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‎.github/workflows/codeql.yml‎

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# For most projects, this workflow file will not need changing; you simply need
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# to commit it to your repository.
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#
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# You may wish to alter this file to override the set of languages analyzed,
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# or to provide custom queries or build logic.
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#
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# ******** NOTE ********
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# We have attempted to detect the languages in your repository. Please check
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# the `language` matrix defined below to confirm you have the correct set of
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# supported CodeQL languages.
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#
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name: "CodeQL Advanced"
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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: '16 0 * * 6'
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jobs:
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analyze:
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name: Analyze (${{ matrix.language }})
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# Runner size impacts CodeQL analysis time. To learn more, please see:
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# - https://gh.io/recommended-hardware-resources-for-running-codeql
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# - https://gh.io/supported-runners-and-hardware-resources
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# - https://gh.io/using-larger-runners (GitHub.com only)
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# Consider using larger runners or machines with greater resources for possible analysis time improvements.
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runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
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permissions:
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# required for all workflows
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security-events: write
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# required to fetch internal or private CodeQL packs
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packages: read
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# only required for workflows in private repositories
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actions: read
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contents: read
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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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- language: python
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build-mode: none
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# CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
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# Use `c-cpp` to analyze code written in C, C++ or both
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# Use 'java-kotlin' to analyze code written in Java, Kotlin or both
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# Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
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# To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
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# see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
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# If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
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# your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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# Add any setup steps before running the `github/codeql-action/init` action.
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# This includes steps like installing compilers or runtimes (`actions/setup-node`
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# or others). This is typically only required for manual builds.
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# - name: Setup runtime (example)
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# uses: actions/setup-example@v1
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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL
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uses: github/codeql-action/init@v3
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with:
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languages: ${{ matrix.language }}
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build-mode: ${{ matrix.build-mode }}
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# If you wish to specify custom queries, you can do so here or in a config file.
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# By default, queries listed here will override any specified in a config file.
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# Prefix the list here with "+" to use these queries and those in the config file.
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# For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
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# queries: security-extended,security-and-quality
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# If the analyze step fails for one of the languages you are analyzing with
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# "We were unable to automatically build your code", modify the matrix above
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# to set the build mode to "manual" for that language. Then modify this step
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# to build your code.
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# ℹ️ Command-line programs to run using the OS shell.
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# 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
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- if: matrix.build-mode == 'manual'
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shell: bash
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run: |
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echo 'If you are using a "manual" build mode for one or more of the' \
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'languages you are analyzing, replace this with the commands to build' \
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'your code, for example:'
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echo ' make bootstrap'
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echo ' make release'
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exit 1
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v3
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with:
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category: "/language:${{matrix.language}}"

‎.github/workflows/python-package.yml‎

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
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name: Package
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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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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10"]
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steps:
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- uses: actions/checkout@v4
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with:
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lfs: true
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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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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sudo apt install netcdf-bin
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python -m pip install --upgrade pip
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python -m pip install .
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python -m pip install .[lint]
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python -m pip install .[test]
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- name: Lint with flake8 flake8-docstrings
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings
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flake8 . --count --exit-zero --ignore E203 --max-complexity=14 --max-line-length=78 --statistics
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- name: Run unit tests
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run: |
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pytest --cov=.
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- name: Run integration tests
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run: |
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wqf --help
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wqf --version
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v5
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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slug: bcdev/fcwq-wqf
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‎.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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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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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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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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.nox/
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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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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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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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db.sqlite3
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db.sqlite3-journal
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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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# PyBuilder
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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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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/latest/usage/project/#working-with-version-control
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.pdm.toml
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.pdm-python
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.pdm-build/
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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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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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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.idea/.gitignore
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.idea/*.iml
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.idea/modules.xml
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.idea/vcs.xml
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# User-specific stuff
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.idea/**/workspace.xml
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.idea/**/tasks.xml
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.idea/**/usage.statistics.xml
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.idea/**/dictionaries
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.idea/**/shelf
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.idea/**/misc.xml
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# AWS User-specific
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.idea/**/aws.xml
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# Generated files
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.idea/**/contentModel.xml
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# File-based project format
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*.iws
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# Datasets
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*.mov
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*.zarr/
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*.zip
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# Graphics
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mov/**/*.*
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pvp/**/*.*
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pvr/**/*.*
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tdr/**/*.*

‎.idea/codeStyles/codeStyleConfig.xml‎

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‎.idea/copyright/mit.xml‎

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‎.idea/copyright/profiles_settings.xml‎

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‎.idea/inspectionProfiles/Project_Default.xml‎

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‎.idea/inspectionProfiles/profiles_settings.xml‎

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