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Add template #1

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merged 38 commits into from
Mar 12, 2025
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e148639
Move to pixi
irm-codebase Mar 4, 2025
467e7a9
Separete pyproject into individual configuration files
irm-codebase Mar 4, 2025
ca4796b
Add pixi tests
irm-codebase Mar 4, 2025
34cb537
Move integration tests within the template
irm-codebase Mar 4, 2025
2d46514
Merge branch 'main' into add-template
irm-codebase Mar 4, 2025
b11be15
update README
irm-codebase Mar 4, 2025
18166bd
Add scheduled workflow for copier template updates.
irm-codebase Mar 5, 2025
353376e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 5, 2025
5aec108
Add PR CI and avoid snakefmt template false positive
irm-codebase Mar 5, 2025
2828bee
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 5, 2025
1fb55eb
Fix CI
irm-codebase Mar 5, 2025
cf6592d
use miniconda incubator in CI
irm-codebase Mar 5, 2025
cb225a9
Add local mamba dependency
irm-codebase Mar 5, 2025
d83d963
switch mamba-> conda
irm-codebase Mar 5, 2025
7146a52
Try pixi local and mini-forge in global
irm-codebase Mar 5, 2025
7524b37
Use pixi with conda dependency
irm-codebase Mar 5, 2025
827c665
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 5, 2025
eecaa11
Avoid windows bug: shell commands must use \"
irm-codebase Mar 5, 2025
e1898c1
Specify locations to skip for the template
irm-codebase Mar 5, 2025
a1a5d99
Add pull request CI test to the template.
irm-codebase Mar 5, 2025
af272a1
update readme and changelog
irm-codebase Mar 5, 2025
573246b
PR fixes: add examples to docs, avoid name confusion
irm-codebase Mar 6, 2025
30e1198
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 6, 2025
d1d896d
Improve the explanation in the README
irm-codebase Mar 6, 2025
86fc03d
Use conda-forge to install clio-tools
irm-codebase Mar 6, 2025
65d0e4b
PR fixes: no pixi shell use, remove unused mkdocs plugin, fix github …
irm-codebase Mar 7, 2025
81f1b95
Fix integration test configuration path
irm-codebase Mar 7, 2025
cf5fb7f
Fix relative path bug
irm-codebase Mar 7, 2025
ff5c1b6
Minor docs updates
brynpickering Mar 7, 2025
bb24ded
Update highlight to tip
brynpickering Mar 7, 2025
977c0ba
Remove attempt at highlighting
brynpickering Mar 7, 2025
13cbe9d
Update tests/utils/simple_answers.yaml
sjpfenninger Mar 11, 2025
1098a91
Update tests/utils/simple_answers.yaml
sjpfenninger Mar 11, 2025
d11f453
Update copier.yaml
irm-codebase Mar 11, 2025
71ff30c
Update README.md
irm-codebase Mar 11, 2025
61d9590
PR fixes: improve instructions, improve integration test.
irm-codebase Mar 11, 2025
bd0428d
Remove mermaid
irm-codebase Mar 11, 2025
e8b7571
Simplify: read the docs is optional, improve README
irm-codebase Mar 12, 2025
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22 changes: 22 additions & 0 deletions .editorconfig
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# Documentation: https://EditorConfig.org
# Inspired by Django .editorconfig file

root = true

[*]
indent_style = space
indent_size = 4
trim_trailing_whitespace = true
end_of_line = lf
insert_final_newline = true
charset = utf-8

[*.{yaml,yml,cff}]
indent_size = 2

[*.md]
trim_trailing_whitespace = true
indent_size = 4

[*.{diff,patch}]
trim_trailing_whitespace = false
2 changes: 2 additions & 0 deletions .gitattributes
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# SCM syntax highlighting & preventing 3-way merges
pixi.lock merge=binary linguist-language=YAML linguist-generated=true
21 changes: 21 additions & 0 deletions .github/workflows/pr-ci.yml
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name: CI

on:
pull_request:
branches: [ main ]

jobs:
build:
name: Build
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
python-version: ["3.12"]
steps:
- uses: actions/checkout@v4
- name: setup-pixi
uses: prefix-dev/setup-pixi@v0.8.3
- name: Run tests
run: pixi run test
28 changes: 28 additions & 0 deletions .gitignore
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### OS-specific
.DS_Store

### Editors
*~
\#*\#
**/.vscode
.$*

### Byte-compiled files
__pycache__
*.pyc
*.egg-info

### Snakemake
.snakemake/
gurobi.log

### Notebooks
.ipynb_checkpoints

# Mutable / cache folders
tmp/
temp/
.cache/
.pytest_cache/
.mypy_cache/
.ruff_cache/
3 changes: 3 additions & 0 deletions .pixi/.gitignore
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*
!.gitignore
!config.toml
1 change: 1 addition & 0 deletions .pixi/config.toml
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pinning-strategy = "latest-up"
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This just affects what happens when somebody runs pixi add, right? Is this a policy that we always want to have >= pinning?

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In general, I think it's best to go for latest-up for development to avoid version conflicts.
It just leads to headaches in many cases (see here for arguments against it plus dog pictures).

pixi will take care of locking regardless. Versions will only change if someone runs pixi upgrade

The exception are environment.yaml files, because rules are closer to applications, and they should use specific versions (pandas = 2.0.2)

40 changes: 40 additions & 0 deletions .pre-commit-config.yaml
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default_language_version:
python: python3

repos:
# Generic 'file quality' testing
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
hooks:
# Machine-friendliness
- id: trailing-whitespace
- id: end-of-file-fixer
# Repo quality
- id: check-added-large-files
args: [--enforce-all]
- id: forbid-submodules
- id: check-case-conflict
- id: check-illegal-windows-names
- id: check-merge-conflict
- id: debug-statements
# Detect config. file issues
- id: check-json
- id: check-yaml
args: [--unsafe]

# Python file formatting
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.9.9
hooks:
- id: ruff
args: [--fix, --exit-non-zero-on-fix]
- id: ruff-format

# Spelling
- repo: https://github.com/codespell-project/codespell
rev: v2.4.1
hooks:
- id: codespell

ci: # https://pre-commit.ci/
autoupdate_schedule: monthly
7 changes: 7 additions & 0 deletions AUTHORS
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This is the list of contributors for copyright purposes.

This does not necessarily list everyone who has contributed to this software's
code or documentation. For a full contributor list, see:
<https://github.com/calliope-project/data-module-template/graphs/contributors>

Ivan Ruiz Manuel, TU Delft <i.ruizmanuel@tudelft.nl>
9 changes: 9 additions & 0 deletions CHANGELOG
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# Changelog

## 0.1.0

### Added

- Module copier template with standard testing and automated docs.
- CI checks for formatting and execution in major platforms
- pixi environment with a lockfile and fully isolated dependencies.
12 changes: 12 additions & 0 deletions CITATION.cff
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# Citation file
# For more information, see:
# https://citation-file-format.github.io/
cff-version: 1.2.0
message: If you use this software or data produced by it, please cite it using the metadata from this file.
title: clio - data module template
repository: https://github.com/calliope-project/data-module-template
license: Apache-2.0
authors:
- given-names: Ivan
family-names: Ruiz Manuel
orcid: https://orcid.org/0000-0003-2288-6423
201 changes: 201 additions & 0 deletions LICENSE
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