From 074df439edb03de2de59d71dd37cd0b432bcbb69 Mon Sep 17 00:00:00 2001 From: Ahmed Ilyas Date: Mon, 9 Sep 2024 16:40:05 +0200 Subject: [PATCH] Use uv project interface in template --- .../.github/workflows/actions.yml | 48 +- {{cookiecutter.plugin_name}}/README.md | 113 +- {{cookiecutter.plugin_name}}/pyproject.toml | 34 +- .../requirements_docs.txt | 4 - {{cookiecutter.plugin_name}}/uv.lock | 2387 +++++++++++++++++ 5 files changed, 2489 insertions(+), 97 deletions(-) delete mode 100644 {{cookiecutter.plugin_name}}/requirements_docs.txt create mode 100644 {{cookiecutter.plugin_name}}/uv.lock diff --git a/{{cookiecutter.plugin_name}}/.github/workflows/actions.yml b/{{cookiecutter.plugin_name}}/.github/workflows/actions.yml index bd7fa86..08db9ff 100644 --- a/{{cookiecutter.plugin_name}}/.github/workflows/actions.yml +++ b/{{cookiecutter.plugin_name}}/.github/workflows/actions.yml @@ -3,42 +3,34 @@ on: [push] jobs: install-and-test: runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python_version: ["3.9", "3.10", "3.11"] steps: - uses: actions/checkout@v4 - - name: Set up Python 3.9 + + - name: Set up Python {% raw -%}${{ matrix.python_version }}{% endraw %} uses: actions/setup-python@v5 with: - python-version: 3.9 - - name: Install dependencies + python-version: {% raw -%}${{ matrix.python_version }}{% endraw %} + + - name: Install uv + uses: astral-sh/setup-uv@v2 + + - name: Install the project + run: uv sync --all-extras + + - name: Run tests run: | - pip install --upgrade pip - pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple - pip install coverage coveralls - - name: Test with pytest - run: | - python -m coverage run -m pytest -sv + uv run pytest --cov + - name: Submit to coveralls continue-on-error: true env: GITHUB_TOKEN: {% raw -%}${{ secrets.GITHUB_TOKEN }}{% endraw %} - run: | - coveralls --service=github - build-and-install: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - name: Set up Python 3.9 - uses: actions/setup-python@v5 - 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 --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple + run: uv run --with coveralls coveralls --service=github + ruff-linting: runs-on: ubuntu-latest steps: @@ -53,4 +45,4 @@ jobs: # - uses: actions/checkout@v4 # - uses: chartboost/ruff-action@v1 # with: - # args: "format . --check" \ No newline at end of file + # args: "format . --check" diff --git a/{{cookiecutter.plugin_name}}/README.md b/{{cookiecutter.plugin_name}}/README.md index a67152b..d126e79 100644 --- a/{{cookiecutter.plugin_name}}/README.md +++ b/{{cookiecutter.plugin_name}}/README.md @@ -4,87 +4,70 @@ This `nomad` plugin was generated with `Cookiecutter` along with `@nomad`'s [`cookiecutter-nomad-plugin`](https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin) template. - ## Development -If you want to develop locally this plugin, clone the project and in the plugin folder, create a virtual environment (you can use Python 3.9, 3.10, or 3.11): +If you want to locally develop this plugin, clone the project. + ```sh git clone https://github.com/{{cookiecutter.github_username}}/{{cookiecutter.plugin_name}}.git cd {{cookiecutter.plugin_name}} -python3.11 -m venv .pyenv -. .pyenv/bin/activate ``` -Make sure to have `pip` upgraded: -```sh -pip install --upgrade pip -``` +We highly recommend using `uv` to manage the project. Consider installing `uv` by following the official installation [guide](https://docs.astral.sh/uv/getting-started/installation/#installing-uv). -We recommend installing `uv` for fast pip installation of the packages: -```sh -pip install uv -``` +Read the short [guide](https://docs.astral.sh/uv/guides/projects/) on how to manage projects. -Install the `nomad-lab` package: -```sh -uv pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple -``` +Install all the dependencies: -**Note!** -Until we have an official pypi NOMAD release with the plugins functionality make -sure to include NOMAD's internal package registry (via `--index-url` in the above command). - -The plugin is still under development. If you would like to contribute, install the package in editable mode (with the added `-e` flag): ```sh -uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple +uv sync --extra-all ``` +**Note!** +If you're not using `uv`, setup a `venv` and pip install the package using `pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple`. +Until we have an official pypi NOMAD release with the plugins functionality make sure to include NOMAD's internal package registry (via --extra-index-url in the above command). ### Run the tests -You can run locally the tests: +You can run the tests using: + ```sh -python -m pytest -sv tests +uv run pytest ``` -where the `-s` and `-v` options toggle the output verbosity. +Or generate a test coverage report: -Our CI/CD pipeline produces a more comprehensive test report using the `pytest-cov` package. You can generate a local coverage report: ```sh -uv pip install pytest-cov -python -m pytest --cov=src tests +uv run pytest --cov ``` ### Run linting and auto-formatting -We use [Ruff](https://docs.astral.sh/ruff/) for linting and formatting the code. Ruff auto-formatting is also a part of the GitHub workflow actions. You can run locally: +We use [Ruff](https://docs.astral.sh/ruff/) for linting and formatting the code. Ruff auto-formatting is also a part of the GitHub workflow actions. You can check linting and formatting using: + ```sh -ruff check . -ruff format . --check +uv run ruff check . +uv run ruff format . --check ``` - ### Debugging For interactive debugging of the tests, use `pytest` with the `--pdb` flag. We recommend using an IDE for debugging, e.g., _VSCode_. If that is the case, add the following snippet to your `.vscode/launch.json`: + ```json { "configurations": [ - { - "name": "", - "type": "debugpy", - "request": "launch", - "cwd": "${workspaceFolder}", - "program": "${workspaceFolder}/.pyenv/bin/pytest", - "justMyCode": true, - "env": { - "_PYTEST_RAISE": "1" - }, - "args": [ - "-sv", - "--pdb", - "", - ] + { + "name": "", + "type": "debugpy", + "request": "launch", + "cwd": "${workspaceFolder}", + "program": "${workspaceFolder}/.venv/bin/pytest", + "justMyCode": true, + "env": { + "_PYTEST_RAISE": "1" + }, + "args": ["-sv", "--pdb", ""] } ] } @@ -94,23 +77,18 @@ where `` must be changed to the local path to the test mod The settings configuration file `.vscode/settings.json` automatically applies the linting and formatting upon saving the modified file. - ### Documentation on Github pages -To view the documentation locally, install the related packages using: -```sh -uv pip install -r requirements_docs.txt -``` +To view the documentation locally, run the docs server: -Run the documentation server: ```sh -mkdocs serve +uv run mkdocs serve ``` - ## Adding this plugin to NOMAD Currently, NOMAD has two distinct flavors that are relevant depending on your role as an user: + 1. [A NOMAD Oasis](#adding-this-plugin-in-your-nomad-oasis): any user with a NOMAD Oasis instance. 2. [Local NOMAD installation and the source code of NOMAD](#adding-this-plugin-in-your-local-nomad-installation-and-the-source-code-of-nomad): internal developers. @@ -121,13 +99,16 @@ Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/ ### Adding this plugin in your local NOMAD installation and the source code of NOMAD Modify the text file under `/nomad/default_plugins.txt` and add: + ```sh {{cookiecutter.plugin_name}}==x.y.z ``` + where `x.y.z` represents the released version of this plugin. Then, go to your NOMAD folder, activate your NOMAD virtual environment and run: + ```sh deactivate cd /nomad @@ -137,15 +118,13 @@ source .pyenv/bin/activate Alternatively and only valid for your local NOMAD installation, you can modify `nomad.yaml` to include this plugin, see [NOMAD Oasis - Install plugins](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html). - ### Build the python package The `pyproject.toml` file contains everything that is necessary to turn the project into a pip installable python package. Run the python build tool to create a package distribution: ```sh -pip install build -python -m build --sdist +uv build ``` You can install the package with pip: @@ -157,15 +136,21 @@ pip install dist/{{cookiecutter.plugin_name}}-{{cookiecutter.version}} Read more about python packages, `pyproject.toml`, and how to upload packages to PyPI on the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/). - ### Template update -We use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests. +We use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests. -To run the check for updates locally, follow the instructions on [`cruft` website](https://cruft.github.io/cruft/#updating-a-project). +To check for updates locally, run: +```sh +uvx cruft update +``` + +**Note!** +`uvx` is included in `uv` installation. ## Main contributors -| Name | E-mail | -|------|------------| -| {{cookiecutter.full_name}} | [{{cookiecutter.email}}](mailto:{{cookiecutter.email}}) + +| Name | E-mail | +| -------------------------- | ------------------------------------------------------- | +| {{cookiecutter.full_name}} | [{{cookiecutter.email}}](mailto:{{cookiecutter.email}}) | diff --git a/{{cookiecutter.plugin_name}}/pyproject.toml b/{{cookiecutter.plugin_name}}/pyproject.toml index 0916c98..ec4dd57 100644 --- a/{{cookiecutter.plugin_name}}/pyproject.toml +++ b/{{cookiecutter.plugin_name}}/pyproject.toml @@ -41,7 +41,34 @@ dependencies = ["nomad-lab>=1.3.0"] Repository = "https://github.com/{{cookiecutter.github_username}}/{{cookiecutter.plugin_name}}" [project.optional-dependencies] -dev = ["ruff", "pytest", "structlog"] +dev = [ + "ruff", + "pytest>=6.0", + "structlog", + "pytest-cov" +] + +docs = [ + "mkdocs", + "mkdocs-material==8.1.1", + "pymdown-extensions", + "mkdocs-click" +] + +[tool.pytest.ini_options] +minversion = "6.0" +addopts = "-q -s -v" +testpaths = ["tests"] + +[tool.coverage.run] +branch = true + +[tool.coverage.paths] +source = ["src"] + +[tool.coverage.report] +show_missing = true +skip_covered = true [tool.ruff] # Exclude a variety of commonly ignored directories. @@ -111,6 +138,11 @@ skip-magic-trailing-comma = false # Like Black, automatically detect the appropriate line ending. line-ending = "auto" +[tool.uv] +extra-index-url = [ + "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple", +] + 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