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Ritvik Vasan
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‎.editorconfig‎

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# http://editorconfig.org
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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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trim_trailing_whitespace = true
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insert_final_newline = true
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charset = utf-8
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end_of_line = lf
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[*.bat]
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indent_style = tab
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end_of_line = crlf
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[LICENSE]
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insert_final_newline = false
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[Makefile]
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indent_style = tab

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug Report
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about: '"Something''s wrong..."'
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title: ''
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labels: ''
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assignees: ''
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---
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## Description
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*A clear description of the bug*
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## Expected Behavior
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*What did you expect to happen instead?*
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## Reproduction
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*A minimal example that exhibits the behavior.*
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## Environment
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*Any additional information about your environment*

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature Request
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about: '"It would be really cool if x did y..."'
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title: ''
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labels: ''
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assignees: ''
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---
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## Use Case
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*Please provide a use case to help us understand your request in context*
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## Solution
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*Please describe your ideal solution*
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## Alternatives
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*Please describe any alternatives you've considered, even if you've dismissed them*

‎.github/PULL_REQUEST_TEMPLATE.md‎

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**Pull request recommendations:**
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- [ ] Name your pull request _your-development-type/short-description_. Ex: _feature/read-tiff-files_
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- [ ] Link to any relevant issue in the PR description. Ex: _Resolves [gh-12], adds tiff file format support_
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- [ ] Provide context of changes.
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- [ ] Provide relevant tests for your feature or bug fix.
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- [ ] Provide or update documentation for any feature added by your pull request.
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Thanks for contributing!

‎.github/workflows/build-docs.yml‎

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name: 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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jobs:
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docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2.3.1
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with:
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persist-credentials: false
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- name: Set up Python
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uses: actions/setup-python@v1
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with:
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python-version: 3.9
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- name: Install Dependencies
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run: |
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pip install --upgrade pip
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pip install .[dev]
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- name: Generate Docs
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run: |
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make gen-docs
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touch docs/_build/html/.nojekyll
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- name: Publish Docs
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uses: JamesIves/github-pages-deploy-action@3.7.1
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with:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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BASE_BRANCH: main # The branch the action should deploy from.
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BRANCH: gh-pages # The branch the action should deploy to.
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FOLDER: docs/_build/html/ # The folder the action should deploy.
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‎.github/workflows/build-main.yml‎

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name: Build Main
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on:
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push:
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branches:
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- main
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schedule:
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# <minute [0,59]> <hour [0,23]> <day of the month [1,31]> <month of the year [1,12]> <day of the week [0,6]>
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# https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07
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# Run every Monday at 18:00:00 UTC (Monday at 10:00:00 PST)
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- cron: '0 18 * * 1'
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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os: [ubuntu-latest, windows-latest, macOS-latest]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Test with pytest
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run: |
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pytest --cov-report xml --cov=pointcloudutils pointcloudutils/tests/
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- name: Upload codecov
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uses: codecov/codecov-action@v1
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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python
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uses: actions/setup-python@v1
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with:
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python-version: 3.9
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Lint with flake8
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run: |
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flake8 pointcloudutils --count --verbose --show-source --statistics
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- name: Check with black
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run: |
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black --check pointcloudutils
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publish:
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if: "contains(github.event.head_commit.message, 'Bump version')"
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needs: [test, lint]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python
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uses: actions/setup-python@v1
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with:
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python-version: 3.9
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install setuptools wheel
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- name: Build Package
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run: |
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python setup.py sdist bdist_wheel
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@master
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with:
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user: AllenCellModeling
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password: ${{ secrets.PYPI_TOKEN }}

‎.github/workflows/test-and-lint.yml‎

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name: Test and Lint
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on: pull_request
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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os: [ubuntu-latest, windows-latest, macOS-latest]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Test with pytest
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run: |
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pytest pointcloudutils/tests/
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- name: Upload codecov
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uses: codecov/codecov-action@v1
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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python
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uses: actions/setup-python@v1
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with:
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python-version: 3.9
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Lint with flake8
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run: |
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flake8 pointcloudutils --count --verbose --show-source --statistics
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- name: Check with black
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run: |
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black --check pointcloudutils

‎.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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# 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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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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# OS generated files
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.DS_Store
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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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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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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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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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docs/pointcloudutils.*rst
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# Dask
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dask-worker-space
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# SageMath parsed files
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*.sage.py
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# dotenv
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.env
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# virtualenv
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.venv
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venv/
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ENV/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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# VSCode
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.vscode

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