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chore: restructure codebase + rename (#26)
* chore: restructure codebase * chore: use name
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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": "00e962a93d725184f3c56a9c923680fc69965d08",
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"checkout": null,
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"context": {
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"cookiecutter": {
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"project_name": "arrayloaders",
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"package_name": "arrayloaders",
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"project_description": "A minibatch loader for anndata store",
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"author_full_name": "Ilan Gold",
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"author_email": "[email protected]",
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"github_user": "scverse",
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"github_repo": "arrayloaders",
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"license": "MIT License",
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"ide_integration": true,
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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": "00e962a93d725184f3c56a9c923680fc69965d08"
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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 arrayloaders
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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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defaults:
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run:
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# to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
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shell: bash -euo pipefail {0}
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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@v4
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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@v5
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with:
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cache-dependency-glob: pyproject.toml
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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/build.yml‎

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‎.github/workflows/doc-changes.yml‎

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‎.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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defaults:
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run:
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# to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
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shell: bash -euo pipefail {0}
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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/arrayloaders
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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@v4
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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@v5
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with:
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cache-dependency-glob: pyproject.toml
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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

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