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Shyue Ping Ong
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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: pip
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directory: "/"
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schedule:
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interval: daily
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time: "7:00"
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open-pull-requests-limit: 10

‎.github/workflows/linting.yml‎

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name: Linting
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on: [push, pull_request]
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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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max-parallel: 4
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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@v3
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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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 --quiet -r requirements-ci.txt
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- name: ruff
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run: |
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ruff --version
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ruff check package
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- name: black
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run: |
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black --version
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black --check --diff --color package
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- name: mypy
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run: |
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mypy --version
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rm -rf .mypy_cache
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mypy package

‎.github/workflows/testing.yml‎

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name: Testing
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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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release:
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types: [published]
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workflow_dispatch:
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inputs:
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task:
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type: choice
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options: [tests, release]
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default: tests
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description: Only run tests or release a new version to PyPI after tests pass.
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jobs:
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test:
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strategy:
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max-parallel: 20
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matrix:
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python-version: ["3.9", "3.10"]
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runs-on: ubuntu-latest
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env:
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PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: "python"
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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@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: pip
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cache-dependency-path: '**/requirements.txt'
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- name: Install dependencies
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run: |
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pip install --quiet -r requirements.txt -r requirements-ci.txt
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pip install -e .
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- name: pytest
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run: |
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pytest --cov=package tests --color=yes
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- name: Coveralls
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uses: coverallsapp/github-action@v2
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build:
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needs: test
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if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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name: Install Python
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with:
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python-version: "3.11"
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- run: python -m pip install build
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- name: Build sdist
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run: |
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python -m build --sdist
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python -m build --wheel
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- uses: actions/upload-artifact@v3
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with:
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path: dist/*.*
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release:
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needs: build
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if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
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runs-on: ubuntu-latest
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permissions:
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# For pypi trusted publishing
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id-token: write
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steps:
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- name: Set up Python 3.11
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uses: actions/setup-python@v4
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with:
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python-version: 3.11
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- name: Get build artifacts
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uses: actions/download-artifact@v3
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with:
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name: artifact
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path: dist
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- name: Publish to PyPi
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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skip-existing: true
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verbose: true

‎.gitignore‎

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__pycache__/
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.DS_Store
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*.o
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*.so
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*.pyc
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*.swp
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*.swo
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*.pyd
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*.c
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dist
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_build
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build
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.project
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.pydevproject
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.settings
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.externalToolBuilders
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.idea
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setuptools*
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.ipynb_checkpoints
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.cache
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.tox
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.eggs/
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.coverage
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.*_cache
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# VS Code
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.vscode/*
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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/

‎LICENSE‎

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BSD 3-Clause License
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The MIT License (MIT)
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Copyright (c) 2011-2012 MIT & The Regents of the University of California,
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through Lawrence Berkeley National Laboratory
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Copyright (c) 2023, Materials Virtual Lab
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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this software and associated documentation files (the "Software"), to deal in
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the Software without restriction, including without limitation the rights to
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use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
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the Software, and to permit persons to whom the Software is furnished to do so,
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subject to the following conditions:
411

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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
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FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
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COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
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IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

‎README.md‎

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# python_template
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A template repository for setting up new python packages
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# Introduction
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This is a template for setting up Python packages in the Materials Virtual Lab. It comes with the standard Github
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workflows, pyproject and linting.

‎package/__init__.py‎

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"""
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Root init file.
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"""

‎pyproject.toml‎

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[build-system]
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requires = [
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# pin NumPy version used in the build
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"oldest-supported-numpy",
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"setuptools>=65.0.0",
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]
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build-backend = "setuptools.build_meta"
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[tool.versioningit.vcs]
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method = "git"
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default-tag = "0.0.1"
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[tool.black]
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line-length = 120
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[tool.ruff]
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target-version = "py38"
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line-length = 120
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select = [
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"B", # flake8-bugbear
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"C4", # flake8-comprehensions
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"D", # pydocstyle
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"E", # pycodestyle error
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"EXE", # flake8-executable
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"F", # pyflakes
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"FA", # flake8-future-annotations
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"FLY", # flynt
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"I", # isort
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"ICN", # flake8-import-conventions
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"ISC", # flake8-implicit-str-concat
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"PD", # pandas-vet
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"PERF", # perflint
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"PIE", # flake8-pie
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"PL", # pylint
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"PT", # flake8-pytest-style
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"PYI", # flakes8-pyi
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"Q", # flake8-quotes
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"RET", # flake8-return
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"RSE", # flake8-raise
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"RUF", # Ruff-specific rules
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"SIM", # flake8-simplify
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"SLOT", # flake8-slots
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"TCH", # flake8-type-checking
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"TID", # tidy imports
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"TID", # flake8-tidy-imports
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"UP", # pyupgrade
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"W", # pycodestyle warning
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"YTT", # flake8-2020
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]
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ignore = [
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"B023", # Function definition does not bind loop variable
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"B028", # No explicit stacklevel keyword argument found
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"B904", # Within an except clause, raise exceptions with ...
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"C408", # unnecessary-collection-call
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"D105", # Missing docstring in magic method
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"D205", # 1 blank line required between summary line and description
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"D212", # Multi-line docstring summary should start at the first line
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"PD901", # pandas-df-variable-name
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"PERF203", # try-except-in-loop
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"PERF401", # manual-list-comprehension (TODO fix these or wait for autofix)
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"PLR", # pylint refactor
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"PLW2901", # Outer for loop variable overwritten by inner assignment target
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"PT013", # pytest-incorrect-pytest-import
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"RUF012", # Disable checks for mutable class args. This is a non-problem.
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"SIM105", # Use contextlib.suppress(OSError) instead of try-except-pass
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]
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pydocstyle.convention = "google"
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isort.required-imports = ["from __future__ import annotations"]
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isort.split-on-trailing-comma = false
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[tool.ruff.per-file-ignores]
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"__init__.py" = ["F401"]
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"*/tests/*" = ["D"]
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"tasks.py" = ["D"]
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"pymatgen/analysis/*" = ["D"]
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"pymatgen/vis/*" = ["D"]
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"pymatgen/io/*" = ["D"]
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"dev_scripts/*" = ["D"]
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[tool.pytest.ini_options]
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addopts = "--durations=30 --quiet -r xXs --color=yes -p no:warnings --import-mode=importlib"
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[tool.coverage.run]
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omit = ["pymatgen/cli"]
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relative_files = true
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[tool.coverage.report]
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exclude_lines = [
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"@deprecated",
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"def __repr__",
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"if 0:",
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"if __name__ == .__main__.:",
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"if self.debug:",
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"if settings.DEBUG",
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"pragma: no cover",
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"raise AssertionError",
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"raise NotImplementedError",
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]
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[tool.mypy]
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ignore_missing_imports = true
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namespace_packages = true
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explicit_package_bases = true
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no_implicit_optional = false
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[[tool.mypy.overrides]]
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module = ["requests.*", "tabulate.*"]
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ignore_missing_imports = true
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[tool.codespell]
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ignore-words-list = """
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titel,alls,ans,nd,mater,nwo,te,hart,ontop,ist,ot,fo,nax,coo,coul,ser,leary,thre,
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fase,rute,reson,titels,ges,scalr,strat,struc,hda,nin,ons,pres,kno,loos,lamda,lew
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"""
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check-filenames = true

‎requirements-ci.txt‎

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ase>=3.22.1
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chemview>=0.6
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netCDF4>=1.5.8
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fdint>=2.0.2
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phonopy>=2.16.3
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h5py>=3.8.0
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BoltzTraP2>=22.3.2
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f90nml>=1.4.3
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# hiphive>=0.6
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seekpath>=2.0.1
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jarvis-tools>=2022.9.16
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galore>=0.7.0
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matgl>=0.5.1

‎requirements.txt‎

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numpy==1.24.3
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sympy==1.11.1
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requests==2.29.0
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monty==2022.9.9
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ruamel.yaml==0.17.32
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scipy==1.9.0
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tabulate==0.9.0
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matplotlib==3.5.2
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palettable==3.3.0
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spglib==2.0.2
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pandas==2.0.3
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networkx==2.8.8
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plotly==5.11.0
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beautifulsoup4==4.12.2
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uncertainties==3.1.7
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Cython==3.0.0
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pybtex==0.24.0
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mp-api==0.33.3
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tqdm==4.65.0
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joblib==1.3.1

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