refactor: ♻️ apply changes from copier template

.copier-answers.yml

@@ -0,0 +1,14 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: '2590293'
+_src_path: gh:seedcase-project/template-python-package
+author_email: ''
+author_family_name: ''
+author_given_name: ''
+copyright_year: '2025'
+github_board_number: '18'
+github_repo: seedcase-sprout
+github_user: seedcase-project
+homepage: https://sprout.seedcase-project.org/
+hosting_provider: netlify
+is_seedcase_project: true
+review_team: '@seedcase-project/developers'

.github/CODEOWNERS

@@ -1,13 +1,2 @@
 # All members on Developers team get added to review PRs
 * @seedcase-project/developers
-
-# Ignore these so we don't get added to sync PRs
-/.github/
-/.vscode/
-/.devcontainer/
-justfile
-.editorconfig
-.gitignore
-ruff.toml
-pyproject.toml
-uv.lock

.github/dependabot.yml

@@ -1,10 +1,19 @@
 version: 2
 updates:
-  - package-ecosystem: pip
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    commit-message:
+      prefix: ci
+      include: scope
+    assignees:
+      - "lwjohnst86"
+
+  - package-ecosystem: uv
     directory: /
     schedule:
       interval: monthly
-    versioning-strategy: increase-if-necessary
     commit-message:
       prefix: build
       include: scope

.github/workflows/dependency-review.yml

@@ -0,0 +1,17 @@
+# Dependency Review Action
+#
+# This Action will scan dependency manifest files that change as part of a Pull Request,
+# surfacing known-vulnerable versions of the packages declared or updated in the PR.
+# Once installed, if the workflow run is marked as required,
+# PRs introducing known-vulnerable packages will be blocked from merging.
+#
+# Source repository: https://github.com/actions/dependency-review-action
+name: "Security: Dependency Review"
+on: pull_request
+
+# Limit token permissions for security
+permissions: read-all
+
+jobs:
+  dependency-review:
+    uses: seedcase-project/.github/.github/workflows/reusable-dependency-review.yml@main

.github/workflows/release-package.yml

@@ -50,7 +50,7 @@ jobs:
       # - https://www.andrlik.org/dispatches/til-use-uv-for-build-and-publish-github-actions/
       # - https://github.com/astral-sh/trusted-publishing-examples
       - name: Set up uv
-        uses: astral-sh/setup-uv@bd01e18f51369d5a26f1651c3cb451d3417e3bba # v6.3.1
+        uses: astral-sh/setup-uv@e92bafb6253dcd438e0484186d7669ea7a8ca1cc # v6.4.3
 
       - name: Build distributions
         # Builds dists from source and stores them in the dist/ directory.

.github/workflows/update-from-template.yml

@@ -0,0 +1,55 @@
+name: Update from template
+
+on:
+  workflow_dispatch:
+  schedule:
+    # Every day at 3:30 at night.
+    - cron: '30 3 * * *'
+
+# Limit token permissions for security
+permissions: read-all
+
+jobs:
+  update-from-template:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@0634a2670c59f64b4a01f0f96f84700a4088b9f0 # v2.12.0
+        with:
+          egress-policy: audit
+
+      - name: Check out repository
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+
+      - name: Install Python
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        with:
+          python-version: "3.13"
+
+      - name: Install dependencies
+        run: |
+          sudo apt install pipx
+          pipx ensurepath
+          pipx install uv rust-just copier
+
+      - name: Set User
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+
+      - name: Pull request with updates from template
+        run: |
+          just update-from-template
+          any_changes=$(git status --porcelain=v1 2>/dev/null | wc -l)
+          if [ "$any_changes" -eq 0 ]; then
+            echo "No updates from the template detected, and no changes found. Stopping and exiting."
+            exit 0
+          fi
+          git checkout -b chore/update-from-template
+          git add .
+          git commit -m "chore(sync): :hammer: update changes from template"
+          gh pr create \
+            --title "chore(sync): :hammer: update changes from template" \
+            --body "This PR is automatically generated by the 'update-from-template' workflow. It syncs the latest changes from the template repository with this repository."

.vscode/extensions.json

@@ -18,6 +18,5 @@
     "tekumara.typos-vscode",
     "EditorConfig.EditorConfig"
   ],
-  // List of extensions recommended by VS Code that should not be recommended for users of this workspace.
   "unwantedRecommendations": []
 }

.vscode/json.code-snippets

@@ -1,18 +1,4 @@
 {
-  // Place your snippets for Quarto here.
-  // Each snippet is defined under a snippet name and has a prefix, body and description.
-  // The prefix is what is used to trigger the snippet and the body will be expanded and inserted.
-  // Possible variables are:
-  //
-  // - $1 and $2 for tab stops,
-  // - $0 for the final cursor position, and
-  // - ${1:label}, ${2:another} for placeholders
-  //
-  // Placeholders with the same ids are connected.
-  //
-  // How to use the code snippets:
-  // After you have set the above settings, a suggestion for one of the code snippets below will pop up automatically, when
-  // you start writing the prefix. Press "Enter" or "Tab" to insert the code snippet.
   "Insert TODO formatting": {
     "scope": "quarto,markdown",
     "prefix": "TODO",

.vscode/launch.json

@@ -1,7 +1,4 @@
 {
-  // Use IntelliSense to learn about possible attributes.
-  // Hover to view descriptions of existing attributes.
-  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
   "version": "0.2.0",
   "configurations": [
     {

.vscode/python.code-snippets

@@ -1,17 +1,4 @@
 {
-  // Place your snippets for python here. Each snippet is defined under a snippet name and has a prefix, body and
-  // description. The prefix is what is used to trigger the snippet and the body will be expanded and inserted. Possible variables are:
-  // $1, $2 for tab stops, $0 for the final cursor position, and ${1:label}, ${2:another} for placeholders. Placeholders with the
-  // same ids are connected.
-  // Example:
-  // "Print to console": {
-  // 	"prefix": "log",
-  // 	"body": [
-  // 		"console.log('$1');",
-  // 		"$2"
-  // 	],
-  // 	"description": "Log output to console"
-  // }
   "Insert a Python test": {
     "prefix": "test-gwt",
     "body": [

.vscode/settings.json

@@ -12,15 +12,17 @@
   "editor.tabCompletion": "on",
   "editor.snippetSuggestions": "inline",
   "conventional-branch.type": [
-    "build", // Changes that affect the build system or external dependencies
-    "ci", // Changes to our CI configuration files and scripts
-    "docs", // Documentation only changes
-    "feat", // A new feature
-    "fix", // A bug fix
-    "refactor", // A code change that neither fixes a bug nor adds a feature
-    "style", // Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc)
-    "test", // Adding missing tests or correcting existing tests
-    "chore", // Misc things, like renaming or deleting files
+    "build",
+    "ci",
+    "docs",
+    "feat",
+    "fix",
+    "refactor",
+    "style",
+    "test",
+    "chore",
+    "perf",
+    "revert"
   ],
   "conventional-branch.format": "{Type}/{Branch}",
   "[quarto][qmd]": {

404.qmd

@@ -1,5 +1,5 @@
 ---
-title: "You’ve entered the garden of missing pages"
+title: "You've entered the garden of missing pages"
 ---
 
 Let's get you back to greener grounds.

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/

CONTRIBUTING.md

@@ -21,17 +21,12 @@ justfile to manage our project, such as to install development
 dependencies. 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, 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
-```
-
-Then, open a terminal so that the working directory is the root of this
-project (`seedcase-sprout/`) and run:
-
-``` bash
-just install-deps
+pipx install uv rust-just
 ```
 
 We keep all our development workflows in the `justfile`, so you can
@@ -41,3 +36,22 @@ 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.

README.md

@@ -8,17 +8,18 @@
 
 ## seedcase-sprout: Grow structured, organised, and FAIR data
 
+[![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.svg)](https://github.com/copier-org/copier)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15800477.svg)](https://doi.org/10.5281/zenodo.15800477)
 [![GitHub
 License](https://img.shields.io/github/license/seedcase-project/seedcase-sprout.svg)](https://github.com/seedcase-project/seedcase-sprout/blob/main/LICENSE.md)
 [![PyPI
-Version](https://img.shields.io/pypi/v/seedcase-sprout.svg)](https://pypi.org/project/seedcase-sprout)
+Version](https://img.shields.io/pypi/v/seedcase-sprout.svg)](https://pypi.org/project/seedcase-sprout/)
 [![GitHub
 Release](https://img.shields.io/github/v/release/seedcase-project/seedcase-sprout.svg)](https://github.com/seedcase-project/seedcase-sprout/releases/latest)
 [![Supported Python Version from PEP 621
-TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fseedcase-project%2Fseedcase-sprout%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)](https://github.com/seedcase-project/seedcase-sprout/blob/main/pyproject.toml)
+TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https://raw.githubusercontent.com/seedcase-project/seedcase-sprout/refs/heads/main/pyproject.toml)](https://github.com/seedcase-project/seedcase-sprout/blob/main/pyproject.toml)
 [![OpenSSF
-Scorecard](https://api.scorecard.dev/projects/github.com/seedcase-project/seedcase-sprout/badge?raw=true.png)](https://scorecard.dev/viewer/?uri=github.com/seedcase-project/seedcase-sprout)
+Scorecard](https://api.scorecard.dev/projects/github.com/seedcase-project/seedcase-sprout/badge?raw=true.svg)](https://scorecard.dev/viewer/?uri=github.com/seedcase-project/seedcase-sprout)
 [![Build
 package](https://github.com/seedcase-project/seedcase-sprout/actions/workflows/build-package.yml/badge.svg)](https://github.com/seedcase-project/seedcase-sprout/actions/workflows/build-package.yml)
 [![Build
@@ -33,7 +34,7 @@ coverage](https://raw.githubusercontent.com/seedcase-project/seedcase-sprout/cov
 state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![OpenSSF Best
-Practices](https://www.bestpractices.dev/projects/10459/badge?raw=true.png)](https://www.bestpractices.dev/projects/10459)
+Practices](https://www.bestpractices.dev/projects/10459/badge?raw=true.svg)](https://www.bestpractices.dev/projects/10459)
 
 Sprout is one component of the [Seedcase
 Project](https://seedcase-project.org) framework that aims to take data
@@ -67,8 +68,8 @@ 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](https://github.com/seedcase-project/.github/blob/main/CODE_OF_CONDUCT.md).
-By participating in this project you agree to abide by its terms.
+Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree
+to abide by its terms.
 
 ## Licensing
 

README.qmd

@@ -48,8 +48,8 @@ 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](https://github.com/seedcase-project/.github/blob/main/CODE_OF_CONDUCT.md).
-By participating in this project you agree to abide by its terms.
+Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree
+to abide by its terms.
 
 ## Licensing
 

_contributors.qmd

@@ -0,0 +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), [\@K-Beicher](https://github.com/K-Beicher), [\@philter87](https://github.com/philter87)

_extensions/seedcase-project/seedcase-theme/_brand.yml

@@ -2,7 +2,13 @@ meta:
   name:
     full: Seedcase Project
     short: Seedcase
+  description: |
+    The Seedcase Project is an organisation dedicated to making an
+    effective and open framework for building modern infrastructures
+    for structured, standardised, and FAIR (findable, accessible,
+    interoperable, and reusable) research data.
   link:
+    home: https://seedcase-project.org
     github: https://github.com/seedcase-project
 
 color:
@@ -19,7 +25,7 @@ typography:
   fonts:
     - family: noto sans
       source: "bunny"
-      # other weights are used inexplicitly for e.g., bold and table headers
+      # other weights are used for e.g., bold and table headers
       weight: [300, 500, 600]
     - family: poppins
       source: "bunny"
@@ -140,3 +146,8 @@ defaults:
       .callout-body {
           font-weight: 300 !important;
       }
+
+      /* Dropdown items on navbar default to 400 weight, but we want them to be lighter. */
+      .dropdown-item {
+          font-weight: 300 !important;
+      }