Use uv project interface in template

{{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"
+  #         args: "format . --check"

{{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": "<descriptive tag>",
-        "type": "debugpy",
-        "request": "launch",
-        "cwd": "${workspaceFolder}",
-        "program": "${workspaceFolder}/.pyenv/bin/pytest",
-        "justMyCode": true,
-        "env": {
-            "_PYTEST_RAISE": "1"
-        },
-        "args": [
-            "-sv",
-            "--pdb",
-            "<path-to-plugin-tests>",
-        ]
+    {
+      "name": "<descriptive tag>",
+      "type": "debugpy",
+      "request": "launch",
+      "cwd": "${workspaceFolder}",
+      "program": "${workspaceFolder}/.venv/bin/pytest",
+      "justMyCode": true,
+      "env": {
+        "_PYTEST_RAISE": "1"
+      },
+      "args": ["-sv", "--pdb", "<path-to-plugin-tests>"]
     }
   ]
 }
@@ -94,23 +77,18 @@ where `<path-to-plugin-tests>` 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
 <other-content-in-default_plugins.txt>
 {{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 <route-to-NOMAD-folder>/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}}) |

{{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",
+]
+
 [tool.setuptools]
 package-dir = { "" = "src" }