Initial commit

.github/workflows/testing.yml

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+name: testing
+
+on:
+  push:
+
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies & package
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[strict,tests,dev]
+          pip install .
+
+      - name: Lint
+        run: |
+          pre-commit run --all-files --show-diff-on-failure
+
+      - name: Test
+        run: |
+          pytest tests

.github/workflows/update-precommit.yml

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+name: pre-commit-auto-update
+
+on:
+  schedule:
+    - cron: '0 0 1,14,28 * *'
+
+jobs:
+  auto-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit autoupdate
+        run: pre-commit autoupdate
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v3
+        with:
+          branch: update/pre-commit-autoupdate
+          title: Auto-update pre-commit hooks
+          commit-message: Auto-update pre-commit hooks
+          body: Update versions of tools in pre-commit config to latest versions.
+          labels: dependencies

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

.pre-commit-config.yaml

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+default_language_version:
+  python: python3
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-yaml
+  - id: fix-encoding-pragma
+    args: [--remove]
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+- repo: https://github.com/myint/autoflake
+  rev: v2.0.1
+  hooks:
+  - id: autoflake
+- repo: https://github.com/psf/black
+  rev: 22.12.0
+  hooks:
+  - id: black
+- repo: https://github.com/asottile/blacken-docs
+  rev: 1.13.0
+  hooks:
+  - id: blacken-docs
+    additional_dependencies: [black]
+    exclude: README.md
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+- repo: https://github.com/pycqa/flake8
+  rev: 6.0.0
+  hooks:
+  - id: flake8
+    entry: pflake8
+    files: ^src/
+    additional_dependencies:
+    - pyproject-flake8==6.0.0
+    - flake8-bugbear==22.12.6
+    - flake8-typing-imports==1.14.0
+    - flake8-docstrings==1.6.0
+    - flake8-rst-docstrings==0.3.0
+    - flake8-rst==0.8.0
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.10.0
+  hooks:
+  - id: python-use-type-annotations
+  - id: rst-backticks
+  - id: rst-directive-colons
+  - id: rst-inline-touching-normal
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.991
+  hooks:
+  - id: mypy
+    files: ^src/
+    additional_dependencies:
+    - tokenize-rt==4.1.0
+    - types-pkg_resources==0.1.2
+    - types-paramiko
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.2
+  hooks:
+  - id: codespell
+    stages: [commit, commit-msg]
+    args: [--ignore-words-list, 'titel,statics,ba,nd,te']
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.3.1
+  hooks:
+    - id: pyupgrade
+      args: [--py38-plus]

LICENSE

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+atomate2-lammps Copyright (c) 2022, Matgenix SRL
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+(1) Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+(3) Neither the name of the Matgenix SRL, nor the names of its contributors may
+be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches, or
+upgrades to the features, functionality or performance of the source code
+("Enhancements") to anyone; however, if you choose to make your Enhancements
+available either publicly, or directly to Matgenix or its contributors, without
+imposing a separate written license agreement for such Enhancements, then you
+hereby grant the following license: a non-exclusive, royalty-free perpetual
+license to install, use, modify, prepare derivative works, incorporate into
+other computer software, distribute, and sublicense such enhancements or
+derivative works thereof, in binary and source code form.

README.md

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+# atomate2-addon-template
+
+This is an example add-on package for [atomate2](https://github.com/materialsproject/atomate2).
+
+It is heavily based on
+the equivalent [add-on template for pymatgen](https://github.com/materialsproject/pymatgen-addon-template).
+
+## License
+
+This add-on is released under the same license as atomate2, modified BSD, the full text of which can be found in this repository.