[WIP] build package; add pymol Contour Plots

.codecov.yml

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+# Codecov configuration to make it a bit less noisy
+coverage:
+  status:
+    patch: false
+    project:
+      default:
+        threshold: 50%
+comment:
+  layout: "header"
+  require_changes: false
+  branches: null
+  behavior: default
+  flags: null
+  paths: null

.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/
+
+# PyCharm
+.idea/
+
+# VS Code
+.vscode/
+
+# macOS
+.DS_Store
+
+# Windows
+Thumbs.db
+ehthumbs.db
+Desktop.ini

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+Moreover, project maintainers will strive to offer feedback and advice to
+ensure quality and consistency of contributions to the code.  Contributions
+from outside the group of project maintainers are strongly welcomed but the
+final decision as to whether commits are merged into the codebase rests with
+the team of project maintainers.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at 'jenke.scheen@choderalab.org'. The project team will
+review and investigate all complaints, and will respond in a way that it deems
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+specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at
+[http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

MANIFEST.in

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+include CODE_OF_CONDUCT.md
+
+global-exclude *.py[cod] __pycache__ *.so

README.md

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-# Py-CoMSIA: Pythonic CoMSIA 3D QSAR
+pycomsia
+==============================
+[//]: # (Badges)
+[![GitHub Actions Build Status](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/pycomsia/workflows/CI/badge.svg)](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/pycomsia/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/pycomsia/branch/main/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/pycomsia/branch/main)
 
-`comsia.py` is a Python implementation of Comparative Molecular Similarity Indices Analysis (CoMSIA), a 3D Quantitative Structure-Activity Relationship (QSAR) method. This tool allows you to analyze molecular fields and predict biological activities based on molecular structures.
 
-## Citing Py-CoMSIA
+A short description of the project (less than one line).
 
-If you use Py-CoMSIA in your work, please cite our publication:
+### Copyright
 
-Haga, C. L., Le, C. N., Yang, X. D., & Phinney, D. G. (2025). Py-CoMSIA: An Open-Source Implementation of Comparative Molecular Similarity Indices Analysis in Python. Pharmaceuticals, 18(3), 440. https://doi.org/10.3390/ph18030440
+Copyright (c) 2026, jscheen
 
-https://www.mdpi.com/1424-8247/18/3/440
 
-## Features
-
-* **CoMSIA Field Calculation:** Calculates steric, electrostatic, hydrophobic, hydrogen bond donor, and hydrogen bond acceptor fields.
-* **PLS Regression:** Utilizes Partial Least Squares (PLS) regression for building QSAR models.
-* **Flexible Input:** Supports both CSV files (SMILES and activity data) and pre-aligned SDF files.
-* **Grid-Based Analysis:** Configurable grid resolution and padding for field calculations.
-* **Field Selection:** Allows you to select specific fields for analysis.
-* **Visualization:** (Optional) Visualization of the CoMSIA fields and PLS results.
-* **Prediction:** Predict activities for new compounds based on the trained model.
-* **Column filtering:** option to filter out columns with low variance.
-
-## Installation
-
-1.  **Clone the repository:**
-
-    ```bash
-    git clone https://github.com/clhaga/pycomsia
-    cd pycomsia
-    ```
-
-2.  **Install dependencies:**
-
-    ```bash
-    pip install -r requirements.txt 
-    ```
-
-## Usage
-
-```bash
-python comsia.py --train_file <train_file> [options]
-```
-
-## Arguments
---train_file (required): Path to the training data. Can be a CSV file with SMILES and activity data or an SDF file containing pre-aligned molecules and activity data.
-
---predict_file: Path to the input CSV or SDF file for prediction.
-
---sdf_activity: Activity to use for SDF file. Required if using an SDF file.
-
---grid_resolution: Resolution of the grid used for field calculation. (default: 1.0)
-
---grid_padding: Padding of the grid used for field calculation. (default: 3.0)
-
---fields: Fields to use for analysis. Options: steric, electrostatic, hydrophobic, donor, acceptor, all. (default: all)
-
---num_components: Number of components for PLS analysis. (default: 12)
-
---column_filter: Column filtering. (default: 0.0)
-
---disable_visualization: Disable visualization. (default: False)
-
-## Data Format
-CSV:
-One molecule per row.
-A column for SMILES strings.
-A column for the activity data.
-
-SDF:
-Molecules should be pre-aligned.
-The SDF file must contain a property field corresponding to the activity data.
-Use --sdf_activity to specify the property name.
-
-## Tests from publication
-
-To run the examples from the publication, simply execute the following:
-
-```bash
-python comsiatest.py
-```
-## Molecule Imager
-
-Creates a png file of molecules in an SDF file with IUPAC names (if available).
-
-```bash
-python moleculeimager.py SDF_file_name.sdf
-```
+#### Acknowledgements
+
+Project based on the 
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.11.