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Development merge (charnley#67)
* init qml reorder * added keyword * mv to other repo * refactor dict * pep8 * folder structure * rm tests * starting to split tests * pep8 and rm py3 * rm py2 * chmod and pytest * mv * readability * merge qml in * pep * py3 * starting to test args * checkpoint * mv tests and more arg parsing * ignore .vim * added qml reorder and qml test * clean * added github action * test dev * added req txt * actions * don't support lower than Python 3.6 * revisit atom types * test with qml * pep * whops * rm comments * added vector distance to qml * fixed type bug, added type assert, added shorthand for reflexes (Thanks Benj) * isort * black formart * black * format tests * format tests * devops * development * devops * isort * deploy * only master
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‎.github/workflows/publish.yml

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name: Deploy PyPi Python Package
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on:
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push:
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branches:
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- master
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tags:
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- 'rmsd-*'
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jobs:
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release:
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name: Create Release
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@master
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- name: Create Release
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id: create_release
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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with:
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tag_name: ${{github.ref}}
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release_name: Release ${{github.ref}}
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body: |
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Release changes
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draft: false
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prerelease: false
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deploy:
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needs: release
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Setup Python
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uses: actions/setup-python@v1
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with:
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python-version: '3.x'
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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 setuptools wheel twine
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- name: Build and publish
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env:
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TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run: |
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python setup.py sdist bdist_wheel
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twine upload dist/*
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‎.github/workflows/test.yml

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name: Test Python package
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on:
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push:
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branches:
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- 'master'
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- 'dev'
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pull_request:
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branches: [ master ]
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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: [3.6, 3.7, 3.8]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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if test -f requirements.txt; then pip install -r requirements.txt; fi
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if test -f requirements.dev.txt; then pip install -r requirements.dev.txt; fi
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python -m pip install git+https://github.com/qmlcode/qml@develop
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- name: Lint with flake8
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run: |
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make lint
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- name: Test with pytest
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run: |
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make test
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‎.gitignore

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# dev
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.vim
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*.py[cod]
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# setup.py output

‎.travis.yml

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language: python
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python:
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- '2.7'
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- '3.6'
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install: pip install -e .
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install:
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- pip install -e .
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- pip install pytest
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script:
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- python tests.py
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- python -m pytest tests
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deploy:
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provider: pypi
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user: charnley

‎Makefile

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python = python
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LINE_LENGTH=79
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BLACKARGS=--line-length ${LINE_LENGTH}
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src=rmsd/*.py tests/*.py
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lint:
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${python} -m isort --check-only ${src}
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${python} -m flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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${python} -m flake8 . --count --exit-zero --max-complexity=10 --statistics
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${python} -m black --check ${BLACKARGS} ${src}
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format:
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${python} -m isort ${src}
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${python} -m autoflake --in-place --remove-unused-variables ${src}
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${python} -m black ${BLACKARGS} ${src}
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test:
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${python} -m pytest -vrs tests

‎README.rst

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Submit issues or pull requests on GitHub.
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Contributions
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-------------
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Please note that we are using ``black`` with line length of 79. Easiest way to
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abide to the code standard is to install the following packages.
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.. code-block:: bash
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pip install black flake8 autoflake isort pytest
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and
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.. code-block:: bash
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make format test lint
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to auto-format and test the code.
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‎example.py

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‎requirements.dev.txt

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flake8
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pytest
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isort
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black

‎requirements.txt

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scipy
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numpy

‎rmsd++/Makefile

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‎rmsd++/README.md

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