Initial commit

.github/dependabot.yml

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

.github/workflows/linting.yml

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+name: Linting
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install --quiet -r requirements-ci.txt
+      - name: ruff
+        run: |
+          ruff --version
+          ruff check package
+      - name: black
+        run: |
+          black --version
+          black --check --diff --color package
+      - name: mypy
+        run: |
+          mypy --version
+          rm -rf .mypy_cache
+          mypy package

.github/workflows/testing.yml

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

.gitignore

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

.pre-commit-config.yaml

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+exclude: ^(docs|.*test_files|cmd_line|tasks.py)
+
+ci:
+  autoupdate_schedule: monthly
+  skip: [mypy]
+  autofix_commit_msg: pre-commit auto-fixes
+  autoupdate_commit_msg: pre-commit autoupdate
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.278
+    hooks:
+      - id: ruff
+        args: [--fix]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+        exclude: pymatgen/analysis/vesta_cutoffs.yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.4.1
+    hooks:
+      - id: mypy
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+      - id: codespell
+        stages: [commit, commit-msg]
+        exclude_types: [html]
+        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
+
+  - repo: https://github.com/MarcoGorelli/cython-lint
+    rev: v0.15.0
+    hooks:
+      - id: cython-lint
+        args: [--no-pycodestyle]
+      - id: double-quote-cython-strings

LICENSE

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+The MIT License (MIT)
+Copyright (c) 2011-2012 MIT & The Regents of the University of California,
+through Lawrence Berkeley National Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+[![GitHub license](https://img.shields.io/github/license/materialsvirtuallab/python_template)](https://github.com/materialsvirtuallab/python_template/blob/main/LICENSE)
+[![Linting](https://github.com/materialsvirtuallab/python_template/workflows/Linting/badge.svg)](https://github.com/materialsvirtuallab/python_template/workflows/Linting/badge.svg)
+[![Testing](https://github.com/materialsvirtuallab/python_template/workflows/Testing/badge.svg)](https://github.com/materialsvirtuallab/python_template/workflows/Testing/badge.svg)
+<!--
+[![Downloads](https://pepy.tech/badge/python_template)](https://pepy.tech/project/python_template)
+[![codecov](https://codecov.io/gh/materialsvirtuallab/python_template/branch/main/graph/badge.svg?token=3V3O79GODQ)]
+(https://codecov.io/gh/materialsvirtuallab/python_template)
+-->
+
+# Introduction
+
+This is a template for setting up Python packages in the Materials Virtual Lab. It comes with the standard Github
+workflows, pyproject and linting.

docs/Gemfile

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+source "https://rubygems.org"
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+# gem "jekyll", "~> 4.3.2"
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.5"
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+gem "github-pages", group: :jekyll_plugins
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.12"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
+# do not have a Java counterpart.
+gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]
+
+gem "webrick", "~> 1.8"

docs/_config.yml

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+title: MVL template
+email: [email protected]
+description: >- # this means to ignore newlines until "baseurl:"
+  This is the template for MAVRL repos.
+# twitter_username: jekyllrb
+github_username:  materialsvirtuallab
+
+# Build settings
+remote_theme: just-the-docs/just-the-docs
+plugins:
+  - jekyll-feed
+
+# favicon_ico: "/assets/favicon.ico"
+
+nav_external_links:
+  - title: "GitHub"
+    url: "https://github.com/materialsvirtuallab/python_template"
+
+aux_links:
+  "Materials Virtual Lab":
+    - "https://materialsvirtuallab.org"

docs/_includes/footer_custom.html

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+<small>&copy; Copyright 2022, Materials Virtual Lab</small>

docs/_includes/nav_footer_custom.html

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+<span class="site-footer">&copy; Copyright 2022, Materials Virtual Lab</span>

docs/index.md

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+[![GitHub license](https://img.shields.io/github/license/materialsvirtuallab/python_template)](https://github.com/materialsvirtuallab/python_template/blob/main/LICENSE)
+[![Linting](https://github.com/materialsvirtuallab/python_template/workflows/Linting/badge.svg)](https://github.com/materialsvirtuallab/python_template/workflows/Linting/badge.svg)
+[![Testing](https://github.com/materialsvirtuallab/python_template/workflows/Testing/badge.svg)](https://github.com/materialsvirtuallab/python_template/workflows/Testing/badge.svg)
+<!-- 
+[![Downloads](https://pepy.tech/badge/python_template)](https://pepy.tech/project/python_template)
+[![codecov](https://codecov.io/gh/materialsvirtuallab/python_template/branch/main/graph/badge.svg?token=3V3O79GODQ)]
+(https://codecov.io/gh/materialsvirtuallab/python_template) 
+-->
+
+# Introduction
+
+This is a template for setting up Python packages in the Materials Virtual Lab. It comes with the standard Github 
+workflows, pyproject.toml, docs, and linting.

package/__init__.py

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+"""Root init file."""