Merge branch 'main' into feat/add-missing-workflows

lwjohnst86 · web-flow · commit ad91b0cef67f · 2025-08-24T09:07:06.000+02:00
diff --git a/.cz.toml b/.cz.toml
@@ -1,5 +1,5 @@
 [tool.commitizen]
-version = "0.15.7"
+version = "0.15.9"
 bump_message = "build(version): :bookmark: update version from $current_version to $new_version"
 version_schema = "semver"
 version_provider = "commitizen"
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -3,7 +3,7 @@ updates:
   - package-ecosystem: github-actions
     directory: /
     schedule:
-      interval: monthly
+      interval: weekly
     commit-message:
       prefix: ci
       include: scope
diff --git a/.github/workflows/release-project.yml b/.github/workflows/release-project.yml
@@ -11,7 +11,7 @@ permissions: read-all
 jobs:
   release:
     # This job outputs env variables `previous_version` and `current_version`.
-    # Only give permissions for this job.
+    # The workflow needs write permissions for `GITHUB_TOKEN` to create a release.
     permissions:
       contents: write
     uses: seedcase-project/.github/.github/workflows/reusable-release-project.yml@main
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -25,6 +25,6 @@ repos:
   # sub-packages, which confuses pre-commit when it tries to find the latest
   # version
   - repo: https://github.com/adhtruong/mirrors-typos
-    rev: v1.35.3
+    rev: v1.35.4
     hooks:
       - id: typos
diff --git a/_contributors.qmd b/_contributors.qmd
@@ -1,4 +1,4 @@
 These are the people who have contributed by submitting changes through pull requests :tada:
 
 
- [\@lwjohnst86](https://github.com/lwjohnst86), [\@signekb](https://github.com/signekb), [\@martonvago](https://github.com/martonvago)
+ [\@lwjohnst86](https://github.com/lwjohnst86), [\@martonvago](https://github.com/martonvago), [\@signekb](https://github.com/signekb)
diff --git a/_extensions/seedcase-project/seedcase-theme/_extension.yml b/_extensions/seedcase-project/seedcase-theme/_extension.yml
@@ -1,7 +1,7 @@
 title: seedcase-theme
 author: Luke W. Johnston
-version: 0.1.0
-quarto-required: ">=1.2.0"
+version: 0.4.1
+quarto-required: ">=1.7.0"
 contributes:
   formats:
     common:
@@ -27,6 +27,7 @@ contributes:
         location: navbar
         type: textbox
       navbar:
+        pinned: true
         background: light
         logo: logos/navbar-logo-seedcase-project.svg
         logo-alt: "Seedcase Project logo: Main page"
@@ -43,7 +44,5 @@ contributes:
             href: https://seedcase-project.org/#acknowledgements
 
     csl: vancouver.csl
-
     format: seedcase-theme-html
-
     brand: _brand.yml
diff --git a/template/.github/dependabot.yml b/template/.github/dependabot.yml
@@ -1,10 +1,17 @@
 version: 2
 updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    commit-message:
+      prefix: ci
+      include: scope
+
   - package-ecosystem: uv
     directory: /
     schedule:
       interval: monthly
-    versioning-strategy: increase-if-necessary
     commit-message:
       prefix: build
       include: scope
diff --git a/template/404.qmd.jinja b/template/404.qmd.jinja
@@ -0,0 +1,19 @@
+---
+{% if is_seedcase_project -%}
+title: "You've entered the garden of missing pages"
+{% else -%}
+title: "The page you are looking for does not exist"
+{% endif -%}
+---
+
+{% if is_seedcase_project -%}
+Let's get you back to greener grounds.
+
+👉 Go to [homepage](/index.qmd).
+
+![](/_extensions/seedcase-project/seedcase-theme/images/404.svg){fig-alt="An illustration of the number 404 surrounded by trees and mountains"}
+
+## Illustration by [Storyset](https://storyset.com/web) {.appendix}
+{%- else -%}
+This page does not exist, go back to the [homepage](/index.qmd) or check the URL for typos.
+{%- endif %}
diff --git a/template/CODE_OF_CONDUCT.md b/template/CODE_OF_CONDUCT.md
@@ -0,0 +1,30 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect
+all people who contribute through reporting issues, posting suggestions,
+updating any material, submitting pull requests, and other activities.
+
+We are committed to making participation in this project a
+harassment-free experience for everyone, regardless of level of
+experience, gender, gender identity and expression, sexual orientation,
+disability, personal appearance, body size, race, ethnicity, age, or
+religion.
+
+Examples of unacceptable behavior by participants include the use of
+sexual language or imagery, derogatory comments or personal attacks,
+trolling, public or private harassment, insults, or other unprofessional
+conduct.
+
+Project maintainers have the right and responsibility to remove, edit,
+or reject comments, commits, code, wiki edits, issues, and other
+contributions that are not aligned to this Code of Conduct. Project
+maintainers who do not follow the Code of Conduct may be removed from
+the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may
+be reported by opening an issue or contacting one or more of the project
+maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant
+(https://contributor-covenant.org), version 1.0.0, available at
+https://contributor-covenant.org/version/1/0/0/
diff --git a/template/CONTRIBUTING.md.jinja b/template/CONTRIBUTING.md.jinja
@@ -0,0 +1,59 @@
+# Contributing
+
+## Issues and bugs :bug:
+
+The easiest way to contribute is to report issues or bugs that you might
+find while using `{{ github_repo }}`. You can do this by creating a
+[new](https://github.com/{{ github_repo_spec }}/issues/new/choose)
+issue on our GitHub repository.
+
+## Adding or modifying content :pencil2:
+
+{% if is_seedcase_project -%}
+If you would like to contribute content, please check out our
+[guidebook](https://guidebook.seedcase-project.org/) for more specific
+details on how we work and develop. It is a regularly evolving document,
+so is at various states of completion.
+{%- endif %}
+
+To contribute to `{{ github_repo }}`, you first need to install
+[uv](https://docs.astral.sh/uv/) and
+[justfile](https://just.systems/man/en/packages.html). We use uv and
+justfile to manage our project, such as to run checks and test the
+template. Both the uv and justfile websites have a more detailed guide
+on using uv, but below are some simple instructions to get you started.
+
+It's easiest to install uv and justfile using
+[pipx](https://pypa.github.io/pipx/), so install that first. Then,
+install uv and justfile by running:
+
+``` bash
+pipx install uv rust-just
+```
+
+We keep all our development workflows in the `justfile`, so you can
+explore it to see what commands are available. To see a list of commands
+available, run:
+
+``` bash
+just
+```
+
+As you contribute, make sure your changes will pass our tests by opening
+a terminal so that the working directory is the root of this project's
+repository and running:
+
+``` bash
+just run-all
+```
+
+When committing changes, please try to follow [Conventional
+Commits](https://decisions.seedcase-project.org/why-conventional-commits)
+as Git messages. Using this convention allows us to be able to
+automatically create a release based on the commit message by using
+[Commitizen](https://decisions.seedcase-project.org/why-semantic-release-with-commitizen).
+If you don't use Conventional Commits when making a commit, we will
+revise the pull request title to follow that format, as we use [squash
+merges](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/squashing-commits/about-squash-merges)
+when merging pull requests, so all other commits in the pull request
+will be squashed into one commit.
diff --git a/template/README.md b/template/README.md
@@ -0,0 +1 @@
+NOTE: Will be overwritten after running `just build-readme`.
diff --git a/template/README.md.jinja b/template/README.md.jinja
diff --git a/template/README.qmd b/template/README.qmd
@@ -0,0 +1,82 @@
+---
+format: gfm
+metadata-files:
+  - _metadata.yml
+---
+
+# {{< meta gh.repo >}}: TODO add more to title
+
+{{< include /docs/includes/_badges.qmd >}}
+
+<!-- TODO: Add description of project -->
+
+::: callout-tip
+This Python package was generated from the
+[`template-python-package`](https://github.com/seedcase-project/template-python-package)
+Seedcase template :tada:
+:::
+
+## Project files and folders
+
+-   `.github/`: Contains GitHub-specific files, such as issue and pull
+    request templates, workflows,
+    [dependabot](https://docs.github.com/en/code-security/getting-started/dependabot-quickstart-guide)
+    configuration, pull request templates, and a
+    [CODEOWNERS](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners)
+    file.
+-   `tools/vulture-allowlist.py`: List of variables that shouldn't be flagged by [Vulture](https://github.com/jendrikseipp/vulture) as unused.
+-   `tools/get-contributors.sh`: Script to get list of project contributors.
+-   `tests/`: Test files for the package.
+-   `src/`: Source code for the package.
+-   `docs/`: Documentation about using and developing the Python package.
+-   `_renderer.py`: Custom [`quartodoc`](https://machow.github.io/quartodoc/) renderer.
+-   `pytest.ini`: Pytest configuration file.
+-   `mypy.ini`: [`mypy`](https://mypy.readthedocs.io/en/stable/) configuration file for type checking Python code.
+-   `.copier-answers.yml`: Contains the answers you gave when copying
+    the project from the template. **You should not modify this file
+    directly.**
+-   `.cz.toml`:
+    [Commitizen](https://commitizen-tools.github.io/commitizen/)
+    configuration file for managing versions and changelogs.
+-   `.pre-commit-config.yaml`: [Pre-commit](https://pre-commit.com/)
+    configuration file for managing and running checks before each
+    commit.
+-   `.typos.toml`: [typos](https://github.com/crate-ci/typos) spell
+    checker configuration file.
+-   `justfile`: [`just`](https://just.systems/man/en/) configuration
+    file for scripting project tasks.
+-   `.editorconfig`: Editor configuration file for
+    [EditorConfig](https://editorconfig.org/) to maintain consistent
+    coding styles across different editors and IDEs.
+-   `CHANGELOG.md`: Changelog file for tracking changes in the project.
+-   `CITATION.cff`: Structured citation metadata for your project.
+-   `CONTRIBUTING.md`: Guidelines for contributing to the project.
+-   `_metadata.yml`: Quarto metadata file for the website, including
+    information about the project, such as the titles and GitHub names.
+-   `pyproject.toml`: Main Python project configuration file defining
+    metadata and dependencies.
+-   `_quarto.yml`: Quarto configuration file for the website, including
+    settings for the website, such as the theme, navigation, and other
+    options.
+-   `ruff.toml`: [Ruff](https://docs.astral.sh/ruff/) configuration file
+    for linting and formatting Python code.
+-   `uv.lock`: Lockfile used by [`uv`](https://docs.astral.sh/uv/) to
+    record exact versions of installed dependencies.
+
+## Contributing
+
+Check out our [contributing document](CONTRIBUTING.md) for information
+on how to contribute to the project, including how to set up your
+development environment.
+
+Please note that this project is released with a [Contributor Code of
+Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree
+to abide by its terms.
+
+## Licensing
+
+This project is licensed under the [MIT License](LICENSE.md).
+
+## Changelog
+
+For a list of changes, see our [changelog](CHANGELOG.md) page.
diff --git a/template/README.qmd.jinja b/template/README.qmd.jinja
diff --git a/template/_metadata.yml.jinja b/template/_metadata.yml.jinja
@@ -0,0 +1,3 @@
+gh:
+  repo: {{ github_repo }}
+  org: {{ github_user }}
diff --git a/template/_quarto.yml.jinja b/template/_quarto.yml.jinja
@@ -5,6 +5,8 @@ project:
   render:
     - "docs/*"
     - "index.qmd"
+    - "404.qmd"
+    - "CONTRIBUTING.md"
 
 website:
   # TODO: Fill in the title of the website.
@@ -32,7 +34,7 @@ website:
       - icon: github
         href: "https://github.com/{{ package_github_repo }}"
         aria-label: "GitHub icon: Source code"
-      {% if is_seedcase_project -%}
+      {%- if is_seedcase_project %}
       - icon: house
         href: "https://seedcase-project.org"
         aria-label: "House icon: Main website for the Seedcase Project"
diff --git a/template/docs/includes/_badges.qmd b/template/docs/includes/_badges.qmd
@@ -0,0 +1,15 @@
+<!-- TODO: Include DOI after uploading -->
+<!-- [![PyPI Version](https://img.shields.io/pypi/v/{{< meta gh.repo >}})](https://pypi.org/project/{{< meta gh.repo >}}/) -->
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-teal.json?raw=true)](https://github.com/copier-org/copier)
+[![Supported Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https://raw.githubusercontent.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/refs/heads/main/pyproject.toml)](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/blob/main/pyproject.toml)
+[![GitHub License](https://img.shields.io/github/license/{{< meta gh.org >}}/{{< meta gh.repo >}}.svg)](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/blob/main/LICENSE.md)
+[![GitHub Release](https://img.shields.io/github/v/release/{{< meta gh.org >}}/{{< meta gh.repo >}}.svg)](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/releases/latest)
+[![Build documentation](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/actions/workflows/build-website.yml/badge.svg)](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/actions/workflows/build-website.yml)
+[![Build package](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/actions/workflows/build-package.yml/badge.svg)](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/actions/workflows/build-package.yml)
+[![OpenSSF Scorecard](https://api.scorecard.dev/projects/github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/badge?raw=true)](https://scorecard.dev/viewer/?uri=github.com/{{< meta gh.org >}}/{{< meta gh.repo >}})
+[![CodeQL](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/actions/workflows/github-code-scanning/codeql/badge.svg?branch=main)](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/actions/workflows/github-code-scanning/codeql)
+[![code coverage](https://raw.githubusercontent.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/coverage/coverage.svg?raw=true)](https://htmlpreview.github.io/?https://raw.githubusercontent.com/{{< meta gh.org >}}/{{< meta gh.repo >}}/coverage/index.html)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/{{< meta gh.org >}}/{{< meta gh.repo >}}/main.svg)](https://results.pre-commit.ci/latest/github/{{< meta gh.org >}}/{{< meta gh.repo >}}/main)
+[![lifecycle](https://lifecycle.r-lib.org/articles/figures/lifecycle-experimental.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+<!-- [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -->

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`	`1`	`These are the people who have contributed by submitting changes through pull requests :tada:`
`2`	`2`
`3`	`3`
`4`		`- [\@lwjohnst86](https://github.com/lwjohnst86), [\@signekb](https://github.com/signekb), [\@martonvago](https://github.com/martonvago)`
	`4`	`+ [\@lwjohnst86](https://github.com/lwjohnst86), [\@martonvago](https://github.com/martonvago), [\@signekb](https://github.com/signekb)`