Initial commit

.github/workflows/python-tests.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python Tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+jobs:
+  build:
+    if: ${{ false }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        exclude:
+          - os: macos-latest
+            python-version: "3.7"
+          - os: macos-latest
+            python-version: "3.8"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install apt dependencies
+      if:  matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt install -y libegl1 libegl1-mesa libegl-mesa0 libgl1-mesa-glx libopengl0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+        check-latest: true
+    - name: Install python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        python -m pip install ovito
+        python -m pip install .
+    - name: Test with pytest
+      run: |
+        pytest

.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/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

LICENSE

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+MIT License
+
+Copyright (c) [[Year]] [[Author]]
+
+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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+# Python Modifier Template
+
+Template for a custom Python-based modifier that hooks into OVITO and can easily be shared with other users.
+
+This repository contains a template for creating your own [Python script modifier](https://docs.ovito.org/python/introduction/custom_modifiers.html), 
+which can be installed into *OVITO Pro* or the [`ovito`](https://pypi.org/project/ovito/) Python module using *pip*.
+
+## Getting Started
+
+1. Click the "Use this template" button to create your own repository based on this template.
+2. Rename `src/PackageName` to reflect the name of your modifier.
+3. Implement your [modifier](https://docs.ovito.org/python/introduction/custom_modifiers.html#advanced-interface) in [`src/PackageName/__init__.py`](src/PackageName/__init__.py). If your modifier needs access to more than one frame of a trajectory, you can uncomment and implement the `input_caching_hints` method. Otherwise, you can delete it. More details on this method can be found in the [OVITO Python docs](https://www.ovito.org/docs/current/python/introduction/custom_modifiers.html#writing-custom-modifiers-advanced-interface). 
+4. Fill in the [`pyproject.toml`](pyproject.toml) file. Fields that need to be replaced with your information are enclosed in descriptive `[[field]]` tags. Please make sure to include ovito>=3.9.1 as a dependency. Depending on your needs, you can add additional fields to the `pyproject.toml` file. Information can be found [here](https://setuptools.pypa.io/en/latest/userguide/index.html).
+5. Fill in the [`README_Template.md`](README_Template.md) file. Again, the `[[fields]]` placeholders should guide you. Feel free to add other sections like "Images", "Citation", or "References" as needed.
+6. Add meaningful examples and data sample files to the `examples` directory to help others understand the use of your modifier.
+7. Pick a license for your project and replace the current (MIT) [`LICENSE`](LICENSE) file with your license. If you keep the MIT license, please update the name and year in the current file.
+8. Once you're done, rename `README_Template.md` to `README.md`, replacing this file.
+
+## Testing
+This repository is configured to enable automated testing using the [pytest](https://docs.pytest.org/en/7.4.x/) framework. Tests are automatically executed after each push to the main branch. To set up and activate automated testing, follow these two steps:
+
+1. Write your tests in the `test/test_modifier.py` file. You can also use other filenames that adhere to the pytest requirements.
+2. Open the `.github/workflows/python-tests.yml` file and remove the `if: ${{ false }}` condition on line 15.
+
+If needed, you can also adjust the operating system and Python versions by modifying the following lines:
+```yaml
+os: [ubuntu-latest, macos-latest, windows-latest]
+python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+```
+
+An example can be found [here](https://github.com/nnn911/GenerateRandomSolution).
+
+As of August 16, 2023, according to the [GitHub documentation](https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions), *"GitHub Actions usage is free for standard GitHub-hosted runners in public repositories, and for self-hosted runners."* Please refer to the GitHub documentation if you are uncertain about incurring costs.
+

README_Template.md

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+# [[Modifier Name]]
+[[One-line description]]
+
+## Description
+[[Full description]]
+
+## Parameters 
+[[Function parameters]]
+
+## Example
+[[Usage example]]
+
+## Installation
+- OVITO Pro [integrated Python interpreter](https://docs.ovito.org/python/introduction/installation.html#ovito-pro-integrated-interpreter):
+  ```
+  ovitos -m pip install --user git+[[Repository Link]].git
+  ``` 
+  The `--user` option is recommended and [installs the package in the user's site directory](https://pip.pypa.io/en/stable/user_guide/#user-installs).
+
+- Other Python interpreters or Conda environments:
+  ```
+  pip install git+[[Repository Link]].git
+  ```
+
+## Technical information / dependencies
+- Tested on OVITO version [[VersionNumber]]
+
+## Contact
+[[Maintainer1Name]] [[Maintainer1Email]]

pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "[[PackageName]]"
+version = "[[Version number]]"
+description = "[[Short description]]"
+keywords = ["ovito", "ovito-extension"]
+authors = [{name = "[[Author 1 name]]", email = "[[Author 1 email]]"}, {name = "[[Author 2 name]]", email = "[[Author 2 email]]"}]
+maintainers = [{name = "[[Maintainer 1 name]]", email = "[[Maintainer 1 email]]"}]
+license = {text = "[[License]]"}
+readme = "README.md"
+requires-python = ">=3.7"
+dependencies = [
+    "ovito >= 3.9.1",
+]
+
+[project.urls]
+repository = "[[Repository Link]]"
+
+[project.entry-points.'OVITO.Modifier']
+"[[Human readable modifier name]]" = "[[PackageName]]:[[ModifierName]]"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "error",
+    "ignore:module 'sre_parse' is deprecated:DeprecationWarning",
+    "ignore:module 'sre_constants' is deprecated:DeprecationWarning",
+]

src/PackageName/__init__.py

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+#### Python Modifier Name ####
+# Description of your Python-based modifier.
+
+from ovito.data import DataCollection
+from ovito.pipeline import ModifierInterface
+from traits.api import *
+
+
+class ModifierName(ModifierInterface):
+    # def input_caching_hints(self, frame: int, input_slots, **kwargs):
+    #     return [frame]
+
+    def modify(self, data: DataCollection, frame: int, **kwargs):
+        pass

tests/test_modifier.py

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+def test_example():
+    assert True