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Feat/medcat-den CU-869an5f00 Add medcat den (#149)
* CU-869an5f00: Initial working commit of MedCAT-den * CU-869an5f00: Add workflow for medcat-den * CU-869an5f00: Add workflow to publish to TestPyPI * CU-869an5f00: Add method to using and registering remote dens * CU-869an5f00: Add a few simple tests for backend registration * CU-869an5f00: Add test to avoid default remote backends * CU-869an5f00: Add better API for registered den getter and existance checker * CU-869an5f00: Ensure existence of build back end at workflow time * CU-869an5f00: Add permissions for PyPI Trusted Publisher release for Test PyPI * CU-869an5f00: Add release workflow * CU-869an5f00: Add entry points based addon support * CU-869an5f00: Fix entry points loading for python 3.9
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‎.github/workflows/medcat-den_main.yml‎

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name: medcat-den - Test
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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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paths:
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- 'medcat-den/**'
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- '.github/workflows/medcat-den**'
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permissions:
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id-token: write
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defaults:
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run:
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working-directory: ./medcat-den
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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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matrix:
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python-version: [ '3.9', '3.10', '3.11', '3.12' ]
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max-parallel: 4
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steps:
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- uses: actions/checkout@v5
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- name: Install uv for Python ${{ matrix.python-version }}
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uses: astral-sh/setup-uv@v6
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with:
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python-version: ${{ matrix.python-version }}
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enable-cache: true
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- name: Install the project
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run: |
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uv sync --all-extras --dev
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uv run python -m ensurepip
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uv run python -m pip install --upgrade pip
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- name: Check types
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run: |
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uv run python -m mypy --follow-imports=normal src/medcat_den
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- name: Ruff linting
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run: |
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uv run ruff check src/medcat_den --preview
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- name: Test
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run: |
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uv run pytest tests
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publish-to-test-PyPI:
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Checkout main
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uses: actions/checkout@v5
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- name: Set up Python
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uses: actions/setup-python@v6
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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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python -m pip install --upgrade build
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- name: Install package in development mode
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run: |
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pip install -e .
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- name: Bump version for TestPyPI
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run: sed -i "s/^version = .*/version = \"1.0.0.dev$(date +%s)\"/" pyproject.toml
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- name: Build package
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run: |
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python -m build
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- name: Publish distribution to TestPyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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repository_url: https://test.pypi.org/legacy/
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packages_dir: medcat-den/dist

‎.github/workflows/medcat-den_release.yml‎

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name: medcat-den release-build
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on:
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push:
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tags:
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- 'medcat-den/v*.*.*'
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permissions:
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id-token: write
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defaults:
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run:
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working-directory: ./medcat-den
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jobs:
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test-and-publish-to-PyPI:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout main
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uses: actions/checkout@v5
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- name: Release Tag
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# If GITHUB_REF=refs/tags/medcat-den/v0.1.2, this returns v0.1.2. Note it's including the "v" though it probably shouldnt
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run: echo "RELEASE_VERSION=${GITHUB_REF##refs/*/}" >> $GITHUB_ENV
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- name: Set up Python
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uses: actions/setup-python@v6
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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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- name: Install client package in development mode
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run: |
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pip install -e .
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- name: Test
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run: |
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pytest tests
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- name: Build client package
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run: |
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python -m build
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- name: Publish production distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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packages_dir: medcat-den/dist

‎medcat-den/.gitignore‎

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# Python gitignore https://github.com/github/gitignore/blob/main/Python.gitignore
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[codz]
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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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# UV
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# Similar to Pipfile.lock, it is generally recommended to include uv.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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#uv.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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#poetry.toml
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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 recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
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# https://pdm-project.org/en/latest/usage/project/#working-with-version-control
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#pdm.lock
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#pdm.toml
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.pdm-python
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.pdm-build/
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# pixi
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# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
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#pixi.lock
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# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
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# in the .venv directory. It is recommended not to include this directory in version control.
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.pixi
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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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.envrc
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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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# Abstra
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# Abstra is an AI-powered process automation framework.
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# Ignore directories containing user credentials, local state, and settings.
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# Learn more at https://abstra.io/docs
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.abstra/
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# Visual Studio Code
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# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
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# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
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# and can be added to the global gitignore or merged into this file. However, if you prefer,
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# you could uncomment the following to ignore the entire vscode folder
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# .vscode/
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# Ruff stuff:
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.ruff_cache/
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# PyPI configuration file
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.pypirc
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# Cursor
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# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
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# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
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# refer to https://docs.cursor.com/context/ignore-files
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.cursorignore
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.cursorindexingignore
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# Marimo
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marimo/_static/
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marimo/_lsp/
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__marimo__/
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# Streamlit
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.streamlit/secrets.toml

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