docs: 📝 apply suggestions from code review

Co-authored-by: Luke W. Johnston <lwjohnst86@users.noreply.github.com>

Author: martonvago

CITATION.cff

@@ -1,4 +1,4 @@
-title: "Template Python package: An opinionated setup for making Python packages."
+title: "Template Python Package: An opinionated setup for making Python packages"
 abstract: "A template for making a Git repository that follows strongly opinionated practices for building and managing Python packages."
 authors:
   - family-names: Johnston
@@ -12,11 +12,13 @@ authors:
   - family-names: Beicher
     given-names: Kristiane
     affiliation: "Steno Diabetes Center Aarhus"
+    orcid: "https://orcid.org/0000-0001-7556-9566"
   - family-names: Vago
     given-names: Marton
     affiliation: "Steno Diabetes Center Aarhus"
 cff-version: 1.2.0
 # doi:
+# date:
 keywords:
   - "copier template"
   - "template"

CONTRIBUTING.md

@@ -21,7 +21,9 @@ 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.
 
-To install uv and justfile, run:
+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
@@ -47,3 +49,14 @@ When testing the template, copier can only use content kept in the Git
 history. Meaning that if you make changes to the template and try to
 test it, it won't be able to test those changes. You have to commit the
 changes first in order for copier to use them.
+
+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.

docs/guide.qmd

@@ -119,13 +119,29 @@ repository with the settings we use, but you can follow them if you want
 to set up your Python package in a similar way. They are also included
 in a message after you've copied the template.
 
-After copying the template, while in the directory of the new Data
-Package, run the following:
+After copying the template, while in the directory of the new Python
+package, run the following:
 
 ``` bash
 just install-precommit
 ```
 
+This sets up the pre-commit hooks to run standard checks on your
+repository whenever you commit files to the history.
+
+If you are using the template to create a Python package for the Seedcase
+Project, run:
+
+``` bash
+just update-quarto-theme
+```
+
+This adds the `seedcase-theme` Quarto theme to the website, which
+provides a consistent look and feel across all Seedcase Project
+websites, including for Python package websites. 
+It's called `update-quarto-theme` here since you can use this
+command to keep the theme updated.
+
 Next, install [`spaid`](https://github.com/seedcase-project/spaid) and
 use the following commands to run the next setup steps:
 
@@ -136,14 +152,26 @@ spaid_gh_ruleset_basic_protect_main -h
 ```
 
 Some configuration is needed after copying this template to a new
-repository, including configuration external to the repository.
-
--   The template file `.github/workflows/release-package.yml` requires
-    the [auto-release-token](https://github.com/apps/auto-release-token)
-    GitHub App to be installed.
--   The GitHub secrets `UPDATE_VERSION_TOKEN`, `ADD_TO_BOARD`, and
-    `NETLIFY_AUTH_TOKEN` and variables `UPDATE_VERSION_APP_ID` and
-    `ADD_TO_BOARD_APP_ID` have to be set up in the repository (or
-    organization) settings. See this
-    [guide](https://guidebook.seedcase-project.org/operations/security#using-github-apps-to-generate-tokens)
-    for more details on how to configure this.
+repository, including configuration external to the repository. Some
+GitHub workflows require installing GitHub Apps, for greater security
+purposes and easier administration when managing multiple repositories.
+The [security
+section](https://guidebook.seedcase-project.org/operations/security#using-github-apps-to-generate-tokens)
+in our [Guidebook](https://guidebook.seedcase-project.org/) provides
+instructions on how to set up GitHub Apps, secrets, and variables.
+Ideally the secrets and variables should be set up in the organization
+settings. The specific workflows in this template that require this
+additional setup are:
+
+-   The workflow `.github/workflows/release-package.yml` requires the
+    [auto-release-token](https://github.com/apps/auto-release-token)
+    GitHub App as well as a creating a GitHub secret called
+    `UPDATE_VERSION_TOKEN` and a variable called `UPDATE_VERSION_APP_ID`
+    that has the App ID.
+-   The workflow `.github/workflows/add-to-project.yml` requires the
+    [add-to-board-token](https://github.com/apps/add-to-board-token)
+    GitHub App, along with the `ADD_TO_BOARD_TOKEN` secret and the
+    `ADD_TO_BOARD_APP_ID` variable of the GitHub App's ID.
+
+If you use Netlify, you will also need to add a `NETLIFY_AUTH_TOKEN` secret
+of your Netlify Token.

index.qmd

@@ -12,26 +12,53 @@ including for developing the package.
 ## Features
 
 -   Use [uv](https://decisions.seedcase-project.org/why-uv/) to manage
-    the Python package.
--   Build management with [just](https://just.systems/man/en/).
--   Check typos with [typos](https://github.com/crate-ci/typos).
+    the Python package and for project management.
+-   Includes a [justfile](https://just.systems/man/en/) for managing
+    common tasks like building the website and running checks.
+-   Uses [typos](https://github.com/crate-ci/typos) to check for common
+    spelling mistakes.
 -   Code formatting and linting with
     [ruff](https://decisions.seedcase-project.org/why-ruff/).
--   Pre-commit hooks with [pre-commit](https://pre-commit.com/).
+-   Run checks with [pre-commit](https://pre-commit.com/) hooks to
+    ensure consistent formatting and style across the project. It
+    includes checks for credentials, typos, and file formatting.
 -   GitHub workflows for automatically adding Pull Requests and Issues
     to a project board.
 -   Pull Request template for easy creation of new Pull Requests.
+-   Includes [GitHub Actions](https://docs.github.com/en/actions) for
+    continuous integration, testing, and delivery for running checks,
+    formatting, releasing, and building the Python package and associated 
+    documentation.
+-   Pull Request template for easy creation of new Pull Requests.
 -   [VS Code](https://code.visualstudio.com/) settings commonly used by
     contributors working in VS Code.
--   [EditorConfig](https://editorconfig.org/) for common cross-editor
-    settings for contributors.
+-   Includes an [EditorConfig](https://editorconfig.org/) file to ensure
+    consistent formatting across different editors.
 -   [`CITATION.cff`](https://citation-file-format.github.io/) file for
     citation information.
--   Website generation with [Quarto](https://quarto.org/).
 -   Python package folder and file structure that takes advantage of
     Python's packaging ecosystem.
 -   [`pyproject.toml`](https://peps.python.org/pep-0518/) for tracking
     dependencies and project metadata.
+-   Uses [Quarto](https://quarto.org/) Markdown for the website content,
+    allowing for easy integration of code, text, and figures.
+-   Uses
+    [Commitizen](https://decisions.seedcase-project.org/why-changelog-with-commitizen)
+    to
+    [check](https://decisions.seedcase-project.org/why-lint-with-commitizen/)
+    commit messages and automatically create the changelog.
+-   Automated Git tagging and GitHub releases with
+    [commitizen](https://decisions.seedcase-project.org/why-semantic-release-with-commitizen/)
+    that are based on messages following [Conventional
+    Commits](https://decisions.seedcase-project.org/why-conventional-commits).
+-   Uses a [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/)
+    license for the website content.
+-   Uses an [MIT](https://decisions.seedcase-project.org/why-mit-license/index.html)
+    license for the code.
+-   Optionally uses the
+    [`seedcase-theme`](https://github.com/{{< meta gh.org >}}/seedcase-theme)
+    Quarto extension for a standard appearance across websites.
+-   Uses [Netlify](https://www.netlify.com/) for hosting the website.
 
 ## Want to contribute?