build: 🔧 update config for non-template package

.github/workflows/build-website.yml

@@ -10,7 +10,7 @@ permissions: read-all
 
 jobs:
   build-website:
-    uses: seedcase-project/.github/.github/workflows/reusable-build-docs-with-python.yml@main
+    uses: seedcase-project/.github/.github/workflows/reusable-build-docs.yml@main
     secrets:
       netlify-token: ${{ secrets.NETLIFY_AUTH_TOKEN }}
       # This is to allow using `gh` CLI

.gitignore

@@ -26,41 +26,6 @@ venv
 __pycache__/
 *.py[cod]
 
-# Python packaging and distribution
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# Python testing and code coverage
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-coverage.*
-.cache
-nosetests.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-
 # MacOS
 .DS_Store
 

.vscode/extensions.json

@@ -7,13 +7,9 @@
     "felipecaputo.git-project-manager",
     "GitHub.vscode-pull-request-github",
     "ms-python.python",
-    "ms-python.vscode-pylance",
-    "matangover.mypy",
-    "njpwerner.autodocstring",
     "quarto.quarto",
     "ms-toolsai.jupyter",
     "vivaxy.vscode-conventional-commits",
-    "charliermarsh.ruff",
     "pshaddel.conventional-branch",
     "tekumara.typos-vscode",
     "EditorConfig.EditorConfig"

.vscode/settings.json

@@ -26,13 +26,13 @@
   "[quarto][qmd]": {
     "editor.formatOnSave": false
   },
-  "[python]": {
-    "editor.defaultFormatter": "charliermarsh.ruff"
-  },
   "python.defaultInterpreterPath": "${workspaceFolder}/.venv",
   "python.languageServer": "Pylance",
   "files.insertFinalNewline": true,
-  "python.testing.pytestEnabled": true,
-  "python.testing.pytestPath": "${workspaceFolder}/.venv/bin/pytest",
-  "mypy.runUsingActiveInterpreter": true,
+  "files.associations": {
+    "*.yml.jinja": "jinja-yaml",
+    "*.cff.jinja": "jinja-yaml",
+    "*.toml.jinja": "jinja-toml",
+    "*.qmd.jinja": "jinja-md"
+  },
 }

README.md

@@ -1,6 +1,11 @@
+
+
 # Template for Seedcase Python packages
 
-This repository contains a template for setting up new Python package projects in Seedcase. The first step is to create a new repository using this template. This can easily be done by clicking the "Use this template" button on the repository page or by using the GitHub CLI:
+This repository contains a template for setting up new Python package
+projects in Seedcase. The first step is to create a new repository using
+this template. This can easily be done by clicking the “Use this
+template” button on the repository page or by using the GitHub CLI:
 
 ``` bash
 # NAME is the name to give the new repository
@@ -9,11 +14,14 @@ gh repo create NAME --template seedcase-project/template-python-project
 
 ## Setting things up after cloning
 
-Search for `NAME` and `REPO` and replace them with the name of your project and the repository name. Then look for any `TODO` items.
+Search for `NAME` and `REPO` and replace them with the name of your
+project and the repository name. Then look for any `TODO` items.
 
 ## Setting things up
 
-Use the commands found in [`spaid`](https://github.com/seedcase-project/spaid) repo to run the next setup steps.
+Use the commands found in
+[`spaid`](https://github.com/seedcase-project/spaid) repo to run the
+next setup steps.
 
 Need to install these packages after:
 

README.qmd

@@ -0,0 +1,23 @@
+# Template for Seedcase Python packages
+
+This repository contains a template for setting up new Python package projects in Seedcase. The first step is to create a new repository using this template. This can easily be done by clicking the "Use this template" button on the repository page or by using the GitHub CLI:
+
+``` bash
+# NAME is the name to give the new repository
+gh repo create NAME --template seedcase-project/template-python-project
+```
+
+## Setting things up after cloning
+
+Search for `NAME` and `REPO` and replace them with the name of your project and the repository name. Then look for any `TODO` items.
+
+## Setting things up
+
+Use the commands found in [`spaid`](https://github.com/seedcase-project/spaid) repo to run the next setup steps.
+
+Need to install these packages after:
+
+``` bash
+uv add --dev pre-commit ruff typos pytest bandit commitizen \
+    genbadge jupyter pytest-cov quartodoc
+```

_publish.yml

@@ -1,5 +1,4 @@
 - source: project
   netlify:
-    # TODO: Include correct ID
-    - id: ""
-      url: "https://NAME-seedcase-project.netlify.app"
+    - id: "8775b18b-3a1a-4dfc-b6c7-a1ef7205d30f"
+      url: "https://seedcase-template-python-package.netlify.app"

justfile

@@ -1,8 +1,11 @@
 @_default:
     just --list --unsorted
 
+@_checks: 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
+run-all: update-quarto-theme update-template _checks test _builds
 
 # Install the pre-commit hooks
 install-precommit:
@@ -13,78 +16,52 @@ 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 .
+# Update the Quarto seedcase-theme extension
+update-quarto-theme:
+  quarto add seedcase-project/seedcase-theme --no-prompt
 
-# Reformat Python code to match coding style and general structure
-format-python:
-  uv run ruff check --fix .
-  uv run ruff format .
+# Update files in the template from the copier parent folder
+update-template:
+  cp .cz.toml .pre-commit-config.yaml .typos.toml .editorconfig 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/
 
-# 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
+
+# Test and check that a Python package can be created from the template
+# TODO: add test for copier
+test:
+  echo "copier test"
+
+# 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
 
-# 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
+# Re-build the README file from the Quarto version
+build-readme:
+  uvx --from quarto quarto render README.qmd --to gfm
 
-# 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
+# Generate a Quarto include file with the contributors
+build-contributors:
+  sh ./tools/get-contributors.sh seedcase-project/template-workshop

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