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refactor: ♻️ convert to using updated template data package (#29)
# Description This PR updates the repo to use the updated `template-data-package`. It also starts the process of using the `*_properties.py` scripts in `main.py`. For this PR, I've followed the Sprout [Creating a Data Package](https://sprout.seedcase-project.org/docs/guide/packages) guide and updated the package properties and `datapackage.json` and `README.md` by uncommenting those steps in `main.py`. I'll do a separate PR that adds the data resources and updates the preprocessing scripts. Closes #23 This PR needs an in-depth review. ## Checklist - [X] Ran `just run-all` (fails bc some comment lines are too long in `scripts/download-data.py` and `scripts/convert-meta.py`, will fix in a separate PR adding the data resources) --------- Co-authored-by: Luke W. Johnston <lwjohnst86@users.noreply.github.com>
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‎.copier-answers.yml‎

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# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
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_commit: 0.15.3
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_src_path: gh:seedcase-project/template-data-package
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author_email: signekb@clin.au.dk
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author_family_name: Brødbæk
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author_given_name: Signe Kirk
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cc0_license: true
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copyright_year: '2025'
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github_board_number: '18'
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package_abbrev: example-rhesus-monkeys
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package_github_repo: seedcase-project/example-rhesus-monkeys
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review_team: '@seedcase-project/developers'

‎.cz.toml‎

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[tool.commitizen]
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version = "0.3.1"
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bump_message = "build(version): :bookmark: update version from $current_version to $new_version [skip ci]"
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version_schema = "semver"
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version_provider = "commitizen"
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bump_message = "build(version): :bookmark: update version from $current_version to $new_version"
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update_changelog_on_bump = true
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version_provider = "uv"
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version_files = [
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"pyproject.toml:version",
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"scripts/package_properties.py:version",
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"datapackage.json:version"
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]
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# Don't regenerate the changelog on every update
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changelog_incremental = true

‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: github-actions
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directory: /
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schedule:
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interval: monthly
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commit-message:
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prefix: ci
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include: scope
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- package-ecosystem: uv
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directory: /
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schedule:
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interval: monthly
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commit-message:
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prefix: build
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include: scope

‎.github/pull_request_template.md‎

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# Description
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3-
These changes EXPLANATION
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Closes #
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This PR needs a quick/an in-depth review.
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## Checklist
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- [ ] Formatted Markdown
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- [ ] Ran `just run-all`
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- [ ] Format Markdown
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- [ ] Run `just run-all`

‎.github/workflows/add-to-project.yml‎

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- reopened
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- opened
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permissions:
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pull-requests: write
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# Limit token permissions for security
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permissions: read-all
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jobs:
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add-to-project:
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uses: seedcase-project/.github/.github/workflows/reusable-add-to-project.yml@main
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permissions:
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pull-requests: write
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with:
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board-number: 18
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app-id: ${{ vars.ADD_TO_BOARD_APP_ID }}

‎.github/workflows/release-package.yml‎

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name: Release package
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on:
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push:
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branches:
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- main
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# Limit token permissions for security
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permissions: read-all
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jobs:
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release:
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# This job outputs env variables `previous_version` and `current_version`.
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# Only give permissions for this job.
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permissions:
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contents: write
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uses: seedcase-project/.github/.github/workflows/reusable-release-project.yml@main
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with:
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app-id: ${{ vars.UPDATE_VERSION_APP_ID }}
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secrets:
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update-version-gh-token: ${{ secrets.UPDATE_VERSION_TOKEN }}

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

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

‎.gitignore‎

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_ignore
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bin/
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dev/
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_temp/
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# Temporary files
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*.tmp
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__pycache__/
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*.py[cod]
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# Raw data files and folders
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*.parquet
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*.csv
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/data-raw/
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/raw/
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/data/
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# MacOS
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.DS_Store
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# Quarto
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/.quarto/
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docs/.quarto/
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# Quartodoc
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objects.json
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*.ipynb
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*.quarto_ipynb
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*_files/
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# Website generation
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_site
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_book
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public
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site
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# Misc files
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*.log

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/gitleaks/gitleaks
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rev: v8.28.0
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rev: v8.27.2
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hooks:
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- id: gitleaks
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v6.0.0
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-merge-conflict
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args: [--assume-in-merge]
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- repo: https://github.com/commitizen-tools/commitizen
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rev: v4.8.3

‎.typos.toml‎

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[files]
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extend-exclude = [
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"*.json",
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"*.csv"
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]

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