milia-py 1.2.0__tar.gz

milia_py-1.2.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [1.2.0] - 2026-06-26
+
+### Added
+
+- QM40 dataset support: 162,954 neutral drug-like ZINC molecules (10-40 heavy
+  atoms) at B3LYP/6-31G(2df,p), with optimized geometries, Mulliken charges,
+  16 scalar quantum-mechanical properties, and per-bond local vibrational mode
+  force constants. Reference: Madushanka, Moura Jr. & Kraka, *Scientific Data*
+  11, 1376 (2024). Includes dataset implementation, handler, preprocessor (ZIP
+  of three CSV files joined by Zinc_id), CSV parser, colocated YAML
+  configuration, and `config_constants` registry entries. Uses the
+  `coordinate_based` molecule-creation strategy (SMILES present, no InChI) and
+  is neutral-only (`supports_charged_molecules()` is `False`).
+
+## [1.1.0] - 2026-02-12
+
+### Added
+
+- Multi-format molecular conversion with RDKit integration (`molecules/`).
+- Automated structural and chemical feature extraction and enrichment.
+- PyTorch Geometric compatible dataset implementation (`miliaDataset`).
+- Modular wavefunction data preprocessing for MOLDEN and FCHK formats.
+- Extensible graph transformation system with experimental setup support.
+- Three-tier plugin architecture for descriptors, transformations, and general extensions.
+- Unified dataset handler pattern with DFT and DMC support (`create_handler`).
+- Schema-validated YAML configuration system (`config/`).
+- Comprehensive CLI with interactive mode and `milia` entry point.
+- GNN model training with hyperparameter optimization support (`models/`).
+- Post-training prediction and inference workflow with checkpoint support (`models/post_training/`).
+- Transfer learning via `FineTuner` and `FreezeStrategy`.
+- Multi-format input support via `DataConverterRegistry`.
+- Molecular descriptor calculation with plugin system (`descriptors/`).
+- Three-tier exception hierarchy with 50+ specialized exception classes.
+- Registry integration for dataset type validation and CLI diagnostics.
+- Full test suite with pytest configuration (`tests/`).
+- MIT license.
+- Production `pyproject.toml` with PEP 517/518/621/639 compliance.
+- Comprehensive `README.md` with installation, quick start, and API reference.
+
+[unreleased]: https://github.com/shahram-boshra/MILIA/compare/v1.2.0...HEAD
+[1.2.0]: https://github.com/shahram-boshra/MILIA/compare/v1.1.0...v1.2.0
+[1.1.0]: https://github.com/shahram-boshra/MILIA/releases/tag/v1.1.0

milia_py-1.2.0/CITATION.cff

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+# =============================================================================
+# CITATION.cff — MILIA
+# =============================================================================
+# Citation File Format (CFF) version 1.2.0
+# Spec: https://citation-file-format.github.io/
+# Schema: https://github.com/citation-file-format/citation-file-format/blob/1.2.0/schema-guide.md
+#
+# GitHub renders this file as a "Cite this repository" sidebar widget.
+# Zenodo uses it for DOI publication via the GitHub–Zenodo integration.
+# Zotero can import references directly from this file.
+#
+# Metadata sourced from pyproject.toml and milia_pipeline/__init__.py.
+# =============================================================================
+
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the metadata from this file."
+title: "MILIA"
+type: software
+
+authors:
+  - family-names: "Boshra"
+    given-names: "Asadollah"
+    alias: "Shahram"
+    email: "a.boshra@gmail.com"
+    orcid: "https://orcid.org/0009-0004-8925-2868"
+  - family-names: "Boshra"
+    given-names: "Ilia"
+    email: "ilia.boshra@gmail.com"
+    orcid: "https://orcid.org/0009-0003-8540-1662"
+
+version: "1.1.0"
+date-released: "2026-02-12"
+license: "MIT"
+
+repository-code: "https://github.com/shahram-boshra/MILIA"
+url: "https://github.com/shahram-boshra/MILIA"
+
+abstract: "Molecular graph processing and machine learning framework for molecular sciences"
+
+keywords:
+  - "molecular machine learning"
+  - "quantum chemistry"
+  - "graph neural networks"
+  - "molecular descriptors"
+  - "pytorch geometric"
+  - "dataset pipeline"
+  - "drug discovery"

milia_py-1.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2026-present Asadollah Boshra (a.boshra@gmail.com)
+
+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.

milia_py-1.2.0/MANIFEST.in

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+# =============================================================================
+# MILIA — MANIFEST.in
+# =============================================================================
+# Controls which files are included in source distributions (sdist) when
+# building with setuptools (pyproject.toml [build-system] backend).
+#
+# Context: setuptools (>=77, per pyproject.toml) auto-includes files implied
+# by [project] metadata (readme, license-files), packages, and package-data.
+# This file explicitly declares additional inclusions for completeness and
+# ensures non-package root-level files critical to the distribution are present.
+#
+# Source: PyPA — Controlling files in the distribution
+#         (setuptools.pypa.io/en/latest/userguide/miscellaneous.html)
+#         PyPA — Including files in source distributions with MANIFEST.in
+#         (packaging.python.org/guides/using-manifest-in/)
+#
+# Order: include → recursive-include → recursive-exclude → prune → global-exclude
+# (per setuptools docs: commands execute in order; later commands override earlier)
+# =============================================================================
+
+# ---- Root-level metadata and documentation files ----------------------------
+# LICENSE and README.md are auto-included by setuptools >=66.1 via pyproject.toml
+# (readme = "README.md", license-files = ["LICENSE"]). Listed explicitly for
+# clarity and forward-compatibility.
+include LICENSE
+include README.md
+include CHANGELOG.md
+include CITATION.cff
+include pyproject.toml
+include setup.py
+
+# ---- Root-level entry point and configuration files -------------------------
+# main.py is the CLI entry point (pyproject.toml: milia = "main:main") but
+# resides at project root, outside the milia_pipeline package. It is NOT
+# discovered by [tool.setuptools.packages.find] (include = ["milia_pipeline*"]),
+# so it must be explicitly included for the sdist to be buildable.
+include main.py
+include research_experiments.yaml
+
+# ---- Configuration directory (outside installable package) ------------------
+# configs/ contains runtime YAML configurations (7 root + 10 dataset-specific).
+# Located at project root, outside milia_pipeline/, so not covered by packages
+# or package-data. Required for users building/running from source.
+recursive-include configs *.yaml
+
+# ---- Installable package source and data ------------------------------------
+# milia_pipeline/ *.py files are auto-included via [tool.setuptools.packages.find].
+# *.yaml and *.yml are auto-included via [tool.setuptools.package-data].
+# Listed explicitly for sdist completeness and clarity.
+recursive-include milia_pipeline *.py
+recursive-include milia_pipeline *.yaml *.yml
+
+# ---- Exclusions — directories not needed in source distribution -------------
+# tests/: 127 test files + fixtures — excluded from sdist per project policy.
+# Tests are available in the Git repository for contributors and CI/CD.
+recursive-exclude tests *
+
+# test_data/: Developer-only fixture files (also in .gitignore).
+# Tests use /tmp/test_data/ with mocks, not this directory.
+recursive-exclude test_data *
+
+# _legacy/: Deprecated code archive (if present). No distribution value.
+prune _legacy
+
+# experiments/: Empty functional placeholder for user experimental extensions.
+prune experiments
+
+# docs/: Documentation source files (Sphinx). Available via Git repository,
+# not needed in sdist. Per pyOpenSci: docs are hosted separately (Read the Docs).
+prune docs
+
+# milia_pipeline.egg-info/: Setuptools build cache artifact. Each clone
+# generates its own via pip install -e . (pypa/setuptools #3348).
+prune milia_pipeline.egg-info
+
+# ---- Global exclusions — compiled/generated artifacts -----------------------
+# Standard safety net: compiled Python files, cache directories, runtime logs.
+global-exclude *.py[codz]
+global-exclude __pycache__
+global-exclude *.log