🧹 Add changes suggested by bots

Author: s-weigand

.github/workflows/test.yml

@@ -31,9 +31,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install uv
@@ -55,9 +55,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install uv
@@ -132,7 +132,7 @@ jobs:
       - name: Install dependencies
         run: |
           uv sync --frozen --group test
-          uv add git+https://github.com/glotaran/pyglotaran
+          uv pip install git+https://github.com/glotaran/pyglotaran
 
       - name: Show installed dependencies
         run: uv pip list
@@ -174,7 +174,7 @@ jobs:
         run: uv pip list
 
       - name: Run tests
-        run: uv run --resolution lowest-direct pytest --nbval --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests
+        run: uv run --resolution lowest-direct pytest --nbval --cov=pyglotaran_extras --cov-report term --cov-report xml --cov-config pyproject.toml tests
 
       - name: Codecov Upload
         continue-on-error: true

CONTRIBUTING.md

@@ -73,7 +73,7 @@ Ready to contribute? Here's how to set up `pyglotaran_extras` for local developm
 
    ```
    $ uv tool install pre-commit --with pre-commit-uv
-   $ pre-commit install && pre-commit install
+   $ pre-commit install
    ```
 
 5. Create a branch for local development:
@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.md.
-3. The pull request should work for Python 3.10 and 3.11. Check
+3. The pull request should work for Python 3.10, 3.11, 3.12, 3.13 and 3.14. Check
    <https://github.com/glotaran/pyglotaran-extras/actions>
    and make sure that the tests pass for all supported Python versions.
 
@@ -111,5 +111,5 @@ Before you submit a pull request, check that it meets these guidelines:
 To run a subset of tests:
 
 ```
-$ uv run pytest tests.test_pyglotaran_extras
+$ uv run pytest tests/plotting
 ```

docs/installation.md

@@ -6,13 +6,21 @@
 
 ## Stable release
 
-To install pyglotaran_extras, run this command in your terminal:
+To install `pyglotaran_extras` for a new project, run this command in your terminal:
 
 ```console
-$ uv pip install pyglotaran_extras
+$ uv init --bare
+$ uv add pyglotaran_extras
 ```
 
 This is the preferred method to install pyglotaran_extras, as it will always install the most recent stable release.
+Additionally this will create a `uv.lock` file allowing you to recreate and share the same environment you use by running `uv sync --frozen`.
+
+Or if you have an existing project and environment
+
+```console
+$ uv pip install pyglotaran_extras
+```
 
 If you don't have [uv] installed, see the [uv installation guide].
 

justfile

@@ -78,7 +78,7 @@ test:
 
 # Check code coverage and open HTML report
 cov:
-    uv run pytest
+    uv run pytest --cov=pyglotaran_extras --cov-report html
     @just _open-browser htmlcov/index.html
 
 # ============================================================================

pyproject.toml

@@ -86,11 +86,6 @@ include = [
   "changelog.md",
 ]
 
-[tool.hatch.envs.default]
-features = [
-  "dev",
-]
-
 [tool.docformatter]
 black = true
 wrap-summaries = 99