From 9ea306ace77d422ba028df5d7bb89b09a236caf5 Mon Sep 17 00:00:00 2001 From: JosePizarro3 Date: Mon, 10 Jun 2024 09:51:25 +0200 Subject: [PATCH 1/3] Added coverage actions Improved README and pyproject.toml --- .github/workflows/actions.yml | 78 ++++++++++++++++++++++------------- README.md | 37 ++++++++++++++++- pyproject.toml | 12 ++++-- 3 files changed, 93 insertions(+), 34 deletions(-) diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml index b6d776e..48eec75 100644 --- a/.github/workflows/actions.yml +++ b/.github/workflows/actions.yml @@ -1,40 +1,62 @@ 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 + pip install --upgrade pip --system + 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 ruff-linting: runs-on: ubuntu-latest steps: diff --git a/README.md b/README.md index 94e3752..7640ac3 100644 --- a/README.md +++ b/README.md @@ -16,18 +16,51 @@ 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 index 80b340e..df861e2 100644 --- 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 = "jose.pizarro@physik.hu-berlin.de" } ] -license = { text = "Apache-2.0" } +maintainers = [ + { name = "Jose M. Pizarro", email = "jose.pizarro@physik.hu-berlin.de" } +] +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] From ca3c781b6c6d9f3b8f50b4ba105433e89e50d3d5 Mon Sep 17 00:00:00 2001 From: JosePizarro3 Date: Mon, 10 Jun 2024 09:52:41 +0200 Subject: [PATCH 2/3] Added coverage badge --- .github/workflows/actions.yml | 1 - README.md | 2 ++ 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml index 48eec75..0782647 100644 --- a/.github/workflows/actions.yml +++ b/.github/workflows/actions.yml @@ -21,7 +21,6 @@ jobs: - name: Install dependencies run: | pip install uv - pip install --upgrade pip --system uv pip install '.[dev]' --system - name: mypy run: | diff --git a/README.md b/README.md index 7640ac3..5006e71 100644 --- 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 From 17b8dcb1b1454258f0733fda3998920da1135b47 Mon Sep 17 00:00:00 2001 From: JosePizarro3 Date: Mon, 10 Jun 2024 09:56:59 +0200 Subject: [PATCH 3/3] Fixed actions --- .github/workflows/actions.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml index 0782647..eec681a 100644 --- a/.github/workflows/actions.yml +++ b/.github/workflows/actions.yml @@ -55,7 +55,7 @@ jobs: python -m build --sdist - name: Install the package run: | - uv pip install dist/*.tar.gz + uv pip install dist/*.tar.gz --system ruff-linting: runs-on: ubuntu-latest steps: