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remove backup ~ files
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‎..zenodo.json.un~‎

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‎.git_archival.txt‎

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ref-names: $Format:%D$
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ref-names: $Format:%D$

‎.gitattributes‎

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# Interpret Jupyter notebooks as Python
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*.ipynb linguist-language=Python
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# For automatic versioning via setuptools_scm_git_archive
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.git_archival.txt export-subst
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# Interpret Jupyter notebooks as Python
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*.ipynb linguist-language=Python
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# For automatic versioning via setuptools_scm_git_archive
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.git_archival.txt export-subst

‎.github/workflows/draft-pdf.yml‎

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on: [push]
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jobs:
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paper:
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runs-on: ubuntu-latest
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name: Paper Draft
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Build draft PDF
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uses: openjournals/openjournals-draft-action@master
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with:
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journal: joss
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# This should be the path to the paper within your repo.
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paper-path: docs/JOSS/paper.md
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- name: Upload
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uses: actions/upload-artifact@v1
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with:
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name: paper
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# This is the output path where Pandoc will write the compiled
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# PDF. Note, this should be the same directory as the input
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# paper.md
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on: [push]
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jobs:
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paper:
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runs-on: ubuntu-latest
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name: Paper Draft
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Build draft PDF
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uses: openjournals/openjournals-draft-action@master
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with:
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journal: joss
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# This should be the path to the paper within your repo.
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paper-path: docs/JOSS/paper.md
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- name: Upload
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uses: actions/upload-artifact@v1
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with:
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name: paper
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# This is the output path where Pandoc will write the compiled
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# PDF. Note, this should be the same directory as the input
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# paper.md
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path: docs/JOSS/paper.pdf

‎.github/workflows/run-tests.yml‎

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name: Tests
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on: [push, pull_request]
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jobs:
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Linting:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.10.13
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uses: actions/setup-python@v3
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with:
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python-version: 3.10.13
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- name: Linting
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run: |
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pip install pre-commit
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pre-commit run --all-files
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Linux:
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needs: Linting
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runs-on: ubuntu-latest
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strategy:
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max-parallel: 8
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matrix:
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python-version: [3.10.13]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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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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pip install -e .[dev]
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# pip install -r requirements-dev.txt
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- name: Test with pytest
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run: |
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py.test test
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- name: Generate coverage report
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run: |
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pip install pytest==7.4.4
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pip install pytest-cov==4.1.0
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pytest --cov=./ --cov-report=xml
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v3
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# - uses: actions/cache@v1
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# with:
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# path: ~/.cache/pip
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# key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-dev.txt') }}
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# restore-keys: |
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# ${{ runner.os }}-pip-
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name: Tests
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on: [push, pull_request]
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jobs:
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Linting:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.10.13
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uses: actions/setup-python@v3
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with:
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python-version: 3.10.13
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- name: Linting
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run: |
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pip install pre-commit
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pre-commit run --all-files
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Linux:
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needs: Linting
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runs-on: ubuntu-latest
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strategy:
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max-parallel: 8
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matrix:
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python-version: [3.10.13]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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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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pip install -e .[dev]
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# pip install -r requirements-dev.txt
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- name: Test with pytest
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run: |
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py.test test
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- name: Generate coverage report
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run: |
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pip install pytest==7.4.4
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pip install pytest-cov==4.1.0
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pytest --cov=./ --cov-report=xml
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v3
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# - uses: actions/cache@v1
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# with:
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# path: ~/.cache/pip
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# key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-dev.txt') }}
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# restore-keys: |
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# ${{ runner.os }}-pip-

‎.gitignore‎

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build
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dist
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*.egg-info
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# automatically generated by setuptools-scm
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pysindy/version.py
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# sphinx gallery files
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docs/examples
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# virtual environment
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venv
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# eggs
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.eggs
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dev
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**/*cache*
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.coverage
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coverage.xml
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.idea
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docs/api
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docs/_build
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.ipynb_checkpoints
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*/.ipynb_checkpoints/*
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*/lightning_logs/*
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lightning_logs
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.DS_Store
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.vscode
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*.pyc
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*.sublime*
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Pipfile
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Pipfile.lock
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/htmlcov/
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build
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dist
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*.egg-info
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# automatically generated by setuptools-scm
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pysindy/version.py
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# sphinx gallery files
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docs/examples
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# virtual environment
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venv
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# eggs
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.eggs
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dev
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**/*cache*
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.coverage
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coverage.xml
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.idea
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docs/api
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docs/_build
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.ipynb_checkpoints
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*/.ipynb_checkpoints/*
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*/lightning_logs/*
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lightning_logs
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.DS_Store
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.vscode
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*.pyc
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*.sublime*
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Pipfile
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Pipfile.lock
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/htmlcov/
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*~

‎.pre-commit-config.yaml‎

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# Settings for pre-commit
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fail_fast: false
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.3.0
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hooks:
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- id: check-added-large-files
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args: ["--maxkb=102400"]
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- id: check-merge-conflict
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- repo: https://github.com/asottile/reorder_python_imports
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rev: v3.9.0
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hooks:
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- id: reorder-python-imports
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exclude: ^(pre_commit/resources/|testing/resources/python3_hooks_repo/)
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args: [--py37-plus, --add-import, 'from __future__ import annotations']
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- repo: https://github.com/ambv/black
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rev: 22.8.0
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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: 5.0.4
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hooks:
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- id: flake8
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args: ["--config=setup.cfg"]
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# Settings for pre-commit
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fail_fast: false
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.3.0
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hooks:
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- id: check-added-large-files
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args: ["--maxkb=102400"]
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- id: check-merge-conflict
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- repo: https://github.com/asottile/reorder_python_imports
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rev: v3.9.0
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hooks:
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- id: reorder-python-imports
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exclude: ^(pre_commit/resources/|testing/resources/python3_hooks_repo/)
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args: [--py37-plus, --add-import, 'from __future__ import annotations']
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- repo: https://github.com/ambv/black
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rev: 22.8.0
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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: 5.0.4
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hooks:
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- id: flake8
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args: ["--config=setup.cfg"]

‎.readthedocs.yaml‎

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# .readthedocs.yaml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Set the version of Python and other tools you might need
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build:
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os: ubuntu-22.04
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tools:
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python: "3.10"
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# You can also specify other tool versions:
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# nodejs: "19"
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# rust: "1.64"
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# golang: "1.19"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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# If using Sphinx, optionally build your docs in additional formats such as PDF
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# formats:
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# - pdf
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# Optionally declare the Python requirements required to build your docs
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#python:
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# install:
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# - requirements: requirements-dev.txt
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# - method: pip
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# path: .
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python:
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install:
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- method: pip
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# .readthedocs.yaml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Set the version of Python and other tools you might need
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build:
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os: ubuntu-22.04
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tools:
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python: "3.10"
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# You can also specify other tool versions:
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# nodejs: "19"
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# rust: "1.64"
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# golang: "1.19"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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# If using Sphinx, optionally build your docs in additional formats such as PDF
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# formats:
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# - pdf
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# Optionally declare the Python requirements required to build your docs
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#python:
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# install:
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# - requirements: requirements-dev.txt
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# - method: pip
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# path: .
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python:
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install:
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- method: pip
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path: .[dev]

‎.requirements-torch.txt.un~‎

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