kbkit 1.0.0__tar.gz

kbkit-1.0.0/.coveragerc

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+[run]
+source = kbkit
+omit = kbkit/__main__.py
+
+[report]
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+    # Don't complain if an ellipsis isn't run (typically in an abstractmethod):
+    ^\s*\.\.\.

kbkit-1.0.0/.editorconfig

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+# http://editorconfig.org/#file-format-details
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_size = 4
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.md]
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab

kbkit-1.0.0/.gitattributes

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+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

kbkit-1.0.0/.github/workflows/build-and-test.yml

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+name: Build and Test
+
+on:
+  pull_request: {}
+  push:
+    branches: main
+
+jobs:
+  build-and-test:
+    strategy:
+      matrix:
+       python-version: ["3.12"]
+       os: [ubuntu-latest]
+
+    name: Python ${{ matrix.os }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          pip install -r requirements.txt
+          pip install pytest pytest-cov ruff mypy coveralls
+          pip install -e .
+
+      - name: Format check
+        run: ruff check src/kbkit
+
+      - name: Type check
+        run: mypy src/kbkit
+
+      - name: Run tests with coverage
+        run: pytest tests/ --cov=. --cov-report=xml --junitxml=junit/test-results.xml
+
+      - name: Upload test results
+        uses: actions/upload-artifact@v4
+        if: ${{ always() }}
+        with:
+          name: test-results-${{ matrix.os }}-${{ matrix.python-version }}
+          path: |
+            junit/test-results.xml
+            coverage.xml
+
+      - name: Upload coverage to Coveralls
+        env:
+          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        run: |
+          coveralls

kbkit-1.0.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build package
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.10.0
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

kbkit-1.0.0/.gitignore

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+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# 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/
+junit/
+test-result*
+
+# 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/
+.envrc
+
+# 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/
+
+# 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/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+
+# Pixi
+.pixi

kbkit-1.0.0/.pre-commit-config.yaml

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+exclude: '.pixi/'
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0  # this is optional, use `pre-commit autoupdate` to get the latest rev!
+  hooks:
+    - id: check-yaml
+    - id: check-toml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+
+- repo: local
+  hooks:
+  - id: ruff
+    name: ruff-format
+    stages: [pre-commit, pre-push]
+    language: system
+    entry: pixi run fmt
+    types: [python]
+    pass_filenames: false
+
+  - id: ruff
+    name: ruff-check
+    stages: [pre-commit, pre-push]
+    language: system
+    entry: pixi run lint
+    types: [python]
+    pass_filenames: false
+
+  - id: Mypy
+    args: [src/kbkit, --ignore-missing-imports, --disable-error-code=assignment]
+    name: mypy
+    stages: [pre-commit, pre-push]
+    language: system
+    entry: pixi run types
+    types: [python]
+    pass_filenames: false
+
+  - id: pytest
+    args: [kbkit]
+    name: pytest
+    stages: [pre-commit, pre-push]
+    language: system
+    entry: pixi run test
+    types: [python]
+    pass_filenames: false

kbkit-1.0.0/.readthedocs.yaml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: requirements.txt
+   - method: pip
+     path: .

kbkit-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Allison Peroutka
+
+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.

kbkit-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: kbkit
+Version: 1.0.0
+Summary: KBKit: Kirkwood-Buff Analysis Toolkit
+Author: Allison Peroutka
+License: MIT License
+        
+        Copyright (c) 2025 Allison Peroutka
+        
+        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.
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: babel<3,>=2.17.0
+Requires-Dist: click<9,>=8.2.1
+Requires-Dist: furo<2026,>=2025.7.19
+Requires-Dist: gromacs<0.0.1,>=0.0.0
+Requires-Dist: ipykernel<7,>=6.30.1
+Requires-Dist: matplotlib<4,>=3.10.5
+Requires-Dist: mdanalysis
+Requires-Dist: mpltern<2,>=1.0.4
+Requires-Dist: mypy
+Requires-Dist: natsort<9,>=8.4.0
+Requires-Dist: nbsphinx<0.10,>=0.9.6
+Requires-Dist: numpy<3,>=2.3.2
+Requires-Dist: pandas<3,>=2.3.1
+Requires-Dist: pandoc<3,>=2.4
+Requires-Dist: pathlib<2,>=1.0.1
+Requires-Dist: pint<0.25
+Requires-Dist: plotly<7,>=6.3.0
+Requires-Dist: pytest-cov>=6.2.1
+Requires-Dist: pytest>=8.4.1
+Requires-Dist: rdkit<2026,>=2025.3.5
+Requires-Dist: scipy<2,>=1.16.1
+Requires-Dist: seaborn<0.14,>=0.13.2
+Requires-Dist: sphinx-copybutton<0.6,>=0.5.2
+Requires-Dist: sphinx-gallery<0.20,>=0.19.0
+Requires-Dist: sphinx-rtd-theme<4,>=3.0.2
+Requires-Dist: sphinx>=7.0
+Requires-Dist: stubs>=1.0.0
+Requires-Dist: sympy<2,>=1.14.0
+Requires-Dist: tree-format<0.2,>=0.1.2
+Requires-Dist: uncertainties<4,>=3.2.3
+Description-Content-Type: text/markdown
+
+# KBKit: Kirkwood-Buff Analysis Toolkit
+
+[![License](https://img.shields.io/github/license/aperoutka/kbkit)](https://github.com/aperoutka/kbkit/blob/master/LICENSE)
+[![Powered by: Pixi](https://img.shields.io/badge/Powered_by-Pixi-facc15)](https://pixi.sh)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
+[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/aperoutka/kbkit/build-and-test.yml?branch=main&logo=github-actions)](https://github.com/aperoutka/kbkit/actions/workflows/build-and-test.yml)
+[![Coverage Status](https://coveralls.io/repos/github/aperoutka/kbkit/badge.svg?branch=main)](https://coveralls.io/github/aperoutka/kbkit?branch=main)
+[![docs](http://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat)](https://kbkit.readthedocs.io/)
+![python 3.12](https://img.shields.io/badge/Python-3.12%2B-blue)
+
+**KBKit** is a Python package for automated Kirkwood-Buff (KB) analysis of molecular simulation data. It provides tools to parse simulation outputs, compute Kirkwood-Buff integrals, and extract thermodynamic properties for binary and multicomponent systems. **KBKit** supports flexible workflows, including:
+
+* Parsing and processing of simulation data (e.g., RDFs, densities)
+* Calculation of KB integrals and related thermodynamic quantities
+* Integration of activity coefficient derivatives (numerical or polynomial)
+* Automated pipelines for batch analysis
+* Calculation of static structure factor and X-ray intensities in the limit of q &rarr; 0
+* Visualization tools for KB integrals, thermodynamic properties, and static structure factors
+
+**KBKit** is designed for researchers in computational chemistry, soft matter, and statistical mechanics who need robust, reproducible KB analysis from simulation data. The package is modular, extensible, and integrates easily with Jupyter notebooks and Python scripts.
+
+## Installation
+
+**KBKit** can be installed from cloning its github repository and creating an anaconda environment with dependencies.
+
+```python
+git clone https://github.com/aperoutka/kbkit.git
+cd kbkit
+conda create --name kbkit python=3.12
+conda activate kbkit
+pip install .
+```
+
+## Examples
+
+Below are several examples on various ways to implement **KBKit**. 
+
+### Calculating Kirkwood-Buff integrals on a single RDF
+
+```python
+from kbkit.analysis import KBIntegrator
+
+# create integrator object from single RDF file
+integrator = KBIntegrator(rdf_file)
+
+# calculate running-KBI
+rkbi = integrator.rkbi()
+
+# calculate KBI in thermodynamic limit
+kbi = integrator.integrate()
+
+# visualize KBI integration and extrapolation
+integrator.plot()
+```
+
+### Run an automated pipeline for batch analysis
+
+```python
+from kbkit.core import KBPipeline
+
+# Set up and run the pipeline
+pipe = KBPipeline(
+    base_path="/path/to/systems",                # directory with system data
+    pure_path="/path/to/pure_components",        # directory with pure component data
+    pure_systems=["acetone_300", "water_300"],   # list of pure systems
+    ensemble="npt",                              # ensemble type: npt or nvt
+    gamma_integration_type="numerical",          # integration method
+    verbose=False                                # logging verbosity
+)
+
+# run kbkit pipeline
+results = pipe.run()
+
+# Access the results properties
+# stored in dataclass (ThermoProperty); attributes: name, value, units
+# example for excess energy
+ge_obj = results.ge
+ge_array = ge_obj.value
+ge_units = ge_obj.units
+print("GE summary: ", ge_array.shape, ge_units)
+
+# Convert units from kJ/mol -> kcal/mol
+# default units will be those from GROMACS
+pipe.convert_units("ge", "kcal/mol")
+```
+
+### Create plots for thermodynamic properties from pipeline
+
+```python
+from kbkit.viz import Plotter
+
+# Map molecule IDs (as present in .top files) to names for figures
+molecule_map = {
+    "ACETO": "Acetone",
+    "TIP4P": "Water",
+}
+x_mol = "ACETO"  # molecule for x-axis labels
+
+plotter = Plotter(pipeline=pipe, x_mol=x_mol, molecule_map=molecule_map)
+
+# Plot Kirkwood-Buff integrals
+plotter.plot("kbi")
+
+# Plot log of activity coefficients
+plotter.plot("lngammas")
+
+# Generate all figures (saved to /path/to/systems/kb_analysis)
+plotter.make_figures()
+```
+
+### Parse GROMACS files
+
+```python
+from kbkit.parsers import TopFileParser, EdrFileParser, GroFileParser
+
+# determines molecules present in simulation and their counts
+top_parser = TopFileParser(top_file.top)
+print("molecule dict: ", top_parser.molecule_counts)
+print("molecule names: ", top_parser.molecules)
+print("total molecule number: ", top_parser.total_molecules)
+
+# determines electron count for each molecule type
+gro_parser = GroFileParser(gro_file.gro)
+print("electron dict: ", gro_parser.electron_count)
+print("box volume: ", gro_parser.compute_box_volume())
+
+# computes energy properties by calling gmx energy
+edr_parser = EdrFileParser(edr_file.edr)
+print("List of available properties: ", edr_parser.available_properties())
+print("Density array over simulation time: ", edr_parser.extract_timeseries("density"))
+print("Average density with std deviation: ", edr_parser.average_property("density", return_std=True))
+```
+
+### Calculate static structure factors and x-ray intensities as q &rarr; 0
+
+```python
+from kbkit.calculators import StaticStructureCalculator
+
+"""
+Requires:
+    - mol fraction matrix: shape(num compositions, num components)
+    - molar_volume: shape(num components), units cm^3/mol
+    - n_electrons: shape(num components)
+"""
+calculator = StaticStructureCalculator(mol_fr, molar_volume, n_electrons)
+
+# update conditions
+# if conditions are not updated all calculations will use previous values
+calculator.update_conditions(T, Hessian, isothermal_compressibility)
+
+# calculate x-ray intensity
+calculator.i0()
+```
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [jevandezande/pixi-cookiecutter](https://github.com/jevandezande/pixi-cookiecutter) project template.