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LucaMarconatoLucaMarconato
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package structure; change license MIT -> BDS3
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‎.codecov.yaml‎

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# Based on pydata/xarray
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codecov:
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require_ci_to_pass: no
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coverage:
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status:
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project:
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default:
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# Require 1% coverage, i.e., always succeed
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target: 1
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patch: false
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changes: false
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comment:
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layout: diff, flags, files
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behavior: once
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require_base: no

‎.cruft.json‎

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "a370e73f7e342f377fee8e902111bbe2bca30b3b",
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"checkout": null,
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"context": {
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"cookiecutter": {
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"project_name": "ngff-transformations",
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"package_name": "ngff_transformations",
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"project_description": "Apply and manipulate NGFF coordinate transformations",
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"author_full_name": "Luca Marconato",
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"author_email": "luca.marconato@scverse.org",
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"github_user": "BioImageTools",
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"github_repo": "ngff-transformations",
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"license": "BSD 3-Clause License",
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"ide_integration": false,
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"_copy_without_render": [
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".github/workflows/build.yaml",
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".github/workflows/test.yaml",
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"docs/_templates/autosummary/**.rst"
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],
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"_exclude_on_template_update": [
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"CHANGELOG.md",
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"LICENSE",
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"README.md",
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"docs/api.md",
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"docs/index.md",
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"docs/notebooks/example.ipynb",
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"docs/references.bib",
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"docs/references.md",
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"src/**",
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"tests/**"
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],
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"_render_devdocs": false,
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"_jinja2_env_vars": {
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"lstrip_blocks": true,
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"trim_blocks": true
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},
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"_template": "https://github.com/scverse/cookiecutter-scverse",
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"_commit": "a370e73f7e342f377fee8e902111bbe2bca30b3b"
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}
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},
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"directory": null
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}

‎.editorconfig‎

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root = true
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[*]
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indent_style = space
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indent_size = 4
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end_of_line = lf
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charset = utf-8
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trim_trailing_whitespace = true
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insert_final_newline = true
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[{*.{yml,yaml,toml},.cruft.json}]
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indent_size = 2
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[Makefile]
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indent_style = tab

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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name: Bug report
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description: Report something that is broken or incorrect
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labels: bug
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body:
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- type: markdown
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attributes:
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value: |
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**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
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detailing how to provide the necessary information for us to reproduce your bug. In brief:
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* Please provide exact steps how to reproduce the bug in a clean Python environment.
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* In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
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* Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
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available datasets or to share a subset of your data.
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- type: textarea
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id: report
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attributes:
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label: Report
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: versions
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attributes:
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label: Versions
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description: |
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Which version of packages.
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Please install `session-info2`, run the following command in a notebook,
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click the “Copy as Markdown” button, then paste the results into the text box below.
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```python
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In[1]: import session_info2; session_info2.session_info(dependencies=True)
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```
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Alternatively, run this in a console:
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```python
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>>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
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```
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render: python
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placeholder: |
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anndata 0.11.3
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---- ----
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charset-normalizer 3.4.1
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coverage 7.7.0
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psutil 7.0.0
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dask 2024.7.1
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jaraco.context 5.3.0
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numcodecs 0.15.1
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jaraco.functools 4.0.1
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Jinja2 3.1.6
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sphinxcontrib-jsmath 1.0.1
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sphinxcontrib-htmlhelp 2.1.0
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toolz 1.0.0
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session-info2 0.1.2
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PyYAML 6.0.2
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llvmlite 0.44.0
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scipy 1.15.2
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pandas 2.2.3
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sphinxcontrib-devhelp 2.0.0
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h5py 3.13.0
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tblib 3.0.0
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setuptools-scm 8.2.0
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more-itertools 10.3.0
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msgpack 1.1.0
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sparse 0.15.5
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wrapt 1.17.2
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jaraco.collections 5.1.0
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numba 0.61.0
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pyarrow 19.0.1
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pytz 2025.1
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MarkupSafe 3.0.2
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crc32c 2.7.1
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sphinxcontrib-qthelp 2.0.0
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sphinxcontrib-serializinghtml 2.0.0
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zarr 2.18.4
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asciitree 0.3.3
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six 1.17.0
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sphinxcontrib-applehelp 2.0.0
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numpy 2.1.3
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cloudpickle 3.1.1
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sphinxcontrib-bibtex 2.6.3
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natsort 8.4.0
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jaraco.text 3.12.1
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setuptools 76.1.0
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Deprecated 1.2.18
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packaging 24.2
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python-dateutil 2.9.0.post0
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---- ----
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Python 3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
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OS Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
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Updated 2025-03-18 15:47

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: false
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contact_links:
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- name: Scverse Community Forum
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url: https://discourse.scverse.org/
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about: If you have questions about “How to do X”, please ask them here.

‎.github/ISSUE_TEMPLATE/feature_request.yml‎

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name: Feature request
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description: Propose a new feature for ngff-transformations
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labels: enhancement
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
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validations:
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required: true

‎.github/workflows/build.yaml‎

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name: Check Build
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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package:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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with:
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Build package
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run: uv build
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- name: Check package
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run: uvx twine check --strict dist/*.whl

‎.github/workflows/release.yaml‎

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name: Release
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on:
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release:
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types: [published]
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# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
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jobs:
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release:
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name: Upload release to PyPI
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/ngff_transformations
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permissions:
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id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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steps:
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- uses: actions/checkout@v5
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with:
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Build package
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run: uv build
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- name: Publish package distributions to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/test.yaml‎

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name: Test
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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schedule:
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- cron: "0 5 1,15 * *"
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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# Get the test environment from hatch as defined in pyproject.toml.
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# This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
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# run locally and on continuous integration.
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# Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
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# more details.
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get-environments:
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runs-on: ubuntu-latest
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outputs:
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envs: ${{ steps.get-envs.outputs.envs }}
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steps:
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- uses: actions/checkout@v5
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with:
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Get test environments
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id: get-envs
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run: |
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ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
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| map(
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select(.key | startswith("hatch-test"))
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| {
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name: .key,
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label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
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python: .value.python
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}
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)')
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echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
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# Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
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test:
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needs: get-environments
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
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name: ${{ matrix.env.label }}
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v5
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with:
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.env.python }}
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- name: create hatch environment
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run: uvx hatch env create ${{ matrix.env.name }}
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- name: run tests using hatch
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env:
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MPLBACKEND: agg
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PLATFORM: ${{ matrix.os }}
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DISPLAY: :42
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run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
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- name: generate coverage report
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run: |
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# See https://coverage.readthedocs.io/en/latest/config.html#run-patch
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test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
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uvx hatch run ${{ matrix.env.name }}:cov-report # report visibly
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uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
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- name: Upload coverage
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uses: codecov/codecov-action@v5
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# Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
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# protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
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check:
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name: Tests pass in all hatch environments
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if: always()
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needs:
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- get-environments
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- test
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runs-on: ubuntu-latest
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steps:
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- uses: re-actors/alls-green@release/v1
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with:
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jobs: ${{ toJSON(needs) }}

‎.gitignore‎

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# Temp files
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.DS_Store
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.idea/
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.ipynb_checkpoints/
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*~
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buck-out/
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# IDEs
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/.idea/
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/.vscode/
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# Compiled files
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.venv/
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__pycache__/
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.*cache/
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# Distribution / packaging
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/dist/
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# Tests and coverage
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/data/
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/node_modules/
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/.coverage*
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# docs
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/docs/generated/
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/docs/_build/
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# others
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.ipynb_checkpoints/

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