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Merge pull request #20 from scverse-bot/template-update-v2-saeyslab-FlowSOM_Python
Update template to v0.5.0
2 parents 772f66a + 0be5e2c commit 7dc115b

24 files changed

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-372
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‎.cruft.json

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "009f1b5205d007026e76b3dd79f57ad946947ceb",
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"checkout": null,
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"commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
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"checkout": "v0.5.0",
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"context": {
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"cookiecutter": {
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"project_name": "FlowSOM",
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"author_full_name": "Artuur Couckuyt",
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"author_email": "[email protected]",
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"github_user": "artuurC",
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"project_repo": "https://github.com/artuurC/FlowSOM",
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"github_repo": "FlowSOM",
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"license": "GNU General Public License Version 3",
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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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"_template": "https://github.com/scverse/cookiecutter-scverse",
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"_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
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}
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},
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"directory": null

‎.editorconfig

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trim_trailing_whitespace = true
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insert_final_newline = true
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[*.{yml,yaml}]
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indent_size = 2
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[.cruft.json]
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[{*.{yml,yaml,toml},.cruft.json}]
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indent_size = 2
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[Makefile]

‎.github/ISSUE_TEMPLATE/bug_report.yml

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- type: textarea
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id: versions
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attributes:
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label: Version information
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label: Versions
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description: |
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Please paste below the output of
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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_info
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session_info.show(html=False, dependencies=True)
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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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-----
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anndata 0.8.0rc2.dev27+ge524389
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session_info 1.0.0
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-----
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asttokens NA
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awkward 1.8.0
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backcall 0.2.0
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cython_runtime NA
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dateutil 2.8.2
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debugpy 1.6.0
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decorator 5.1.1
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entrypoints 0.4
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executing 0.8.3
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h5py 3.7.0
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ipykernel 6.15.0
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jedi 0.18.1
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mpl_toolkits NA
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natsort 8.1.0
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numpy 1.22.4
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packaging 21.3
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pandas 1.4.2
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parso 0.8.3
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pexpect 4.8.0
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pickleshare 0.7.5
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pkg_resources NA
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prompt_toolkit 3.0.29
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psutil 5.9.1
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ptyprocess 0.7.0
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pure_eval 0.2.2
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pydev_ipython NA
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pydevconsole NA
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pydevd 2.8.0
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pydevd_file_utils NA
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pydevd_plugins NA
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pydevd_tracing NA
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pygments 2.12.0
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pytz 2022.1
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scipy 1.8.1
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setuptools 62.5.0
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setuptools_scm NA
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six 1.16.0
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stack_data 0.3.0
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tornado 6.1
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traitlets 5.3.0
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wcwidth 0.2.5
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zmq 23.1.0
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-----
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IPython 8.4.0
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jupyter_client 7.3.4
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jupyter_core 4.10.0
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-----
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Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
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Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
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-----
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Session information updated at 2022-07-07 17:55
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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/workflows/build.yaml

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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@v3
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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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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python-version: "3.10"
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cache: "pip"
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cache-dependency-path: "**/pyproject.toml"
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- name: Install build dependencies
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run: python -m pip install --upgrade pip wheel twine build
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cache-dependency-glob: pyproject.toml
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- name: Build package
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run: python -m build
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run: uv build
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- name: Check package
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run: twine check --strict dist/*.whl
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run: uvx twine check --strict dist/*.whl

‎.github/workflows/release.yaml

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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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with:
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filter: blob:none
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fetch-depth: 0
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- uses: actions/setup-python@v4
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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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python-version: "3.x"
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cache: "pip"
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- run: pip install build
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- run: python -m build
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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

‎.github/workflows/test.yaml

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push:
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branches: [main]
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pull_request:
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branches: "*"
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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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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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820

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jobs:
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test:
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: bash -e {0} # -e to fail on error
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strategy:
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fail-fast: false
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matrix:
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include:
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# - os: ubuntu-latest
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# python: "3.9"
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- os: ubuntu-latest
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python: "3.11"
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# - os: ubuntu-latest
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# python: "3.11"
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# pip-flags: "--pre"
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# name: PRE-RELEASE DEPENDENCIES
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python: "3.10"
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- os: ubuntu-latest
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python: "3.12"
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- os: ubuntu-latest
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python: "3.12"
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pip-flags: "--pre"
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name: PRE-RELEASE DEPENDENCIES
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name: ${{ matrix.name }} Python ${{ matrix.python }}
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python }}
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# cache: "pip"
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# cache-dependency-path: "**/pyproject.toml"
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- name: Install test dependencies
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run: |
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python -m pip install --upgrade pip wheel
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- name: Install dependencies
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run: |
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python -m pip install ${{ matrix.pip-flags }} ".[dev,test]"
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- name: Test
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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: 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: |
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python -m coverage run -m pytest -v --color=yes
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- name: Report coverage
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run: |
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python -m coverage report
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run: uvx hatch test --cover --python ${{ matrix.python }}
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- name: Upload coverage
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uses: codecov/codecov-action@v3
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}

‎.gitignore

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# Compiled files
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.venv/
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__pycache__/
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.mypy_cache/
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.ruff_cache/
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.*cache/
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# Distribution / packaging
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/build/
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/dist/
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/*.egg-info/
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# Tests and coverage
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/.pytest_cache/
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/.cache/
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/data/
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/node_modules/
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# docs
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/docs/generated/
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/docs/_build/
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# IDEs
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/.idea/
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/.vscode/

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