From a758d446e86b9748b3f0d9b00c269e8fe61c3099 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 10:28:00 +0100
Subject: [PATCH 01/30] feat: :sparkles: add files with copier variables to
 template folder

---
 .gitignore                                    |   1 +
 copier.yaml                                   | 125 ++++++++++++++++
 justfile                                      | 134 ++++++++++--------
 template/.github/CODEOWNERS.jinja             |  13 ++
 template/.github/dependabot.yml.jinja         |  14 ++
 .../workflows/add-to-project.yml.jinja        |  27 ++++
 template/CITATION.cff.jinja                   |  24 ++++
 template/LICENSE.md.jinja                     |  21 +++
 template/README.md.jinja                      |   3 +
 template/_quarto.yml.jinja                    |  73 ++++++++++
 ...oject %}site-counter.html{% endif %}.jinja |   3 +
 template/index.qmd.jinja                      |   5 +
 template/pyproject.toml.jinja                 |  38 +++++
 .../{{package_name_snake_case}}/__init__.py   |   1 +
 .../src/{{package_name_snake_case}}/py.typed  |   0
 template/{{_copier_conf.answers_file}}.jinja  |   2 +
 16 files changed, 421 insertions(+), 63 deletions(-)
 create mode 100644 copier.yaml
 create mode 100644 template/.github/CODEOWNERS.jinja
 create mode 100644 template/.github/dependabot.yml.jinja
 create mode 100644 template/.github/workflows/add-to-project.yml.jinja
 create mode 100644 template/CITATION.cff.jinja
 create mode 100644 template/LICENSE.md.jinja
 create mode 100644 template/README.md.jinja
 create mode 100644 template/_quarto.yml.jinja
 create mode 100644 template/docs/{% if seedcase_project %}site-counter.html{% endif %}.jinja
 create mode 100644 template/index.qmd.jinja
 create mode 100644 template/pyproject.toml.jinja
 create mode 100644 template/src/{{package_name_snake_case}}/__init__.py
 rename src/PACKAGE-NAME/__init__.py => template/src/{{package_name_snake_case}}/py.typed (100%)
 create mode 100644 template/{{_copier_conf.answers_file}}.jinja

diff --git a/.gitignore b/.gitignore
index 6346a65..21ac9de 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,7 @@
 _ignore
 bin/
 dev/
+_temp/
 
 # Temporary files
 *.tmp
diff --git a/copier.yaml b/copier.yaml
new file mode 100644
index 0000000..38e0de0
--- /dev/null
+++ b/copier.yaml
@@ -0,0 +1,125 @@
+_subdirectory: template
+
+# Post-copy commands:
+_tasks:
+  # Add dev dependencies
+  - command: "git init -b main && uv add --dev pre-commit ruff typos pytest bandit commitizen genbadge jupyter pytest-cov quartodoc types-tabulate mypy vulture"
+    when: "{{ _copier_operation == 'copy' }}"
+  # If Seedcase project, add seedcase-theme extension
+  - command: "uv run quarto add --no-prompt seedcase-project/seedcase-theme"
+    when: "{{ _copier_operation == 'copy' and is_seedcase_project }}"
+  # If Seedcase project, use seedcase-theme as project type
+  - command: >-
+      uv run python -c "from pathlib import Path; file = Path('_quarto.yml'); file.write_text(file.read_text().replace('type: website', 'type: seedcase-theme', 1))"
+    when: "{{ _copier_operation == 'copy' and is_seedcase_project }}"
+
+
+# Message to show after generating or regenerating the project successfully
+_message_after_copy: |
+
+  Your project "{{ package_name }}" has been created successfully!
+
+  Next steps:
+
+  1. Change directory to the project root:
+
+    $ cd {{ _copier_conf.dst_path }}
+
+  2. Install the pre-commit hooks:
+
+    $ just install-precommit
+
+  3. Install [`spaid`](https://github.com/seedcase-project/spaid) and run these commands to upload and configure your project on GitHub:
+
+    $ spaid_gh_create_repo_from_local -h
+    $ spaid_gh_set_repo_settings -h
+    $ spaid_gh_ruleset_basic_protect_main -h
+
+  4. Configure GitHub following this
+    [guide](https://guidebook.seedcase-project.org/operations/security#using-github-apps-to-generate-tokens):
+
+    - Install the [auto-release-token](https://github.com/apps/auto-release-token) GitHub App
+    - Create these secrets: UPDATE_VERSION_TOKEN, ADD_TO_BOARD, NETLIFY_AUTH_TOKEN
+    - Create these variables: UPDATE_VERSION_APP_ID, ADD_TO_BOARD_APP_ID
+
+  5. List and complete all TODO items in the repository:
+
+    $ just list-todos
+
+# Questions:
+github_user:
+  type: str
+  help: "What is the GitHub username of the person or organisation who owns the package?"
+  validator: |
+    {% if github_user and not (github_user | regex_search('^[\w.-]+$')) %}
+    Must contain only alphanumeric characters and `_`, `-`, or `.`.
+    {% endif %}
+
+package_name:
+  type: str
+  help: "What is the name of the package?"
+  default: "{{ _copier_conf.dst_path | basename }}"
+  validator: |
+    {% if package_name and not (package_name | regex_search('^[\w.-]+$')) %}
+    Must contain only alphanumeric characters and `_`, `-`, or `.`.
+    {% endif %}
+
+package_name_snake_case:
+  type: str
+  default: "{{package_name | replace('-', '_') | replace('.', '_')}}"
+  when: false
+
+package_github_repo:
+  type: str
+  default: "{{ github_user ~ '/' ~ package_name }}"
+  when: false
+
+is_seedcase_project:
+  type: bool
+  help: "Is this package part of the Seedcase Project?"
+  default: "{{ github_user == 'seedcase-project' }}"
+
+seedcase_short_name:
+  type: str
+  help: "What is the short name of the package?"
+  default: "{{ package_name[9:] if ('seedcase-' in package_name) else '' }}"
+  when: "{{ is_seedcase_project }}"
+
+homepage:
+  type: str
+  help: "What is the homepage of your project?"
+  default: "{{ 'https://%s.seedcase-project.org' % seedcase_short_name if is_seedcase_project else '' }}"  
+
+author_given_name:
+  type: str
+  help: "What is your first/given name?"
+
+author_family_name:
+  type: str
+  help: "What is your last/family name?"
+
+author_email:
+  type: str
+  help: "What is your email address?"
+
+review_team:
+  type: str
+  help: What GitHub team is responsible for reviewing pull requests?
+  default: "{{ '@%s/developers' % github_user if github_user else '' }}"
+
+github_board_number:
+  type: str
+  help: "What is the number of the GitHub project board to add issues and PRs to?"
+  validator: |
+    {% if github_board_number and not github_board_number.isdigit() %}
+    The board number must be an integer.
+    {% endif %}
+
+copyright_year:
+  type: str
+  default: "{{ copyright_year | default('%Y' | strftime) }}"
+  when: false
+
+dependabot_pr_assignee:
+  type: str
+  help: "What is the GitHub username of the person to assign to PRs opened by dependabot?"
diff --git a/justfile b/justfile
index b009dfd..f26f5ba 100644
--- a/justfile
+++ b/justfile
@@ -2,7 +2,7 @@
     just --list --unsorted
 
 # Run all build-related recipes in the justfile
-run-all: install-deps format-python check-python check-unused test-python check-security check-spelling check-commits build-website
+run-all: check-spelling check-commits test build-website
 
 # Install the pre-commit hooks
 install-precommit:
@@ -13,78 +13,86 @@ install-precommit:
   # Update versions of pre-commit hooks
   uvx pre-commit autoupdate
 
-# Install Python package dependencies
-install-deps:
-  uv sync --all-extras --dev
-
-# Run the Python tests
-test-python:
-  uv run pytest
-  # Make the badge from the coverage report
-  uv run genbadge coverage \
-    -i coverage.xml \
-    -o htmlcov/coverage.svg
-
-# Check Python code for any errors that need manual attention
-check-python:
-  # Check formatting
-  uv run ruff check .
-  # Check types
-  uv run mypy .
-
-# Reformat Python code to match coding style and general structure
-format-python:
-  uv run ruff check --fix .
-  uv run ruff format .
-
-# Build the documentation website using Quarto
-build-website:
-  # To let Quarto know where python is.
-  export QUARTO_PYTHON=.venv/bin/python3
-  # Delete any previously built files from quartodoc.
-  # -f is to not give an error if the files don't exist yet.
-  rm -f docs/reference/*.qmd
-  uv run quartodoc build
-  uv run quarto render --execute
-
-# Run checks on commits with non-main branches
+# Check the commit messages on the current branch that are not on the main branch
 check-commits:
   #!/bin/zsh
   branch_name=$(git rev-parse --abbrev-ref HEAD)
   number_of_commits=$(git rev-list --count HEAD ^main)
   if [[ ${branch_name} != "main" && ${number_of_commits} -gt 0 ]]
   then
-    uv run cz check --rev-range main..HEAD
+    uvx --from commitizen cz check --rev-range main..HEAD
   else
-    echo "Can't either be on ${branch_name} or have more than ${number_of_commits}."
+    echo "On `main` or current branch doesn't have any commits."
   fi
 
-# Run basic security checks on the package
-check-security:
-  uv run bandit -r src/
-
 # Check for spelling errors in files
 check-spelling:
-  uv run typos
+  uvx typos
 
-# Build the documentation as PDF using Quarto
-build-pdf:
-  # To let Quarto know where python is.
-  export QUARTO_PYTHON=.venv/bin/python3
-  uv run quarto install tinytex
-  # For generating images from Mermaid diagrams
-  uv run quarto install chromium
-  uv run quarto render --profile pdf --to pdf
-  find docs -name "mermaid-figure-*.png" -delete
+# Test and check that a Python package can be created from the template
+test:
+  #!/bin/zsh
+  test_name="test-python-package"
+  test_dir="$(pwd)/_temp/$test_name"
+  template_dir="$(pwd)"
+  commit=$(git rev-parse HEAD)
+  rm -rf $test_dir
+  # vcs-ref means the current commit/head, not a tag.
+  uvx copier copy $template_dir $test_dir \
+    --vcs-ref=$commit \
+    --defaults \
+    --trust \
+    --data github_user="first-last" \
+    --data package_name=$test_name \
+    --data is_seedcase_project=true \
+    --data author_given_name="First" \
+    --data author_family_name="Last" \
+    --data author_email="first.last@example.com" \
+    --data review_team="@first-last/developers" \
+    --data github_board_number=22 \
+    --data dependabot_pr_assignee="mango90"
+  # Run checks in the generated test Python package
+  cd $test_dir
+  git add .
+  git commit -m "test: initial copy"
+  just check-python check-spelling
+  # TODO: Find some way to test the `update` command
+  # Check that recopy works
+  echo "Testing recopy command -----------"
+  rm .cz.toml
+  git add .
+  git commit -m "test: preparing to recopy from the template"
+  uvx copier recopy \
+    --vcs-ref=$commit \
+    --defaults \
+    --overwrite \
+    --trust
+  # Check that copying onto an existing Python package works
+  echo "Using the template in an existing package command -----------"
+  rm .cz.toml .copier-answers.yml LICENSE.md
+  git add .
+  git commit -m "test: preparing to copy onto an existing package"
+  uvx copier copy \
+    $template_dir $test_dir \
+    --vcs-ref=$commit \
+    --defaults \
+    --trust \
+    --overwrite \
+    --data github_user="first-last" \
+    --data package_name=$test_name \
+    --data is_seedcase_project=true \
+    --data author_given_name="First" \
+    --data author_family_name="Last" \
+    --data author_email="first.last@example.com" \
+    --data review_team="@first-last/developers" \
+    --data github_board_number=22 \
+    --data dependabot_pr_assignee="mango90"
 
-# Check for unused code in the package and its tests
-check-unused:
-  # exit code=0: No unused code was found
-  # exit code=3: Unused code was found
-  # Three confidence values:
-  # - 100 %: function/method/class argument, unreachable code
-  # - 90 %: import
-  # - 60 %: attribute, class, function, method, property, variable
-  # There are some things should be ignored though, with the allowlist.
-  # Create an allowlist with `vulture --make-allowlist`
-  uv run vulture src/ tests/ **/vulture-allowlist.py
+# Clean up any leftover and temporary build files
+cleanup:
+  #!/bin/zsh
+  rm -rf _temp
+
+# Build the website using Quarto
+build-website:
+  uvx --from quarto quarto render
diff --git a/template/.github/CODEOWNERS.jinja b/template/.github/CODEOWNERS.jinja
new file mode 100644
index 0000000..172a7e0
--- /dev/null
+++ b/template/.github/CODEOWNERS.jinja
@@ -0,0 +1,13 @@
+# All members on Developers team get added to review PRs
+* {{ review_team }}
+
+# Ignore these so we don't get added to sync PRs
+/.github/
+/.vscode/
+/.devcontainer/
+justfile
+.editorconfig
+.gitignore
+ruff.toml
+pyproject.toml
+uv.lock
diff --git a/template/.github/dependabot.yml.jinja b/template/.github/dependabot.yml.jinja
new file mode 100644
index 0000000..76c25b2
--- /dev/null
+++ b/template/.github/dependabot.yml.jinja
@@ -0,0 +1,14 @@
+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: monthly
+    versioning-strategy: increase-if-necessary
+    commit-message:
+      prefix: build
+      include: scope
+{%- if dependabot_pr_assignee %}
+    assignees:
+      - "{{ dependabot_pr_assignee }}"
+{% endif %}
diff --git a/template/.github/workflows/add-to-project.yml.jinja b/template/.github/workflows/add-to-project.yml.jinja
new file mode 100644
index 0000000..955b8d5
--- /dev/null
+++ b/template/.github/workflows/add-to-project.yml.jinja
@@ -0,0 +1,27 @@
+name: Add to project board
+
+on:
+  issues:
+    types:
+      - opened
+      - reopened
+      - transferred
+  pull_request:
+    types:
+      - reopened
+      - opened
+
+# Limit token permissions for security
+permissions: read-all
+
+jobs:
+  add-to-project:
+    uses: seedcase-project/.github/.github/workflows/reusable-add-to-project.yml@main
+    permissions:
+      pull-requests: write
+    with:
+      board-number: {{ github_board_number }}
+      app-id: {{ '${{ vars.ADD_TO_BOARD_APP_ID }}' }}
+    secrets:
+      add-to-board-token: {{ '${{ secrets.ADD_TO_BOARD }}' }}
+      gh-token: {{ '${{ secrets.GITHUB_TOKEN }}' }}
diff --git a/template/CITATION.cff.jinja b/template/CITATION.cff.jinja
new file mode 100644
index 0000000..c03cb5b
--- /dev/null
+++ b/template/CITATION.cff.jinja
@@ -0,0 +1,24 @@
+# TODO: Add title of Python package.
+title: ""
+# TODO: Add abstract of Python package.
+abstract: ""
+authors:
+  - family-names: {{ author_family_name }}
+    given-names: {{ author_given_name }}
+  # TODO: Add ORCID and affiliation for the author.
+    orcid: ""
+    affiliation: ""
+  # TODO: Add more authors as needed.
+  # - family-names: ""
+  #   given-names: ""
+  #   orcid: ""
+  #   affiliation: ""
+cff-version: 1.2.0
+# doi:
+keywords:
+  # TODO: Add keywords relevant to the project.
+  - ""
+license: MIT
+message: "If you use this Python package, please cite it using these metadata."
+repository-code: "https://github.com/{{ package_github_repo }}"
+url: "{{ homepage }}"
diff --git a/template/LICENSE.md.jinja b/template/LICENSE.md.jinja
new file mode 100644
index 0000000..8b1ba0a
--- /dev/null
+++ b/template/LICENSE.md.jinja
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) {{ copyright_year }} {{ package_name }} authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/template/README.md.jinja b/template/README.md.jinja
new file mode 100644
index 0000000..117f38b
--- /dev/null
+++ b/template/README.md.jinja
@@ -0,0 +1,3 @@
+# {{ package_name }}
+
+<!-- TODO: Add README for project. -->
diff --git a/template/_quarto.yml.jinja b/template/_quarto.yml.jinja
new file mode 100644
index 0000000..ce79abd
--- /dev/null
+++ b/template/_quarto.yml.jinja
@@ -0,0 +1,73 @@
+project:
+  type: website
+  # Delete auto-generated files from `quartodoc`
+  post-render: rm -f docs/reference/*.qmd
+  render:
+    - "docs/*"
+    - "index.qmd"
+
+website:
+  title: "{{ 'Seedcase ' ~ (seedcase_short_name | title) if is_seedcase_project else package_name }}"
+  site-url: "{{ homepage }}"
+  repo-url: "https://github.com/{{ package_github_repo }}"
+  page-navigation: true
+  navbar:
+    pinned: true
+    title: false
+    {%- if is_seedcase_project %}
+    logo: "_extensions/seedcase-project/seedcase-theme/logos/navbar-logo-seedcase-{{ seedcase_short_name }}.svg"
+    logo-alt: "Seedcase {{ seedcase_short_name | title }} logo: Main page"
+    {%- else %}
+    # TODO: add logo
+    logo: ""
+    logo-alt: "{{ package_name }} logo: Main page"
+    {%- endif %}  
+    left:
+      - text: "Guide"
+        href: docs/guide/index.qmd
+      - text: "Design"
+        href: docs/design/index.qmd
+    tools:
+      - icon: github
+        href: "https://github.com/{{ package_github_repo }}"
+        aria-label: "GitHub icon: Source code"
+      - icon: house
+        href: "{{ 'https://seedcase-project.org' if is_seedcase_project else homepage }}"
+        aria-label: "House icon: {{ 'Seedcase Project' if is_seedcase_project else package_name }} home page"
+  sidebar:
+    - id: design
+      pinned: true
+      style: "floating"
+      contents:
+        - text: "Design"
+          href: docs/design/index.qmd
+    - id: guide
+      contents:
+        - section: "Guide"
+          href: docs/guide/index.qmd
+
+quartodoc:
+  sidebar: "docs/reference/_sidebar.yml"
+  style: "pkgdown"
+  dir: "docs/reference"
+  package: "{{ package_name_snake_case }}"
+  parser: google
+  dynamic: true
+  renderer:
+    style: _renderer.py
+    table_style: description-list
+    show_signature_annotations: true
+
+metadata-files:
+  - docs/reference/_sidebar.yml
+{% if is_seedcase_project %}
+format:
+  seedcase-theme-html:
+    include-before-body:
+      - "docs/site-counter.html"
+{%- endif %}  
+
+editor:
+  markdown:
+    wrap: 72
+    canonical: true
diff --git a/template/docs/{% if seedcase_project %}site-counter.html{% endif %}.jinja b/template/docs/{% if seedcase_project %}site-counter.html{% endif %}.jinja
new file mode 100644
index 0000000..5156b87
--- /dev/null
+++ b/template/docs/{% if seedcase_project %}site-counter.html{% endif %}.jinja	
@@ -0,0 +1,3 @@
+<!-- TODO: Set up GoatCounter -->
+<script data-goatcounter="https://seedcase-project-{{ seedcase_short_name }}.goatcounter.com/count" async
+  src="//gc.zgo.at/count.js"></script>
diff --git a/template/index.qmd.jinja b/template/index.qmd.jinja
new file mode 100644
index 0000000..d567c08
--- /dev/null
+++ b/template/index.qmd.jinja
@@ -0,0 +1,5 @@
+---
+title: "Welcome to {{ 'Seedcase ' ~ (seedcase_short_name | title) if is_seedcase_project else package_name }}!"
+---
+
+{{ "{{< include /docs/includes/_wip.qmd >}}" }}
diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
new file mode 100644
index 0000000..7ae59ce
--- /dev/null
+++ b/template/pyproject.toml.jinja
@@ -0,0 +1,38 @@
+[project]
+name = "{{ package_name }}"
+version = "0.1.0"
+# TODO: Add a description of the package.
+description = ""
+authors = [
+  {name = "{{ author_given_name }} {{ author_family_name }}", email = "{{ author_email }}" },
+  # TODO: Add more authors as needed.
+]
+maintainers = [
+  {name = "{{ author_given_name }} {{ author_family_name }}", email = "{{ author_email }}" },
+  # TODO: Add more maintainers as needed.
+]
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE.md"]
+requires-python = ">=3.12"
+dependencies = []
+
+[project.urls]
+homepage = "{{ homepage }}"
+{%- if package_github_repo %}
+repository = "https://github.com/{{ package_github_repo }}"
+changelog = "https://github.com/{{ package_github_repo }}/blob/main/CHANGELOG.md"
+issues = "https://github.com/{{ package_github_repo }}/issues"
+{% endif %}
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.pytest.ini_options]
+addopts = [
+  # A short traceback mode to make it easier to view
+  "--tb=short",
+  # Use the `src/` package
+  "--import-mode=importlib",
+]
diff --git a/template/src/{{package_name_snake_case}}/__init__.py b/template/src/{{package_name_snake_case}}/__init__.py
new file mode 100644
index 0000000..89c3d35
--- /dev/null
+++ b/template/src/{{package_name_snake_case}}/__init__.py
@@ -0,0 +1 @@
+"""Module containing all source code."""
diff --git a/src/PACKAGE-NAME/__init__.py b/template/src/{{package_name_snake_case}}/py.typed
similarity index 100%
rename from src/PACKAGE-NAME/__init__.py
rename to template/src/{{package_name_snake_case}}/py.typed
diff --git a/template/{{_copier_conf.answers_file}}.jinja b/template/{{_copier_conf.answers_file}}.jinja
new file mode 100644
index 0000000..a8c521e
--- /dev/null
+++ b/template/{{_copier_conf.answers_file}}.jinja
@@ -0,0 +1,2 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+{{ dict(_copier_answers, copyright_year=copyright_year) | to_nice_yaml -}}

From 9c68f25ce4f39ee5cbeb295416d1d6e13a911d88 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 13:12:24 +0100
Subject: [PATCH 02/30] docs: :memo: edit index page

---
 template/index.qmd.jinja | 2 --
 1 file changed, 2 deletions(-)

diff --git a/template/index.qmd.jinja b/template/index.qmd.jinja
index d567c08..2eec46c 100644
--- a/template/index.qmd.jinja
+++ b/template/index.qmd.jinja
@@ -1,5 +1,3 @@
 ---
 title: "Welcome to {{ 'Seedcase ' ~ (seedcase_short_name | title) if is_seedcase_project else package_name }}!"
 ---
-
-{{ "{{< include /docs/includes/_wip.qmd >}}" }}

From b75f8f90c8d469331996235821df221a68030ee7 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 15:51:51 +0100
Subject: [PATCH 03/30] build: :wrench: update justfile

---
 .vscode/settings.json                         |  1 +
 justfile                                      |  4 ++--
 .../{README.md.jinja => README.qmd.jinja}     |  0
 template/{justfile => justfile.jinja}         | 23 +++++++++++++++++--
 template/tools/get-contributors.sh            | 18 +++++++++++++++
 5 files changed, 42 insertions(+), 4 deletions(-)
 rename template/{README.md.jinja => README.qmd.jinja} (100%)
 rename template/{justfile => justfile.jinja} (78%)
 create mode 100644 template/tools/get-contributors.sh

diff --git a/.vscode/settings.json b/.vscode/settings.json
index fc0bb11..6ec6d96 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -30,6 +30,7 @@
   "python.languageServer": "Pylance",
   "files.insertFinalNewline": true,
   "files.associations": {
+    "justfile.jinja": "django-txt",
     "*.yml.jinja": "jinja-yaml",
     "*.cff.jinja": "jinja-yaml",
     "*.toml.jinja": "jinja-toml",
diff --git a/justfile b/justfile
index e121875..2fc0660 100644
--- a/justfile
+++ b/justfile
@@ -26,7 +26,7 @@ update-template:
   mkdir -p template/tools
   cp tools/get-contributors.sh template/tools/
   cp .github/pull_request_template.md template/.github/
-  cp .github/workflows/build-website.yml .github/workflows/dependency-review.yml template/.github/workflows/
+  cp .github/workflows/dependency-review.yml template/.github/workflows/
 
 # Check the commit messages on the current branch that are not on the main branch
 check-commits:
@@ -118,4 +118,4 @@ build-readme:
 
 # Generate a Quarto include file with the contributors
 build-contributors:
-  sh ./tools/get-contributors.sh seedcase-project/template-workshop
+  sh ./tools/get-contributors.sh seedcase-project/template-python-project
diff --git a/template/README.md.jinja b/template/README.qmd.jinja
similarity index 100%
rename from template/README.md.jinja
rename to template/README.qmd.jinja
diff --git a/template/justfile b/template/justfile.jinja
similarity index 78%
rename from template/justfile
rename to template/justfile.jinja
index 279c94f..1e0e4f6 100644
--- a/template/justfile
+++ b/template/justfile.jinja
@@ -1,8 +1,15 @@
 @_default:
     just --list --unsorted
 
+@_checks: check-python check-unused test-python check-security check-spelling check-commits
+@_builds: build-contributors build-website build-readme
+
 # Run all build-related recipes in the justfile
-run-all: install-deps format-python check-python check-unused test-python check-security check-spelling check-commits build-website
+{%- if is_seedcase_project %}
+run-all: install-deps update-quarto-theme format-python _checks _builds
+{%- else %} 
+run-all: install-deps format-python _checks _builds
+{%- endif %} 
 
 # List all TODO items in the repository
 list-todos:
@@ -16,7 +23,11 @@ install-precommit:
   uvx pre-commit run --all-files
   # Update versions of pre-commit hooks
   uvx pre-commit autoupdate
-
+{% if is_seedcase_project %}
+# Update the Quarto seedcase-theme extension
+update-quarto-theme:
+  quarto add seedcase-project/seedcase-theme --no-prompt
+{% endif %} 
 # Install Python package dependencies
 install-deps:
   uv sync --all-extras --dev
@@ -92,3 +103,11 @@ check-unused:
   # There are some things should be ignored though, with the allowlist.
   # Create an allowlist with `vulture --make-allowlist`
   uv run vulture src/ tests/ **/vulture-allowlist.py
+
+# Re-build the README file from the Quarto version
+build-readme:
+  uvx --from quarto quarto render README.qmd --to gfm
+
+# Generate a Quarto include file with the contributors
+build-contributors:
+  sh ./tools/get-contributors.sh {{ package_github_repo }}
diff --git a/template/tools/get-contributors.sh b/template/tools/get-contributors.sh
new file mode 100644
index 0000000..65bfbb4
--- /dev/null
+++ b/template/tools/get-contributors.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+# Get a list of contributors to this repository and save it to
+# _contributors.qmd.tmp file. It also:
+#
+# - Formats users into Markdown links to their GitHub profiles.
+# - Removes any usernames with the word "bot" in them.
+# - Removes the trailing comma from the list.
+repo_spec=${1}
+echo "These are the people who have contributed by submitting changes through pull requests :tada:\n\n" > _contributors.qmd.tmp
+gh api \
+  -H "Accept: application/vnd.github+json" \
+  -H "X-GitHub-Api-Version: 2022-11-28" \
+  /repos/$repo_spec/contributors \
+  --template '{{range .}} [\@{{.login}}]({{.html_url}}){{"\n"}}{{end}}' | \
+  grep -v "\[bot\]" | \
+  tr '\n' ', ' | \
+  sed -e 's/,$//' >> _contributors.qmd.tmp

From 6a604818ec4d4f4fdab610f7f828ab315a875be9 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 15:58:53 +0100
Subject: [PATCH 04/30] build: :wrench: use just recipe in copier task

---
 copier.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/copier.yaml b/copier.yaml
index 38e0de0..5267c6f 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -6,7 +6,7 @@ _tasks:
   - command: "git init -b main && uv add --dev pre-commit ruff typos pytest bandit commitizen genbadge jupyter pytest-cov quartodoc types-tabulate mypy vulture"
     when: "{{ _copier_operation == 'copy' }}"
   # If Seedcase project, add seedcase-theme extension
-  - command: "uv run quarto add --no-prompt seedcase-project/seedcase-theme"
+  - command: "just update-quarto-theme"
     when: "{{ _copier_operation == 'copy' and is_seedcase_project }}"
   # If Seedcase project, use seedcase-theme as project type
   - command: >-

From a6585eba1b26823fd6a5c4c46792c78e4fc445f7 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 16:10:19 +0100
Subject: [PATCH 05/30] build: :wrench: update justfile

---
 justfile                | 12 +++++++-----
 template/justfile.jinja |  5 +++--
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/justfile b/justfile
index 2fc0660..2e96a02 100644
--- a/justfile
+++ b/justfile
@@ -2,10 +2,12 @@
     just --list --unsorted
 
 @_checks: check-spelling check-commits
+# Test Seedcase and non-Seedcase projects
+@_tests: (test "true") (test "false")
 @_builds: build-contributors build-website build-readme
 
 # Run all build-related recipes in the justfile
-run-all: update-quarto-theme update-template _checks test _builds
+run-all: update-quarto-theme update-template _checks _tests _builds
 
 # Install the pre-commit hooks
 install-precommit:
@@ -45,10 +47,10 @@ check-spelling:
   uvx typos
 
 # Test and check that a Python package can be created from the template
-test:
+test is_seedcase_project:
   #!/bin/zsh
   test_name="test-python-package"
-  test_dir="$(pwd)/_temp/$test_name"
+  test_dir="$(pwd)/_temp/{{ is_seedcase_project }}/$test_name"
   template_dir="$(pwd)"
   commit=$(git rev-parse HEAD)
   rm -rf $test_dir
@@ -59,7 +61,7 @@ test:
     --trust \
     --data github_user="first-last" \
     --data package_name=$test_name \
-    --data is_seedcase_project=true \
+    --data is_seedcase_project={{ is_seedcase_project }} \
     --data author_given_name="First" \
     --data author_family_name="Last" \
     --data author_email="first.last@example.com" \
@@ -95,7 +97,7 @@ test:
     --overwrite \
     --data github_user="first-last" \
     --data package_name=$test_name \
-    --data is_seedcase_project=true \
+    --data is_seedcase_project={{ is_seedcase_project }} \
     --data author_given_name="First" \
     --data author_family_name="Last" \
     --data author_email="first.last@example.com" \
diff --git a/template/justfile.jinja b/template/justfile.jinja
index 1e0e4f6..e0db7b2 100644
--- a/template/justfile.jinja
+++ b/template/justfile.jinja
@@ -2,13 +2,14 @@
     just --list --unsorted
 
 @_checks: check-python check-unused test-python check-security check-spelling check-commits
+@_tests: test-python
 @_builds: build-contributors build-website build-readme
 
 # Run all build-related recipes in the justfile
 {%- if is_seedcase_project %}
-run-all: install-deps update-quarto-theme format-python _checks _builds
+run-all: install-deps update-quarto-theme format-python _checks _tests _builds
 {%- else %} 
-run-all: install-deps format-python _checks _builds
+run-all: install-deps format-python _checks _tests _builds
 {%- endif %} 
 
 # List all TODO items in the repository

From c3b8a6027e21ec310c1e543b04e316607bb3fbcf Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 16:11:14 +0100
Subject: [PATCH 06/30] test: preparing to recopy from the template

---
 .cz.toml | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 .cz.toml

diff --git a/.cz.toml b/.cz.toml
deleted file mode 100644
index ff8c8fb..0000000
--- a/.cz.toml
+++ /dev/null
@@ -1,6 +0,0 @@
-[tool.commitizen]
-bump_message = "build(version): :bookmark: update version from $current_version to $new_version"
-update_changelog_on_bump = true
-version_provider = "uv"
-# Don't regenerate the changelog on every update
-changelog_incremental = true

From eccca84266f20f4ab95def607965f720f18c3ba5 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 16:11:15 +0100
Subject: [PATCH 07/30] test: preparing to copy onto an existing package

---
 LICENSE.md | 21 ---------------------
 1 file changed, 21 deletions(-)
 delete mode 100644 LICENSE.md

diff --git a/LICENSE.md b/LICENSE.md
deleted file mode 100644
index aeed825..0000000
--- a/LICENSE.md
+++ /dev/null
@@ -1,21 +0,0 @@
-# MIT License
-
-Copyright (c) 2023-2025 Aarhus University
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

From 3f9094006fdf446140f754f32742dbfe6c6cb066 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 16:22:25 +0100
Subject: [PATCH 08/30] docs: :memo: build README.md from .qmd

---
 template/README.md.jinja | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 template/README.md.jinja

diff --git a/template/README.md.jinja b/template/README.md.jinja
new file mode 100644
index 0000000..52ae523
--- /dev/null
+++ b/template/README.md.jinja
@@ -0,0 +1,5 @@
+
+
+# {{ package_name }}
+
+<!-- TODO: Add README for project. -->

From 07738016f00d7682210dfa39f1dacb15cae970b4 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 16:27:05 +0100
Subject: [PATCH 09/30] docs: :memo: tweak post-copy message

---
 copier.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/copier.yaml b/copier.yaml
index 5267c6f..d53e5f3 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -39,7 +39,7 @@ _message_after_copy: |
     [guide](https://guidebook.seedcase-project.org/operations/security#using-github-apps-to-generate-tokens):
 
     - Install the [auto-release-token](https://github.com/apps/auto-release-token) GitHub App
-    - Create these secrets: UPDATE_VERSION_TOKEN, ADD_TO_BOARD, NETLIFY_AUTH_TOKEN
+    - Create these secrets: UPDATE_VERSION_TOKEN, ADD_TO_BOARD, NETLIFY_AUTH_TOKEN (if using Netlify)
     - Create these variables: UPDATE_VERSION_APP_ID, ADD_TO_BOARD_APP_ID
 
   5. List and complete all TODO items in the repository:

From c8e797404923f08c39024a66de3f9ec4458c6b15 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 16:29:00 +0100
Subject: [PATCH 10/30] docs: :memo: remove TODO from README.md

---
 template/README.md.jinja | 1 -
 1 file changed, 1 deletion(-)

diff --git a/template/README.md.jinja b/template/README.md.jinja
index 52ae523..d57964e 100644
--- a/template/README.md.jinja
+++ b/template/README.md.jinja
@@ -2,4 +2,3 @@
 
 # {{ package_name }}
 
-<!-- TODO: Add README for project. -->

From c72d8048b96fe8a488d5b7730d90ae0a49772684 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 5 Aug 2025 15:34:54 +0000
Subject: [PATCH 11/30] chore(pre-commit): :pencil2: automatic fixes

---
 copier.yaml                | 2 +-
 template/README.md.jinja   | 1 -
 template/_quarto.yml.jinja | 4 ++--
 template/justfile.jinja    | 6 +++---
 4 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/copier.yaml b/copier.yaml
index d53e5f3..84c6838 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -88,7 +88,7 @@ seedcase_short_name:
 homepage:
   type: str
   help: "What is the homepage of your project?"
-  default: "{{ 'https://%s.seedcase-project.org' % seedcase_short_name if is_seedcase_project else '' }}"  
+  default: "{{ 'https://%s.seedcase-project.org' % seedcase_short_name if is_seedcase_project else '' }}"
 
 author_given_name:
   type: str
diff --git a/template/README.md.jinja b/template/README.md.jinja
index d57964e..ba17175 100644
--- a/template/README.md.jinja
+++ b/template/README.md.jinja
@@ -1,4 +1,3 @@
 
 
 # {{ package_name }}
-
diff --git a/template/_quarto.yml.jinja b/template/_quarto.yml.jinja
index ce79abd..9333a7a 100644
--- a/template/_quarto.yml.jinja
+++ b/template/_quarto.yml.jinja
@@ -21,7 +21,7 @@ website:
     # TODO: add logo
     logo: ""
     logo-alt: "{{ package_name }} logo: Main page"
-    {%- endif %}  
+    {%- endif %}
     left:
       - text: "Guide"
         href: docs/guide/index.qmd
@@ -65,7 +65,7 @@ format:
   seedcase-theme-html:
     include-before-body:
       - "docs/site-counter.html"
-{%- endif %}  
+{%- endif %}
 
 editor:
   markdown:
diff --git a/template/justfile.jinja b/template/justfile.jinja
index e0db7b2..cde9811 100644
--- a/template/justfile.jinja
+++ b/template/justfile.jinja
@@ -8,9 +8,9 @@
 # Run all build-related recipes in the justfile
 {%- if is_seedcase_project %}
 run-all: install-deps update-quarto-theme format-python _checks _tests _builds
-{%- else %} 
+{%- else %}
 run-all: install-deps format-python _checks _tests _builds
-{%- endif %} 
+{%- endif %}
 
 # List all TODO items in the repository
 list-todos:
@@ -28,7 +28,7 @@ install-precommit:
 # Update the Quarto seedcase-theme extension
 update-quarto-theme:
   quarto add seedcase-project/seedcase-theme --no-prompt
-{% endif %} 
+{% endif %}
 # Install Python package dependencies
 install-deps:
   uv sync --all-extras --dev

From 865a4c50980bfe53b22ff3ae17197746bc84d1f7 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 17:33:49 +0100
Subject: [PATCH 12/30] fix: :bug: add back files that disappeared

---
 .cz.toml   |  6 ++++++
 LICENSE.md | 21 +++++++++++++++++++++
 2 files changed, 27 insertions(+)
 create mode 100644 .cz.toml
 create mode 100644 LICENSE.md

diff --git a/.cz.toml b/.cz.toml
new file mode 100644
index 0000000..ff8c8fb
--- /dev/null
+++ b/.cz.toml
@@ -0,0 +1,6 @@
+[tool.commitizen]
+bump_message = "build(version): :bookmark: update version from $current_version to $new_version"
+update_changelog_on_bump = true
+version_provider = "uv"
+# Don't regenerate the changelog on every update
+changelog_incremental = true
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..aeed825
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2023-2025 Aarhus University
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

From a4065508b7c7d6f71fd089a3eadf9c7db83ec25e Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Tue, 5 Aug 2025 17:47:58 +0100
Subject: [PATCH 13/30] refactor: :recycle: always have goat counter

---
 template/_quarto.yml.jinja                                   | 5 ++---
 template/docs/site-counter.html.jinja                        | 3 +++
 ... if seedcase_project %}site-counter.html{% endif %}.jinja | 3 ---
 3 files changed, 5 insertions(+), 6 deletions(-)
 create mode 100644 template/docs/site-counter.html.jinja
 delete mode 100644 template/docs/{% if seedcase_project %}site-counter.html{% endif %}.jinja

diff --git a/template/_quarto.yml.jinja b/template/_quarto.yml.jinja
index 9333a7a..b79e8ad 100644
--- a/template/_quarto.yml.jinja
+++ b/template/_quarto.yml.jinja
@@ -60,12 +60,11 @@ quartodoc:
 
 metadata-files:
   - docs/reference/_sidebar.yml
-{% if is_seedcase_project %}
+
 format:
-  seedcase-theme-html:
+  {{ "seedcase-theme-html" if is_seedcase_project else "html" }}:
     include-before-body:
       - "docs/site-counter.html"
-{%- endif %}
 
 editor:
   markdown:
diff --git a/template/docs/site-counter.html.jinja b/template/docs/site-counter.html.jinja
new file mode 100644
index 0000000..b92291e
--- /dev/null
+++ b/template/docs/site-counter.html.jinja
@@ -0,0 +1,3 @@
+<!-- TODO: Set up GoatCounter -->
+<script data-goatcounter="https://{{ github_user }}-{{ package_name }}.goatcounter.com/count" async
+  src="//gc.zgo.at/count.js"></script>
diff --git a/template/docs/{% if seedcase_project %}site-counter.html{% endif %}.jinja b/template/docs/{% if seedcase_project %}site-counter.html{% endif %}.jinja
deleted file mode 100644
index 5156b87..0000000
--- a/template/docs/{% if seedcase_project %}site-counter.html{% endif %}.jinja	
+++ /dev/null
@@ -1,3 +0,0 @@
-<!-- TODO: Set up GoatCounter -->
-<script data-goatcounter="https://seedcase-project-{{ seedcase_short_name }}.goatcounter.com/count" async
-  src="//gc.zgo.at/count.js"></script>

From 694508f99a79f11b090ed419a75d260c84b9d922 Mon Sep 17 00:00:00 2001
From: martonvago <57952344+martonvago@users.noreply.github.com>
Date: Wed, 6 Aug 2025 11:11:30 +0100
Subject: [PATCH 14/30] refactor: :recycle: apply suggestions from code review

Co-authored-by: Luke W. Johnston <lwjohnst86@users.noreply.github.com>
---
 copier.yaml                           |  4 ++--
 justfile                              |  2 --
 template/.github/CODEOWNERS.jinja     | 10 ----------
 template/.github/dependabot.yml.jinja |  2 +-
 template/_quarto.yml.jinja            |  3 ++-
 template/index.qmd.jinja              |  2 +-
 template/justfile.jinja               |  2 +-
 template/pyproject.toml.jinja         |  8 --------
 8 files changed, 7 insertions(+), 26 deletions(-)

diff --git a/copier.yaml b/copier.yaml
index 84c6838..10106a2 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -3,7 +3,7 @@ _subdirectory: template
 # Post-copy commands:
 _tasks:
   # Add dev dependencies
-  - command: "git init -b main && uv add --dev pre-commit ruff typos pytest bandit commitizen genbadge jupyter pytest-cov quartodoc types-tabulate mypy vulture"
+  - command: "git init -b main; uv add --dev pre-commit ruff typos pytest bandit commitizen genbadge jupyter pytest-cov quartodoc types-tabulate mypy vulture"
     when: "{{ _copier_operation == 'copy' }}"
   # If Seedcase project, add seedcase-theme extension
   - command: "just update-quarto-theme"
@@ -109,7 +109,7 @@ review_team:
 
 github_board_number:
   type: str
-  help: "What is the number of the GitHub project board to add issues and PRs to?"
+  help: "What is the GitHub project board number to add issues and PRs to?"
   validator: |
     {% if github_board_number and not github_board_number.isdigit() %}
     The board number must be an integer.
diff --git a/justfile b/justfile
index 2e96a02..d6d658a 100644
--- a/justfile
+++ b/justfile
@@ -60,7 +60,6 @@ test is_seedcase_project:
     --defaults \
     --trust \
     --data github_user="first-last" \
-    --data package_name=$test_name \
     --data is_seedcase_project={{ is_seedcase_project }} \
     --data author_given_name="First" \
     --data author_family_name="Last" \
@@ -96,7 +95,6 @@ test is_seedcase_project:
     --trust \
     --overwrite \
     --data github_user="first-last" \
-    --data package_name=$test_name \
     --data is_seedcase_project={{ is_seedcase_project }} \
     --data author_given_name="First" \
     --data author_family_name="Last" \
diff --git a/template/.github/CODEOWNERS.jinja b/template/.github/CODEOWNERS.jinja
index 172a7e0..bad0bef 100644
--- a/template/.github/CODEOWNERS.jinja
+++ b/template/.github/CODEOWNERS.jinja
@@ -1,13 +1,3 @@
 # All members on Developers team get added to review PRs
 * {{ review_team }}
 
-# Ignore these so we don't get added to sync PRs
-/.github/
-/.vscode/
-/.devcontainer/
-justfile
-.editorconfig
-.gitignore
-ruff.toml
-pyproject.toml
-uv.lock
diff --git a/template/.github/dependabot.yml.jinja b/template/.github/dependabot.yml.jinja
index 76c25b2..627835e 100644
--- a/template/.github/dependabot.yml.jinja
+++ b/template/.github/dependabot.yml.jinja
@@ -1,6 +1,6 @@
 version: 2
 updates:
-  - package-ecosystem: pip
+  - package-ecosystem: uv
     directory: /
     schedule:
       interval: monthly
diff --git a/template/_quarto.yml.jinja b/template/_quarto.yml.jinja
index b79e8ad..dba6b7d 100644
--- a/template/_quarto.yml.jinja
+++ b/template/_quarto.yml.jinja
@@ -7,7 +7,8 @@ project:
     - "index.qmd"
 
 website:
-  title: "{{ 'Seedcase ' ~ (seedcase_short_name | title) if is_seedcase_project else package_name }}"
+  # TODO: Fill in the title of the website.
+  title: ""
   site-url: "{{ homepage }}"
   repo-url: "https://github.com/{{ package_github_repo }}"
   page-navigation: true
diff --git a/template/index.qmd.jinja b/template/index.qmd.jinja
index 2eec46c..2769a9f 100644
--- a/template/index.qmd.jinja
+++ b/template/index.qmd.jinja
@@ -1,3 +1,3 @@
 ---
-title: "Welcome to {{ 'Seedcase ' ~ (seedcase_short_name | title) if is_seedcase_project else package_name }}!"
+title: "Welcome!"
 ---
diff --git a/template/justfile.jinja b/template/justfile.jinja
index cde9811..7f4a1dc 100644
--- a/template/justfile.jinja
+++ b/template/justfile.jinja
@@ -1,7 +1,7 @@
 @_default:
     just --list --unsorted
 
-@_checks: check-python check-unused test-python check-security check-spelling check-commits
+@_checks: check-python check-unused check-security check-spelling check-commits
 @_tests: test-python
 @_builds: build-contributors build-website build-readme
 
diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index 7ae59ce..a12e4c8 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -28,11 +28,3 @@ issues = "https://github.com/{{ package_github_repo }}/issues"
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
-
-[tool.pytest.ini_options]
-addopts = [
-  # A short traceback mode to make it easier to view
-  "--tb=short",
-  # Use the `src/` package
-  "--import-mode=importlib",
-]

From 88fc9be7e53aef10056cc8a0a6c6484147dc6fcc Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 6 Aug 2025 10:12:37 +0000
Subject: [PATCH 15/30] chore(pre-commit): :pencil2: automatic fixes

---
 template/.github/CODEOWNERS.jinja | 1 -
 1 file changed, 1 deletion(-)

diff --git a/template/.github/CODEOWNERS.jinja b/template/.github/CODEOWNERS.jinja
index bad0bef..9681e53 100644
--- a/template/.github/CODEOWNERS.jinja
+++ b/template/.github/CODEOWNERS.jinja
@@ -1,3 +1,2 @@
 # All members on Developers team get added to review PRs
 * {{ review_team }}
-

From 4ce030f829bb2830b4ca9247d7e293101d59b583 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:19:17 +0100
Subject: [PATCH 16/30] refactor: :recycle: do not auto-add seedcase-theme

---
 copier.yaml    | 8 --------
 docs/guide.qmd | 2 ++
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/copier.yaml b/copier.yaml
index 84c6838..bb3be03 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -5,14 +5,6 @@ _tasks:
   # Add dev dependencies
   - command: "git init -b main && uv add --dev pre-commit ruff typos pytest bandit commitizen genbadge jupyter pytest-cov quartodoc types-tabulate mypy vulture"
     when: "{{ _copier_operation == 'copy' }}"
-  # If Seedcase project, add seedcase-theme extension
-  - command: "just update-quarto-theme"
-    when: "{{ _copier_operation == 'copy' and is_seedcase_project }}"
-  # If Seedcase project, use seedcase-theme as project type
-  - command: >-
-      uv run python -c "from pathlib import Path; file = Path('_quarto.yml'); file.write_text(file.read_text().replace('type: website', 'type: seedcase-theme', 1))"
-    when: "{{ _copier_operation == 'copy' and is_seedcase_project }}"
-
 
 # Message to show after generating or regenerating the project successfully
 _message_after_copy: |
diff --git a/docs/guide.qmd b/docs/guide.qmd
index c1c60fb..57c42a3 100644
--- a/docs/guide.qmd
+++ b/docs/guide.qmd
@@ -136,6 +136,8 @@ Project, run:
 just update-quarto-theme
 ```
 
+Then set `seedcase-theme` as your project `type` in `_quarto.yml`.
+
 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.

From becdbe4e80a3b3c97c4de90eada62c48e978b013 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:24:46 +0100
Subject: [PATCH 17/30] docs: :memo: tweak post-install message

---
 copier.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/copier.yaml b/copier.yaml
index f4e5b01..91be0e3 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -30,9 +30,10 @@ _message_after_copy: |
   4. Configure GitHub following this
     [guide](https://guidebook.seedcase-project.org/operations/security#using-github-apps-to-generate-tokens):
 
-    - Install the [auto-release-token](https://github.com/apps/auto-release-token) GitHub App
-    - Create these secrets: UPDATE_VERSION_TOKEN, ADD_TO_BOARD, NETLIFY_AUTH_TOKEN (if using Netlify)
-    - Create these variables: UPDATE_VERSION_APP_ID, ADD_TO_BOARD_APP_ID
+    - Install the [auto-release-token](https://github.com/apps/auto-release-token)
+      and [add-to-board-token](https://github.com/apps/add-to-board-token) GitHub Apps
+    - Create an `UPDATE_VERSION_TOKEN` and `ADD_TO_BOARD_TOKEN` secret for the GitHub Apps
+    - Create an `UPDATE_VERSION_APP_ID` and `ADD_TO_BOARD_APP_ID` variable of the GitHub Apps' IDs
 
   5. List and complete all TODO items in the repository:
 

From 02181b8d9c77b05310d9834cc8d27c75d44ac1c2 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:26:08 +0100
Subject: [PATCH 18/30] chore: :wrench: change justfile.jinja file association

---
 .vscode/settings.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 6ec6d96..346d266 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -30,7 +30,7 @@
   "python.languageServer": "Pylance",
   "files.insertFinalNewline": true,
   "files.associations": {
-    "justfile.jinja": "django-txt",
+    "justfile.jinja": "plaintext",
     "*.yml.jinja": "jinja-yaml",
     "*.cff.jinja": "jinja-yaml",
     "*.toml.jinja": "jinja-toml",

From 471e8c3438f7688dfed7e170cf91c00b47b03b15 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:35:28 +0100
Subject: [PATCH 19/30] refactor: :recycle: extract github_user from
 package_github_repo

---
 copier.yaml | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/copier.yaml b/copier.yaml
index 91be0e3..bfe6617 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -40,14 +40,20 @@ _message_after_copy: |
     $ just list-todos
 
 # Questions:
-github_user:
+package_github_repo:
   type: str
-  help: "What is the GitHub username of the person or organisation who owns the package?"
+  help: "What is or will be the GitHub repository spec for the project?"
+  placeholder: "user/repo"
   validator: |
-    {% if github_user and not (github_user | regex_search('^[\w.-]+$')) %}
-    Must contain only alphanumeric characters and `_`, `-`, or `.`.
+    {% if package_github_repo and not (package_github_repo | regex_search('^[\w.-]+\/[\w.-]+$')) %}
+    Must be in the format `user/repo` and contain only alphanumeric characters and `_`, `-`, or `.`.
     {% endif %}
 
+github_user:
+  type: str
+  default: "{{ package_github_repo.split('/')[0] if package_github_repo else '' }}"
+  when: false
+
 package_name:
   type: str
   help: "What is the name of the package?"
@@ -62,11 +68,6 @@ package_name_snake_case:
   default: "{{package_name | replace('-', '_') | replace('.', '_')}}"
   when: false
 
-package_github_repo:
-  type: str
-  default: "{{ github_user ~ '/' ~ package_name }}"
-  when: false
-
 is_seedcase_project:
   type: bool
   help: "Is this package part of the Seedcase Project?"

From 431f2a405fabe9cafc07676abf553b5e1537c806 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:39:24 +0100
Subject: [PATCH 20/30] refactor: :recycle: remove seedcase_short_name

---
 copier.yaml                | 8 +-------
 template/_quarto.yml.jinja | 4 ++--
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/copier.yaml b/copier.yaml
index bfe6617..92ad684 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -73,16 +73,10 @@ is_seedcase_project:
   help: "Is this package part of the Seedcase Project?"
   default: "{{ github_user == 'seedcase-project' }}"
 
-seedcase_short_name:
-  type: str
-  help: "What is the short name of the package?"
-  default: "{{ package_name[9:] if ('seedcase-' in package_name) else '' }}"
-  when: "{{ is_seedcase_project }}"
-
 homepage:
   type: str
   help: "What is the homepage of your project?"
-  default: "{{ 'https://%s.seedcase-project.org' % seedcase_short_name if is_seedcase_project else '' }}"
+  default: "{{ 'https://%s.seedcase-project.org' % package_name if is_seedcase_project else '' }}"
 
 author_given_name:
   type: str
diff --git a/template/_quarto.yml.jinja b/template/_quarto.yml.jinja
index dba6b7d..70efacc 100644
--- a/template/_quarto.yml.jinja
+++ b/template/_quarto.yml.jinja
@@ -16,8 +16,8 @@ website:
     pinned: true
     title: false
     {%- if is_seedcase_project %}
-    logo: "_extensions/seedcase-project/seedcase-theme/logos/navbar-logo-seedcase-{{ seedcase_short_name }}.svg"
-    logo-alt: "Seedcase {{ seedcase_short_name | title }} logo: Main page"
+    logo: "_extensions/seedcase-project/seedcase-theme/logos/navbar-logo-{{ package_name }}.svg"
+    logo-alt: "{{ package_name }} logo: Main page"
     {%- else %}
     # TODO: add logo
     logo: ""

From ab59e84f44fab177d7f5e1e2fc7bc2db900d537f Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:41:33 +0100
Subject: [PATCH 21/30] refactor: :recycle: do not template PR assignee

---
 copier.yaml                                               | 4 ----
 justfile                                                  | 6 ++----
 template/.github/{dependabot.yml.jinja => dependabot.yml} | 4 ----
 3 files changed, 2 insertions(+), 12 deletions(-)
 rename template/.github/{dependabot.yml.jinja => dependabot.yml} (67%)

diff --git a/copier.yaml b/copier.yaml
index 92ad684..7bcd79b 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -107,7 +107,3 @@ copyright_year:
   type: str
   default: "{{ copyright_year | default('%Y' | strftime) }}"
   when: false
-
-dependabot_pr_assignee:
-  type: str
-  help: "What is the GitHub username of the person to assign to PRs opened by dependabot?"
diff --git a/justfile b/justfile
index d6d658a..8d523a3 100644
--- a/justfile
+++ b/justfile
@@ -65,8 +65,7 @@ test is_seedcase_project:
     --data author_family_name="Last" \
     --data author_email="first.last@example.com" \
     --data review_team="@first-last/developers" \
-    --data github_board_number=22 \
-    --data dependabot_pr_assignee="mango90"
+    --data github_board_number=22
   # Run checks in the generated test Python package
   cd $test_dir
   git add .
@@ -100,8 +99,7 @@ test is_seedcase_project:
     --data author_family_name="Last" \
     --data author_email="first.last@example.com" \
     --data review_team="@first-last/developers" \
-    --data github_board_number=22 \
-    --data dependabot_pr_assignee="mango90"
+    --data github_board_number=22
 
 # Clean up any leftover and temporary build files
 cleanup:
diff --git a/template/.github/dependabot.yml.jinja b/template/.github/dependabot.yml
similarity index 67%
rename from template/.github/dependabot.yml.jinja
rename to template/.github/dependabot.yml
index 627835e..3a50f8a 100644
--- a/template/.github/dependabot.yml.jinja
+++ b/template/.github/dependabot.yml
@@ -8,7 +8,3 @@ updates:
     commit-message:
       prefix: build
       include: scope
-{%- if dependabot_pr_assignee %}
-    assignees:
-      - "{{ dependabot_pr_assignee }}"
-{% endif %}

From a0b401e38a2591825a9ec2bcdeb43a133235568e Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:52:35 +0100
Subject: [PATCH 22/30] refactor: :recycle: make house icon Seedcase-only

---
 template/_quarto.yml.jinja | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/template/_quarto.yml.jinja b/template/_quarto.yml.jinja
index 70efacc..751e1a5 100644
--- a/template/_quarto.yml.jinja
+++ b/template/_quarto.yml.jinja
@@ -32,9 +32,11 @@ website:
       - icon: github
         href: "https://github.com/{{ package_github_repo }}"
         aria-label: "GitHub icon: Source code"
+      {% if is_seedcase_project -%}
       - icon: house
-        href: "{{ 'https://seedcase-project.org' if is_seedcase_project else homepage }}"
-        aria-label: "House icon: {{ 'Seedcase Project' if is_seedcase_project else package_name }} home page"
+        href: "https://seedcase-project.org"
+        aria-label: "House icon: Main website for the Seedcase Project"
+      {% endif %}
   sidebar:
     - id: design
       pinned: true

From 2bb14f04cfd72ad3d2db9e25d9bc2479e4fbfa90 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:55:10 +0100
Subject: [PATCH 23/30] chore: :truck: remove .jinja from index file

---
 template/{index.qmd.jinja => index.qmd} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename template/{index.qmd.jinja => index.qmd} (100%)

diff --git a/template/index.qmd.jinja b/template/index.qmd
similarity index 100%
rename from template/index.qmd.jinja
rename to template/index.qmd

From 99e456a8448e26b77dcdcc912871ad974119b246 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:55:53 +0100
Subject: [PATCH 24/30] build: :wrench: add recipes to justfile

---
 template/justfile.jinja | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/template/justfile.jinja b/template/justfile.jinja
index 7f4a1dc..ab72553 100644
--- a/template/justfile.jinja
+++ b/template/justfile.jinja
@@ -112,3 +112,11 @@ build-readme:
 # Generate a Quarto include file with the contributors
 build-contributors:
   sh ./tools/get-contributors.sh {{ package_github_repo }}
+
+# Check for and apply updates from the template
+update-from-template:
+  uvx copier update --trust --defaults
+
+# Reset repo changes to match the template
+reset-from-template:
+  uvx copier recopy --trust --defaults

From e34cc61b57871bb443cb2bd7e9490c6c86651ede Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:56:20 +0100
Subject: [PATCH 25/30] test: preparing to recopy from the template

---
 .cz.toml | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 .cz.toml

diff --git a/.cz.toml b/.cz.toml
deleted file mode 100644
index ff8c8fb..0000000
--- a/.cz.toml
+++ /dev/null
@@ -1,6 +0,0 @@
-[tool.commitizen]
-bump_message = "build(version): :bookmark: update version from $current_version to $new_version"
-update_changelog_on_bump = true
-version_provider = "uv"
-# Don't regenerate the changelog on every update
-changelog_incremental = true

From 1184ed27e7ccaf3111ff02a32008d4f74d0f636d Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 11:56:20 +0100
Subject: [PATCH 26/30] test: preparing to copy onto an existing package

---
 LICENSE.md | 21 ---------------------
 1 file changed, 21 deletions(-)
 delete mode 100644 LICENSE.md

diff --git a/LICENSE.md b/LICENSE.md
deleted file mode 100644
index aeed825..0000000
--- a/LICENSE.md
+++ /dev/null
@@ -1,21 +0,0 @@
-# MIT License
-
-Copyright (c) 2023-2025 Aarhus University
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

From 28b072ae32144f0744aa2b18923fa7c8397cd335 Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 12:02:03 +0100
Subject: [PATCH 27/30] fix: :bug: fix copier test

---
 .cz.toml | 6 ++++++
 justfile | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)
 create mode 100644 .cz.toml

diff --git a/.cz.toml b/.cz.toml
new file mode 100644
index 0000000..ff8c8fb
--- /dev/null
+++ b/.cz.toml
@@ -0,0 +1,6 @@
+[tool.commitizen]
+bump_message = "build(version): :bookmark: update version from $current_version to $new_version"
+update_changelog_on_bump = true
+version_provider = "uv"
+# Don't regenerate the changelog on every update
+changelog_incremental = true
diff --git a/justfile b/justfile
index 8d523a3..9fdf690 100644
--- a/justfile
+++ b/justfile
@@ -59,7 +59,7 @@ test is_seedcase_project:
     --vcs-ref=$commit \
     --defaults \
     --trust \
-    --data github_user="first-last" \
+    --data package_github_repo="first-last/repo" \
     --data is_seedcase_project={{ is_seedcase_project }} \
     --data author_given_name="First" \
     --data author_family_name="Last" \
@@ -93,7 +93,7 @@ test is_seedcase_project:
     --defaults \
     --trust \
     --overwrite \
-    --data github_user="first-last" \
+    --data package_github_repo="first-last/repo" \
     --data is_seedcase_project={{ is_seedcase_project }} \
     --data author_given_name="First" \
     --data author_family_name="Last" \

From 267be141639ce0e8186f551d5acd675d790b780d Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Wed, 6 Aug 2025 12:08:53 +0100
Subject: [PATCH 28/30] fix: :bug: add back LICENSE

---
 LICENSE.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 LICENSE.md

diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..aeed825
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2023-2025 Aarhus University
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

From 4d0a3f4f1ec3608088720a42f55ac185f647943d Mon Sep 17 00:00:00 2001
From: martonvago <marci.vago@gmail.com>
Date: Thu, 7 Aug 2025 16:54:41 +0100
Subject: [PATCH 29/30] build: :wrench: use latest get-contributors.sh in
 template

---
 template/tools/get-contributors.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/template/tools/get-contributors.sh b/template/tools/get-contributors.sh
index 65bfbb4..40aea37 100644
--- a/template/tools/get-contributors.sh
+++ b/template/tools/get-contributors.sh
@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
 
 # Get a list of contributors to this repository and save it to
-# _contributors.qmd.tmp file. It also:
+# _contributors.qmd file (overwritten if it exists). It also:
 #
 # - Formats users into Markdown links to their GitHub profiles.
 # - Removes any usernames with the word "bot" in them.
 # - Removes the trailing comma from the list.
 repo_spec=${1}
-echo "These are the people who have contributed by submitting changes through pull requests :tada:\n\n" > _contributors.qmd.tmp
+echo "These are the people who have contributed by submitting changes through pull requests :tada:\n\n" > _contributors.qmd
 gh api \
   -H "Accept: application/vnd.github+json" \
   -H "X-GitHub-Api-Version: 2022-11-28" \
@@ -15,4 +15,4 @@ gh api \
   --template '{{range .}} [\@{{.login}}]({{.html_url}}){{"\n"}}{{end}}' | \
   grep -v "\[bot\]" | \
   tr '\n' ', ' | \
-  sed -e 's/,$//' >> _contributors.qmd.tmp
+  sed -e 's/,$//' >> _contributors.qmd

From 5173c990951b3b7faa0a79391fa5b5c568ac6c12 Mon Sep 17 00:00:00 2001
From: "Luke W. Johnston" <lwjohnst86@users.noreply.github.com>
Date: Fri, 8 Aug 2025 09:16:00 +0200
Subject: [PATCH 30/30] refactor: strip empty jinja lines

---
 template/_quarto.yml.jinja | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/template/_quarto.yml.jinja b/template/_quarto.yml.jinja
index 751e1a5..cf7c3ab 100644
--- a/template/_quarto.yml.jinja
+++ b/template/_quarto.yml.jinja
@@ -36,7 +36,7 @@ website:
       - icon: house
         href: "https://seedcase-project.org"
         aria-label: "House icon: Main website for the Seedcase Project"
-      {% endif %}
+      {%- endif %}
   sidebar:
     - id: design
       pinned: true