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Merge pull request #63 from Tieqiong/cookierelease
cookie release
2 parents 2462d39 + 4e3f684 commit 0512015

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Diff for: ‎.codecov.yml

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fixes:
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- ".*/site-packages/::src/"
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# codecov can find this file anywhere in the repo, so we don't need to clutter
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# the root folder.
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#comment: false
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codecov:
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notify:
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require_ci_to_pass: no
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coverage:
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status:
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patch:
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default:
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target: '70'
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if_no_uploads: error
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if_not_found: success
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if_ci_failed: failure
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project:
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default: false
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library:
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target: auto
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if_no_uploads: error
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if_not_found: success
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if_ci_failed: error
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paths: '!*/tests/.*'
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tests:
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target: 97.9%
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paths: '*/tests/.*'
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if_not_found: success
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flags:
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tests:
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paths:
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- tests/

Diff for: ‎.coveragerc

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# Configuration of the coverage.py tool for reporting test coverage.
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[report]
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# RE patterns for lines to be excluded from consideration.
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exclude_lines =
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## Have to re-enable the standard pragma
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pragma: no cover
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## Don't complain if tests don't hit defensive assertion code:
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raise AssertionError
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raise NotImplementedError
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^[ ]*assert False
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## Don't complain if non-runnable code isn't run:
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^[ ]*@unittest.skip\b
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^[ ]{4}unittest.main()
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if __name__ == .__main__.:
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[run]
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source =
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diffpy.structure
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[report]
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omit =
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## Exclude from codecov report:
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*/tests/debug.py
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*/apps/*.py
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# TODO remove in version 3.1
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*/applications/*.py
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*/python?.?/*
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*/site-packages/nose/*
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# ignore _version.py and versioneer.py
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.*version.*
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*_version.py
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exclude_lines =
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if __name__ == '__main__':

Diff for: ‎.flake8

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[flake8]
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exclude =
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.git,
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__pycache__,
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build,
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dist,
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doc/source/conf.py
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max-line-length = 115
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# Ignore some style 'errors' produced while formatting by 'black'
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# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
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extend-ignore = E203

Diff for: ‎.gitarchive.cfg

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This file was deleted.

Diff for: ‎.gitattributes

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/.gitattributes export-ignore
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/.gitignore export-ignore
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/.travis.yml export-ignore
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/conda-recipe/ export-ignore
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/devutils export-ignore
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/doc export-ignore
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.gitarchive.cfg export-subst
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*.bat text eol=crlf
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diffpy.structure/_version.py export-subst

Diff for: ‎.github/workflows/docs.yml

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name: Build Documentation
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on:
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push:
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branches:
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- main
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release:
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jobs:
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test:
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: build
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auto-update-conda: true
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- name: install requirements
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run: >-
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conda install -n build -c conda-forge
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--file requirements/build.txt
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--file requirements/run.txt
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--file requirements/docs.txt
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--quiet --yes
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- name: install the package
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run: python -m pip install . --no-deps
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- name: build documents
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run: make -C doc html
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./doc/build/html

Diff for: ‎.github/workflows/main.yml

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name: CI
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on:
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push:
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branches:
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- main
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- CI
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pull_request:
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workflow_dispatch:
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jobs:
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miniconda:
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name: Miniconda ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ["ubuntu-latest"]
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steps:
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- name: check out diffpy.structure
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uses: actions/checkout@v3
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with:
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repository: diffpy/diffpy.structure
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path: .
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fetch-depth: 0 # avoid shallow clone with no tags
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- name: initialize miniconda
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# this uses a marketplace action that sets up miniconda in a way that makes
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# it easier to use. I tried setting it up without this and it was a pain
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uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: test
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# environment.yml file is needed by this action. Because I don't want
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# maintain this but rather maintain the requirements files it just has
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# basic things in it like conda and pip
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environment-file: ./environment.yml
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python-version: 3
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auto-activate-base: false
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- name: install diffpy.structure requirements
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shell: bash -l {0}
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run: |
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conda config --set always_yes yes --set changeps1 no
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conda config --add channels conda-forge
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conda activate test
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conda install --file requirements/run.txt
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conda install --file requirements/test.txt
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pip install .
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- name: Validate diffpy.structure
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shell: bash -l {0}
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run: |
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conda activate test
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coverage run -m pytest -vv -s
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coverage report -m
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codecov

Diff for: ‎.github/workflows/pre-commit.yml

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name: pre-commit
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on:
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pull_request:
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push:
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workflow_dispatch:
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jobs:
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pre-commit:
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# pull requests are a duplicate of a branch push if within the same repo.
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if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
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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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- uses: actions/setup-python@v4
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- uses: pre-commit/[email protected]
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with:
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extra_args: --all-files

Diff for: ‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Packages
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*.egg
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*.egg-info
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dist
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build
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eggs
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parts
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bin
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var
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sdist
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temp
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develop-eggs
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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venv/
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*.egg-info/
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.installed.cfg
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lib
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lib64
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tags
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*.egg
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bin/
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temp/
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tags/
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errors.err
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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MANIFEST
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.tox
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*,cover
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.hypothesis/
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# Translations
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*.mo
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*.pot
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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.settings
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# Django stuff:
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*.log
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# Sphinx documentation
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docs/build/
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docs/source/generated/
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# pytest
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.pytest_cache/
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# PyBuilder
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target/
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# Editor files
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# mac
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.DS_Store
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*~
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# vim
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*.swp
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*.swo
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# pycharm
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.idea/
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# VSCode
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.vscode/
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# Ipython Notebook
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.ipynb_checkpoints
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# version information
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setup.cfg

Diff for: ‎.isort.cfg

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[settings]
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line_length = 115
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multi_line_output = 3
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include_trailing_comma = True

Diff for: ‎.pre-commit-config.yaml

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default_language_version:
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python: python3
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ci:
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autofix_commit_msg: |
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[pre-commit.ci] auto fixes from pre-commit hooks
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autofix_prs: true
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autoupdate_branch: 'pre-commit-autoupdate'
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autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
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autoupdate_schedule: monthly
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skip: [no-commit-to-branch]
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submodules: false
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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hooks:
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- id: check-yaml
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- id: end-of-file-fixer
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- id: trailing-whitespace
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exclude: '\.(rst|txt)$'
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- repo: https://github.com/psf/black
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rev: 24.4.2
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hooks:
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- id: black
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- repo: https://github.com/pycqa/flake8
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rev: 7.0.0
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hooks:
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- id: flake8
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- repo: https://github.com/pycqa/isort
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rev: 5.13.2
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hooks:
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- id: isort
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args: ["--profile", "black"]
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- repo: https://github.com/kynan/nbstripout
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rev: 0.7.1
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hooks:
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- id: nbstripout
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: no-commit-to-branch
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name: Prevent Commit to Main Branch
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args: ["--branch", "main"]
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stages: [pre-commit]

Diff for: ‎.readthedocs.yml

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