Merge remote-tracking branch 'origin/main' into sc/tox-warnings-on-freshly-cut-cookie

samcunliffe · samcunliffe · commit bdfbfa8cf19b · 2025-07-24T08:53:28.000+01:00
diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -43,7 +43,8 @@
         "question",
         "review",
         "talk",
-        "test"
+        "test",
+        "tutorial"
       ]
     },
     {
@@ -77,7 +78,8 @@
         "eventOrganizing",
         "review",
         "talk",
-        "test"
+        "test",
+        "tutorial"
       ]
     },
     {
@@ -105,7 +107,8 @@
         "doc",
         "question",
         "review",
-        "test"
+        "test",
+        "tutorial"
       ]
     },
     {
@@ -268,7 +271,10 @@
         "doc",
         "content",
         "maintenance",
-        "review"
+        "review",
+        "talk",
+        "tutorial",
+        "eventOrganizing"
       ]
     },
     {
@@ -288,7 +294,8 @@
       "contributions": [
         "bug",
         "a11y",
-        "review"
+        "review",
+        "tutorial"
       ]
     },
     {
@@ -310,6 +317,15 @@
         "a11y",
         "code"
       ]
+    },
+    {
+      "login": "jamesbriant",
+      "name": "James Briant",
+      "avatar_url": "https://avatars.githubusercontent.com/u/6298711?v=4",
+      "profile": "http://james.briant.co.uk",
+      "contributions": [
+        "bug"
+      ]
     }
   ]
 }
diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ Python packages with our recommended tooling set up and ready to go.
 
 > [!NOTE]
 > If you're making a package within a community that has an existing
-> package template (e.g., [`scikit-hep`](https://github.com/scikit-hep/cookie)),
+> package template (e.g., [`SciKit-Surgery`](https://github.com/SciKit-Surgery/PythonTemplate)),
 > we recommend using their template instead of this one.
 
 ## Using our Python package template
@@ -77,11 +77,11 @@ uv pip install -e ".[dev]"
   <tbody>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://paddyroddy.github.io"><img src="https://avatars.githubusercontent.com/u/15052188?v=4?s=100" width="100px;" alt="Patrick J. Roddy"/><br /><sub><b>Patrick J. Roddy</b></sub></a><br /><a href="#ideas-paddyroddy" title="Ideas, Planning, & Feedback">🤔</a> <a href="#bug-paddyroddy" title="Bug reports">🐛</a> <a href="#code-paddyroddy" title="Code">💻</a> <a href="#content-paddyroddy" title="Content">🖋</a> <a href="#doc-paddyroddy" title="Documentation">📖</a> <a href="#eventOrganizing-paddyroddy" title="Event Organizing">📋</a> <a href="#projectManagement-paddyroddy" title="Project Management">📆</a> <a href="#question-paddyroddy" title="Answering Questions">💬</a> <a href="#review-paddyroddy" title="Reviewed Pull Requests">👀</a> <a href="#talk-paddyroddy" title="Talks">📢</a> <a href="#test-paddyroddy" title="Tests">⚠️</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="http://scnlf.me"><img src="https://avatars.githubusercontent.com/u/1836192?v=4?s=100" width="100px;" alt="Sam Cunliffe"/><br /><sub><b>Sam Cunliffe</b></sub></a><br /><a href="#ideas-samcunliffe" title="Ideas, Planning, & Feedback">🤔</a> <a href="#bug-samcunliffe" title="Bug reports">🐛</a> <a href="#code-samcunliffe" title="Code">💻</a> <a href="#content-samcunliffe" title="Content">🖋</a> <a href="#doc-samcunliffe" title="Documentation">📖</a> <a href="#eventOrganizing-samcunliffe" title="Event Organizing">📋</a> <a href="#projectManagement-samcunliffe" title="Project Management">📆</a> <a href="#question-samcunliffe" title="Answering Questions">💬</a> <a href="#review-samcunliffe" title="Reviewed Pull Requests">👀</a> <a href="#talk-samcunliffe" title="Talks">📢</a> <a href="#test-samcunliffe" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="http://scnlf.me"><img src="https://avatars.githubusercontent.com/u/1836192?v=4?s=100" width="100px;" alt="Sam Cunliffe"/><br /><sub><b>Sam Cunliffe</b></sub></a><br /><a href="#ideas-samcunliffe" title="Ideas, Planning, & Feedback">🤔</a> <a href="#bug-samcunliffe" title="Bug reports">🐛</a> <a href="#code-samcunliffe" title="Code">💻</a> <a href="#content-samcunliffe" title="Content">🖋</a> <a href="#doc-samcunliffe" title="Documentation">📖</a> <a href="#eventOrganizing-samcunliffe" title="Event Organizing">📋</a> <a href="#projectManagement-samcunliffe" title="Project Management">📆</a> <a href="#question-samcunliffe" title="Answering Questions">💬</a> <a href="#review-samcunliffe" title="Reviewed Pull Requests">👀</a> <a href="#talk-samcunliffe" title="Talks">📢</a> <a href="#test-samcunliffe" title="Tests">⚠️</a> <a href="#tutorial-samcunliffe" title="Tutorials">✅</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://www.davidstansby.com"><img src="https://avatars.githubusercontent.com/u/6197628?v=4?s=100" width="100px;" alt="David Stansby"/><br /><sub><b>David Stansby</b></sub></a><br /><a href="#ideas-dstansby" title="Ideas, Planning, & Feedback">🤔</a> <a href="#bug-dstansby" title="Bug reports">🐛</a> <a href="#code-dstansby" title="Code">💻</a> <a href="#content-dstansby" title="Content">🖋</a> <a href="#doc-dstansby" title="Documentation">📖</a> <a href="#eventOrganizing-dstansby" title="Event Organizing">📋</a> <a href="#projectManagement-dstansby" title="Project Management">📆</a> <a href="#review-dstansby" title="Reviewed Pull Requests">👀</a> <a href="#test-dstansby" title="Tests">⚠️</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="http://matt-graham.github.io"><img src="https://avatars.githubusercontent.com/u/6746980?v=4?s=100" width="100px;" alt="Matt Graham"/><br /><sub><b>Matt Graham</b></sub></a><br /><a href="#bug-matt-graham" title="Bug reports">🐛</a> <a href="#code-matt-graham" title="Code">💻</a> <a href="#content-matt-graham" title="Content">🖋</a> <a href="#doc-matt-graham" title="Documentation">📖</a> <a href="#design-matt-graham" title="Design">🎨</a> <a href="#eventOrganizing-matt-graham" title="Event Organizing">📋</a> <a href="#review-matt-graham" title="Reviewed Pull Requests">👀</a> <a href="#talk-matt-graham" title="Talks">📢</a> <a href="#test-matt-graham" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="http://matt-graham.github.io"><img src="https://avatars.githubusercontent.com/u/6746980?v=4?s=100" width="100px;" alt="Matt Graham"/><br /><sub><b>Matt Graham</b></sub></a><br /><a href="#bug-matt-graham" title="Bug reports">🐛</a> <a href="#code-matt-graham" title="Code">💻</a> <a href="#content-matt-graham" title="Content">🖋</a> <a href="#doc-matt-graham" title="Documentation">📖</a> <a href="#design-matt-graham" title="Design">🎨</a> <a href="#eventOrganizing-matt-graham" title="Event Organizing">📋</a> <a href="#review-matt-graham" title="Reviewed Pull Requests">👀</a> <a href="#talk-matt-graham" title="Talks">📢</a> <a href="#test-matt-graham" title="Tests">⚠️</a> <a href="#tutorial-matt-graham" title="Tutorials">✅</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/sfmig"><img src="https://avatars.githubusercontent.com/u/33267254?v=4?s=100" width="100px;" alt="sfmig"/><br /><sub><b>sfmig</b></sub></a><br /><a href="#bug-sfmig" title="Bug reports">🐛</a> <a href="#code-sfmig" title="Code">💻</a> <a href="#content-sfmig" title="Content">🖋</a> <a href="#review-sfmig" title="Reviewed Pull Requests">👀</a> <a href="#test-sfmig" title="Tests">⚠️</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/p-j-smith"><img src="https://avatars.githubusercontent.com/u/29753790?v=4?s=100" width="100px;" alt="Paul Smith"/><br /><sub><b>Paul Smith</b></sub></a><br /><a href="#bug-p-j-smith" title="Bug reports">🐛</a> <a href="#code-p-j-smith" title="Code">💻</a> <a href="#content-p-j-smith" title="Content">🖋</a> <a href="#doc-p-j-smith" title="Documentation">📖</a> <a href="#question-p-j-smith" title="Answering Questions">💬</a> <a href="#review-p-j-smith" title="Reviewed Pull Requests">👀</a> <a href="#test-p-j-smith" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/p-j-smith"><img src="https://avatars.githubusercontent.com/u/29753790?v=4?s=100" width="100px;" alt="Paul Smith"/><br /><sub><b>Paul Smith</b></sub></a><br /><a href="#bug-p-j-smith" title="Bug reports">🐛</a> <a href="#code-p-j-smith" title="Code">💻</a> <a href="#content-p-j-smith" title="Content">🖋</a> <a href="#doc-p-j-smith" title="Documentation">📖</a> <a href="#question-p-j-smith" title="Answering Questions">💬</a> <a href="#review-p-j-smith" title="Reviewed Pull Requests">👀</a> <a href="#test-p-j-smith" title="Tests">⚠️</a> <a href="#tutorial-p-j-smith" title="Tutorials">✅</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://docs.renovatebot.com/"><img src="https://avatars.githubusercontent.com/u/38656520?v=4?s=100" width="100px;" alt="Renovate Bot"/><br /><sub><b>Renovate Bot</b></sub></a><br /><a href="#maintenance-renovatebot" title="Maintenance">🚧</a></td>
     </tr>
     <tr>
@@ -103,11 +103,12 @@ uv pip install -e ".[dev]"
       <td align="center" valign="top" width="14.28%"><a href="https://pre-commit.ci"><img src="https://avatars.githubusercontent.com/u/64617429?v=4?s=100" width="100px;" alt="pre-commit.ci"/><br /><sub><b>pre-commit.ci</b></sub></a><br /><a href="#maintenance-pre-commit-ci" title="Maintenance">🚧</a></td>
     </tr>
     <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://saransh-cpp.github.io/"><img src="https://avatars.githubusercontent.com/u/74055102?v=4?s=100" width="100px;" alt="Saransh Chopra"/><br /><sub><b>Saransh Chopra</b></sub></a><br /><a href="#doc-Saransh-cpp" title="Documentation">📖</a> <a href="#content-Saransh-cpp" title="Content">🖋</a> <a href="#maintenance-Saransh-cpp" title="Maintenance">🚧</a> <a href="#review-Saransh-cpp" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://saransh-cpp.github.io/"><img src="https://avatars.githubusercontent.com/u/74055102?v=4?s=100" width="100px;" alt="Saransh Chopra"/><br /><sub><b>Saransh Chopra</b></sub></a><br /><a href="#doc-Saransh-cpp" title="Documentation">📖</a> <a href="#content-Saransh-cpp" title="Content">🖋</a> <a href="#maintenance-Saransh-cpp" title="Maintenance">🚧</a> <a href="#review-Saransh-cpp" title="Reviewed Pull Requests">👀</a> <a href="#talk-Saransh-cpp" title="Talks">📢</a> <a href="#tutorial-Saransh-cpp" title="Tutorials">✅</a> <a href="#eventOrganizing-Saransh-cpp" title="Event Organizing">📋</a></td>
       <td align="center" valign="top" width="14.28%"><a href="http://drandrewmitchell.com"><img src="https://avatars.githubusercontent.com/u/22335636?v=4?s=100" width="100px;" alt="Andrew Mitchell"/><br /><sub><b>Andrew Mitchell</b></sub></a><br /><a href="#bug-MitchellAcoustics" title="Bug reports">🐛</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://www.ucl.ac.uk/advanced-research-computing/advanced-research-computing-centre"><img src="https://avatars.githubusercontent.com/u/24316371?v=4?s=100" width="100px;" alt="Kimberly Meechan"/><br /><sub><b>Kimberly Meechan</b></sub></a><br /><a href="#bug-K-Meech" title="Bug reports">🐛</a> <a href="#a11y-K-Meech" title="Accessibility">️️️️♿️</a> <a href="#review-K-Meech" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://www.ucl.ac.uk/advanced-research-computing/advanced-research-computing-centre"><img src="https://avatars.githubusercontent.com/u/24316371?v=4?s=100" width="100px;" alt="Kimberly Meechan"/><br /><sub><b>Kimberly Meechan</b></sub></a><br /><a href="#bug-K-Meech" title="Bug reports">🐛</a> <a href="#a11y-K-Meech" title="Accessibility">️️️️♿️</a> <a href="#review-K-Meech" title="Reviewed Pull Requests">👀</a> <a href="#tutorial-K-Meech" title="Tutorials">✅</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/jamesprime"><img src="https://avatars.githubusercontent.com/u/17751241?v=4?s=100" width="100px;" alt="James Prime"/><br /><sub><b>James Prime</b></sub></a><br /><a href="#a11y-jamesprime" title="Accessibility">️️️️♿️</a> <a href="#ideas-jamesprime" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/cuteshaun"><img src="https://avatars.githubusercontent.com/u/28014041?v=4?s=100" width="100px;" alt="Andrii Tsapko"/><br /><sub><b>Andrii Tsapko</b></sub></a><br /><a href="#a11y-cuteshaun" title="Accessibility">️️️️♿️</a> <a href="#code-cuteshaun" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="http://james.briant.co.uk"><img src="https://avatars.githubusercontent.com/u/6298711?v=4?s=100" width="100px;" alt="James Briant"/><br /><sub><b>James Briant</b></sub></a><br /><a href="#bug-jamesbriant" title="Bug reports">🐛</a></td>
     </tr>
   </tbody>
 </table>
diff --git a/docs/pages/linting.md b/docs/pages/linting.md
@@ -32,3 +32,11 @@ for some of these.
 | Name                                           | Short description                                                             |                     🚦                      |
 | ---------------------------------------------- | ----------------------------------------------------------------------------- | :-----------------------------------------: |
 | [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | <span class="label label-green">Best</span> |
+
+### Dependency checking
+
+| Name                                                              | Short description                                                |                      🚦                      |
+| ----------------------------------------------------------------- | ---------------------------------------------------------------- | :------------------------------------------: |
+| [deptry](https://deptry.com/)                                     | Checks for unused dependencies and undeclared dependencies.      | <span class="label label-yellow">Good</span> |
+| [fawltydeps](https://tweag.github.io/FawltyDeps/)                 | Checks for unused dependencies and undeclared dependencies.      | <span class="label label-yellow">Good</span> |
+| [pip-check-reqs](https://github.com/adamtheturtle/pip-check-reqs) | Checks requirements file (requires converting `pyproject.toml`). | <span class="label label-yellow">Good</span> |
diff --git a/docs/pages/templates.md b/docs/pages/templates.md
@@ -29,7 +29,7 @@ their package template.
 | ------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------- |
 | [Napari](https://github.com/napari/cookiecutter-napari-plugin)     | Cookiecutter template for authoring (npe2-based) napari plugins.                                                                                |
 | [SciKit-Surgery](https://github.com/SciKit-Surgery/PythonTemplate) | Cookiecutter template developed by the Wellcome EPSRC Centre for Interventional and Surgical Sciences.                                          |
-| [Scientific Python](https://github.com/scientific-python/cookie)   | Cookiecutter template developed by [SciKit-HEP](https://github.com/scikit-hep) but now adopted by the more general Scientific Python community. |
+| [Scientific Python](https://github.com/scientific-python/cookie)   | Cookiecutter template developed by [Scikit-HEP](https://github.com/scikit-hep) but now adopted by the more general Scientific Python community. |
 
 ### Template engines
 
diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
@@ -66,7 +66,7 @@ def main(initialise_git_repository: str, deploy_docs_to_github_pages: str) -> in
                 '-d "{{cookiecutter.project_short_description}}" '
                 "--public "
                 "-r origin "
-                "--source {{cookiecutter.project_slug}}\n"
+                "--source {{cookiecutter.project_slug}}\n",
             )
         except FileNotFoundError:
             # GitHub CLI isn't installed
@@ -78,7 +78,7 @@ def main(initialise_git_repository: str, deploy_docs_to_github_pages: str) -> in
                 "https://docs.github.com/en/get-started/quickstart/create-a-repo.\n\n"
                 "Then run:\n\n"
                 "git remote add origin git@github.com:"
-                "{{cookiecutter.__repo_name}}.git\n"
+                "{{cookiecutter.__repo_name}}.git\n",
             )
         except subprocess.CalledProcessError as e:
             # some other error
@@ -98,7 +98,7 @@ def main(initialise_git_repository: str, deploy_docs_to_github_pages: str) -> in
             "{{cookiecutter.__repo_url}}/settings/pages\n\n"
             "and under 'Built and deployment' selecting 'Deploy from a branch' for "
             "the 'Source' drop-down and 'gh-pages' for the 'Branch' drop-down, "
-            "leaving the branch path drop-down with its default value of '/ (root)'."
+            "leaving the branch path drop-down with its default value of '/ (root)'.",
         )
 
     return _EXIT_SUCCESS
@@ -109,5 +109,5 @@ def main(initialise_git_repository: str, deploy_docs_to_github_pages: str) -> in
         main(
             "{{ cookiecutter.initialise_git_repository }}",
             "{{ cookiecutter.deploy_docs_to_github_pages }}",
-        )
+        ),
     )
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -7,20 +7,50 @@
 import pytest
 
 
+@pytest.fixture(scope="function")  # noqa: PT003
+def default_config() -> dict[str, str]:
+    """
+    Get the minimal default configuration for cutting a cookie in tests.
+
+    This is used if `generate_package` is called without arguments.
+    """
+    return {
+        "github_owner": "test-user",
+        "project_short_description": "description",
+        "project_name": "Cookiecutter Test",
+        "project_slug": "cookiecutter-test",
+    }
+
+
+@pytest.fixture(scope="function")  # noqa: PT003
+def default_config_with(default_config: dict[str, str]) -> typing.Callable:
+    """Extend or modify the default configuration with one additional value."""
+
+    def _wrapped_with(**kwargs: str) -> dict[str, str]:
+        return default_config | kwargs
+
+    return _wrapped_with
+
+
 def _generate_package(
     config: dict[str, str], path: pathlib.Path
-) -> subprocess.CompletedProcess[str]:
+) -> tuple[subprocess.CompletedProcess[str], pathlib.Path]:
     """
     Generate a project from the cookiecutter template.
 
-    Arguments:
-    ---------
-    config: dict
+    Parameters
+    ----------
+    config
         A dictionary with values for the cookiecutter template,
         as defined in the cookiecutter.json
-    path: Path
+    path
         Directory to create package in.
 
+    Returns
+    -------
+    subprocess.CompletedProcess, pathlib.Path
+        The result of the cookiecutter command and the path to the generated package.
+
     """
     args = [f"{key}={val}" for key, val in config.items()]
     cmd = ["cookiecutter", ".", "--no-input", "--output-dir", f"{path}"]
@@ -30,10 +60,18 @@ def _generate_package(
         shell=False,
         capture_output=True,
         text=True,
-    )
+    ), path / config["project_slug"]
 
 
 @pytest.fixture
-def generate_package() -> typing.Callable:
+def generate_package(
+    default_config: dict[str, str], tmp_path: pathlib.Path
+) -> typing.Callable:
     """Generate project from cookiecutter template."""
-    return _generate_package
+
+    def _wrapped_with_tmp_path(
+        config: dict[str, str] = default_config,
+    ) -> tuple[subprocess.CompletedProcess, pathlib.Path]:
+        return _generate_package(config, tmp_path)
+
+    return _wrapped_with_tmp_path
diff --git a/tests/test_git_init.py b/tests/test_git_init.py
diff --git a/tests/test_package_generation.py b/tests/test_package_generation.py

Original file line number	Diff line number	Diff line change
`@@ -43,7 +43,8 @@`
`43`	`43`	`"question",`
`44`	`44`	`"review",`
`45`	`45`	`"talk",`
`46`		`- "test"`
	`46`	`+ "test",`
	`47`	`+ "tutorial"`
`47`	`48`	`]`
`48`	`49`	`},`
`49`	`50`	`{`
`@@ -77,7 +78,8 @@`
`77`	`78`	`"eventOrganizing",`
`78`	`79`	`"review",`
`79`	`80`	`"talk",`
`80`		`- "test"`
	`81`	`+ "test",`
	`82`	`+ "tutorial"`
`81`	`83`	`]`
`82`	`84`	`},`
`83`	`85`	`{`
`@@ -105,7 +107,8 @@`
`105`	`107`	`"doc",`
`106`	`108`	`"question",`
`107`	`109`	`"review",`
`108`		`- "test"`
	`110`	`+ "test",`
	`111`	`+ "tutorial"`
`109`	`112`	`]`
`110`	`113`	`},`
`111`	`114`	`{`
`@@ -268,7 +271,10 @@`
`268`	`271`	`"doc",`
`269`	`272`	`"content",`
`270`	`273`	`"maintenance",`
`271`		`- "review"`
	`274`	`+ "review",`
	`275`	`+ "talk",`
	`276`	`+ "tutorial",`
	`277`	`+ "eventOrganizing"`
`272`	`278`	`]`
`273`	`279`	`},`
`274`	`280`	`{`
`@@ -288,7 +294,8 @@`
`288`	`294`	`"contributions": [`
`289`	`295`	`"bug",`
`290`	`296`	`"a11y",`
`291`		`- "review"`
	`297`	`+ "review",`
	`298`	`+ "tutorial"`
`292`	`299`	`]`
`293`	`300`	`},`
`294`	`301`	`{`
`@@ -310,6 +317,15 @@`
`310`	`317`	`"a11y",`
`311`	`318`	`"code"`
`312`	`319`	`]`
	`320`	`+ },`
	`321`	`+ {`
	`322`	`+ "login": "jamesbriant",`
	`323`	`+ "name": "James Briant",`
	`324`	`+ "avatar_url": "https://avatars.githubusercontent.com/u/6298711?v=4",`
	`325`	`+ "profile": "http://james.briant.co.uk",`
	`326`	`+ "contributions": [`
	`327`	`+ "bug"`
	`328`	`+ ]`
`313`	`329`	`}`
`314`	`330`	`]`
`315`	`331`	`}`