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Adding CI testing, linter and uv build system (#5)
* setup uv, format and linting via ruff * add pytest * add gitignore * decrease required python version * unable to install package below python 3.9 * sort imports * update relevant imports * update imports in the examples * add compute_energy import * clear outputs (reduce file size)
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‎.github/workflows/test.yaml

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# This workflow will install Python dependencies, run tests
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: tests
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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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jobs:
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pytest:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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python-version:
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- "3.13"
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- "3.12"
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- "3.11"
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- "3.10"
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- "3.9"
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os:
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- ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Install uv and set the python version
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uses: astral-sh/setup-uv@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install the project
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run: uv sync --all-extras --dev
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- name: Pytest
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run: |
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uv run python --version
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uv run pytest

‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# UV
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# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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#uv.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/latest/usage/project/#working-with-version-control
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.pdm.toml
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.pdm-python
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.pdm-build/
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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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/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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# Ruff stuff:
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.ruff_cache/
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# PyPI configuration file
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.pypirc

‎.python-version

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3.11

‎README.ipynb

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‎README.md

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Let us initialize a molecule of dimethyl ether (DME):
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```python
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from autoadsorbate import Fragment
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f = Fragment(smile = 'COC', to_initialize = 5)
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```
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```python
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from autoadsorbate.utils import docs_plot_conformers
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from autoadsorbate import docs_plot_conformers
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conformer_trajectory = f.conformers
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fig = docs_plot_conformers(conformer_trajectory)
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```
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```python
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from autoadsorbate.Smile import get_marked_smiles
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from autoadsorbate import get_marked_smiles
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marked_smile = get_marked_smiles(['COC'])[0]
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marked_smile
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```
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We can visualize these structures:
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```python
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from autoadsorbate import docs_plot_conformers
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fig = docs_plot_conformers(conformer_trajectory)
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```
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```python
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from autoadsorbate.utils import docs_plot_sites
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from autoadsorbate import docs_plot_sites
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oriented_conformer_trajectory = [f.get_conformer(i) for i, _ in enumerate(f.conformers)]
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fig = docs_plot_conformers(oriented_conformer_trajectory)
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from autoadsorbate import docs_plot_sites
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fig = docs_plot_sites(s)
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```
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Simple methods of brute force SMILES enumeration are implemented as well. For example, only using a few lines of code we can initialize multiple conformers of all reaction intermediaries in the nitrogen hydrogenation reaction. A template of the required information can be found here:
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```python
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from autoadsorbate.string_utils import _example_config
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from autoadsorbate import _example_config
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_example_config
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```
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```python
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from autoadsorbate import construct_smiles
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config = {
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From the list of initialized conformers we can remove the ones that are effectively identical:
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from autoadsorbate import get_drop_snapped
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```python
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from autoadsorbate import Surface, Fragment
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slab = fcc211(symbol = 'Cu', size=(6,3,3), vacuum=10) # any ase.Atoms object
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s=Surface(slab, touch_sphere_size=2.7) # finding all surface atoms

‎README.rst

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