral.sh/ruff/)).

diff --git a/pyproject.toml b/pyproject.toml
@@ -7,12 +7,15 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = 'pySSMF'
-version = '0.1.0'
 description = 'A Python package to solve the Slave-Spin Mean-Field equations for tight-binding models in strongly correlated systems'
 authors = [
     { name = "Jose M. Pizarro", email = "[email protected]" }
 ]
-license = { text = "Apache-2.0" }
+maintainers = [
+    { name = "Jose M. Pizarro", email = "[email protected]" }
+]
+dynamic = ["version"]
+license = { file = "LICENSE" }
 requires-python = ">=3.9"
 readme = "README.md"
 dependencies = [
@@ -29,11 +32,12 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     'mypy==1.5.1',
-    'pytest==3.10.0',
+    'pytest',
+    'pytest-timeout',
+    'pytest-cov',
     'ruff',
     "structlog==22.3.0",
     "lxml_html_clean>=0.1.0",
-    "PyQt5==5.15.10",
 ]
 
 [tool.ruff]