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irm-codebasepre-commit-ci[bot]
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Update copier CI action and add snakemake linting (#9)
* Ensure the module looks nice in the snakemake catalog * Improve .gitignore file omissions * Use templated github workflows for releases, PRs, and tempalte version checking * Add useful tools to pixi (ipdb, ipykernel) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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‎.github/workflows/release.yml‎

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name: Release
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on:
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release:
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types: [released]
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jobs:
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add-latest-tag:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Run latest-tag
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uses: EndBug/latest-tag@v1.6.2
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with:
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# Name of the tag.
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ref: latest

‎.github/workflows/template-check-version.yml‎

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# Adapted from https://github.com/arup-group/actions-city-modelling-lab/blob/main/.github/workflows/template-check.yml
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# MIT licensed
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name: Reusable workflow for keeping up-to-date with template changes.
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on:
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workflow_call:
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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copier-issue:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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issues: write
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env:
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UPDATE: "false"
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steps:
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- uses: actions/checkout@v4
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with:
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ref: "latest" # This avoids comparing against development versions.
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- name: Setup pixi
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uses: prefix-dev/setup-pixi@v0.8.3
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- name: Add copier
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run: pixi add copier
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- name: Add dummy GitHub credentials
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run: |
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git config --global user.name Copier update
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git config --global user.email check@dummy.bot.com
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- name: Run copier update
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run: pixi run copier update --skip-answered --defaults
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- name: Check for template changes
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run: test -z "$(git status --porcelain)" || echo "UPDATE=true" >> $GITHUB_ENV
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- name: Open issue
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if: env.UPDATE == 'true'
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run: |
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gh issue --repo ${{ github.repository }} \
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create --title "Template update" --body "The template has been updated. Please run `copier update` and merge changes."
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/template-pr-ci.yml‎

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name: Reusable Pull Request CI tests for modules
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on:
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workflow_call:
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jobs:
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build:
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name: Build
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, windows-latest, macos-latest]
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python-version: ["3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: setup-pixi
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uses: prefix-dev/setup-pixi@v0.8.3
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- name: Run tests
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run: pixi run test
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- name: Run linting
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run: pixi run snakemake --lint

‎.github/workflows/template-release.yml‎

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name: Reusable release workflow for modules
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on:
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workflow_call:
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jobs:
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add-latest-tag:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Run latest-tag
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uses: EndBug/latest-tag@v1.6.2
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with:
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# Name of the tag.
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ref: latest

‎README.md‎

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> - **Please be sure to maintain the following files to ensure `clio` compatibility**
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> - These are:
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> - `INTERFACE.yaml`: a simple description of the module's input/output structure.
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> - `config/example.yaml`: a basic functioning example of how to configure this module.
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> - `config/config.yaml`: a basic functioning example of how to configure this module.
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> - `workflow/internal/config.schema.yaml`: the module's configuration schema, used by `snakemake` for [validation](https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html).
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> - `AUTHORS` / `CITATION.cff` / `LICENSE`: licensing and attribution of this module's code and methods.
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> - If the optional auto-generated documentation was selected, `docs/hooks/clio_standard.py` will use these files to automatically generate a basic Read the Docs website.

‎copier.yaml‎

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_min_copier_version: '9.4.1'
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_subdirectory: template
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_skip_if_exists:
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- config/example.yaml
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- docs/ # documentation must be present, but we do not enforce its shape
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- tests/ # Tests must be present, but we do not enforce their content
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- "!tests/clio_test.py" # except for the set of standard tests
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- workflow/ # A workflow must be present, but it can have anything within it
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- "!workflow/profiles/default/config.yaml" # except that the profile must not change
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# Respect user changes, except for a few standard files.
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- config/*
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- "!config/README.md" # Necessary for the snakemake workflow catalog
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- docs/*
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- resources/*
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- results/*
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- tests/*
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- "!tests/clio_test.py" # Standard integration tests
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- workflow/
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- "!workflow/profiles" # Profiles should be equal across projects
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- AUTHORS
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- CITATION.cff
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- INTERFACE.yaml
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- pixi.toml
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- README.md
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_templates_suffix: .jinja
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_answers_file: .copier-answers.yml
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‎pixi.toml‎

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[project]
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name = "data-module-template"
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version = "0.1.0"
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authors = ["See AUTHORS file"]
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description = "A template for `clio` data modules."
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license = "Apache-2.0"

‎template/.github/issue_template.md‎

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## Problem description
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<!-- Describe the problem or error here -->
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## Steps to reproduce the problem
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<!-- Describe the steps needed to reproduce the problem here -->
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<!-- We recommend including the configuration and user resources used. -->
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## Module version
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<!-- Exact module version used -->

‎template/.github/pull_request_template.md‎

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Fixes #
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## Summary of changes in this pull request
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*
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*
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*
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## Reviewer checklist
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* [ ] `INTERFACE.yaml` is up-to-date with all relevant user resources and results.
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* [ ] The integration example is up-to-date with a minimal use-case of the module.
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* [ ] Module documentation is up-to-date.

‎template/.github/workflows/check-latest-template-spec.yml‎

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