synkit 1.6.2b1__tar.gz → 1.6.3__tar.gz

synkit-1.6.3/.gitignore

@@ -0,0 +1,128 @@
+# Python bytecode, environments, and tool caches
+**/__pycache__/
+*.py[cod]
+.coverage
+.mypy_cache/
+.pytest_cache/
+.ruff_cache/
+.tox/
+.venv/
+venv/
+*cachedir
+*/catboost_info/
+
+# Build and generated documentation output
+/build/
+/dist/
+/docs/
+*.egg-info/
+# Optional Mapper kernel artifacts are rebuilt from the shipped C++ source.
+libsynkit_distance_*.so
+libsynkit_distance_*.json
+
+# Generated logs, reports, notebooks, and data files
+*.log
+*.pdf
+*.rdf
+*.ipynb
+!Experiment/CRN/notebooks/crn_glycolysis_case_study.ipynb
+*.csv
+*.json
+*.json.gz
+*.pkl.gz
+*.txt
+
+# Package resources and repository evidence retained despite the broad rules
+!Experiment/CRN/LICENSES/*.txt
+!synkit/CRN/Benchmark/data/kegg_modules.json
+!Data/Conformance/stereomolgraph_graph_conformance.json
+!Data/Mech/polar.json
+!Data/Mech/radical.json
+!Data/Mech/stereo.json
+!Data/Schema/
+!Data/Schema/attribute_propagation_v1_5.json
+!/scripts/python_file_size_baseline.json
+!Test/Synthesis/Reactor/fixtures/small_rewrite_conformance.json
+
+# Lewis benchmark inputs and reviewed evidence
+!Experiment/Lewis/Data/all.csv
+!Experiment/Lewis/Data/benchmark.json.gz
+!Experiment/Lewis/Data/combinatorial_all.csv
+!Experiment/Lewis/Data/hydrogen.pkl.gz
+!Experiment/Lewis/mech_path/Data/MechanismBench/electrocyclic_machinery.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/polar.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/radical.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/stereo.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/stereo_branch_coverage.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/stereo_couplings.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/evidence/mechanismbench_evidence.json
+!Experiment/Lewis/mech_path/Data/reconstruction_audit/polar-failures.csv
+!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-arrow-review.csv
+!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-failures.csv
+!Experiment/Lewis/rule_replay/Data/bidirectional-replay/results.json
+!Experiment/Lewis/rule_replay/Data/relative-lone-pair/results.json
+
+# Stereo benchmark inputs and reproducible reports
+!Experiment/Stereo/Data/**/*.csv
+!Experiment/Stereo/Data/**/*.json
+!Experiment/Stereo/Data/manifest.json
+!Experiment/Stereo/Data/Perception/full_detection_report.json
+!Experiment/Stereo/Data/Perception/perception_conformance_cases.json
+
+# Historical reaction-stereo records consumed by experiment audits
+!Experiment/StereoReaction/evidence/stereo_rxn_closeout.json
+!Experiment/StereoReaction/evidence/stereo_rxn_validation.json
+
+# Large or reproducible data products
+/Data/Benchmark/*
+!/Data/Benchmark/mech/
+/Data/Benchmark/mech/*
+!/Data/Benchmark/mech/README.md
+!/Data/Benchmark/mech/polar-failures.csv
+!/Data/Benchmark/mech/radical-failures.csv
+!/Data/Benchmark/partial_expand/
+!/Data/Benchmark/partial_expand/**
+/Data/Benchmark/partial_expand/results/
+!/Data/Benchmark/Stereo/
+!/Data/Benchmark/Stereo/**
+/Data/Fragment/*
+/Data/Study/CRN/case_formose/*
+/Data/USPTO/*
+/Experiment/Lewis/Runs/
+
+# Generated FLOWER intermediates and long-run evidence
+/Experiment/Lewis/FLOWER/batches/
+/Experiment/Lewis/FLOWER/full_reactions/
+/Experiment/Lewis/FLOWER/replay-debug/
+/Experiment/Lewis/FLOWER/replay-results*/
+/Experiment/Lewis/FLOWER/replay-runs/
+!Experiment/Lewis/FLOWER/full-reaction-batches/manifest.json
+!Experiment/Lewis/FLOWER/full-reaction-replay-summary.json
+
+# Resumable local benchmark state
+/Experiment/RBL/*checkpoint*.jsonl
+
+# Development and scratch paths
+/Test/Conformance/
+/crn/
+/debug/
+/dev/
+# Manuscripts, evidence, figures, and local cleanup archives
+/paper/
+/sprint/
+/synkit/Graph/dev/
+
+# Local one-off scripts and prompts
+.gitignore
+measure_candidate_stages.py
+request.md
+run.sh
+run_rdcanon.py
+run_valid_bug_cases.py
+test_partial.py
+test_run.py
+test_syn.py
+test_syn_reactor.py
+
+# Local benchmark outputs and frozen source copies stay local.
+/benchmark_results/

synkit-1.6.3/Experiment/CRN/LICENSES/BIOMODELS.txt

@@ -0,0 +1,13 @@
+BioModels input notice
+======================
+
+The optional interoperability study downloads models from BioModels. The
+BioModels dataset, including encoded models and annotations, is made available
+under the Creative Commons CC0 1.0 Public Domain Dedication:
+
+https://www.ebi.ac.uk/biomodels/termsofuse
+
+Downloaded model files are cached locally under
+``Experiment/CRN/data/biomodels`` but are excluded from SynKit distribution
+artifacts. Evidence reports retain identifiers, source URLs, file sizes and
+SHA-256 checksums.

synkit-1.6.3/Experiment/CRN/LICENSES/KEGG.txt

@@ -0,0 +1,15 @@
+KEGG-derived cache notice
+=========================
+
+The file ``synkit/CRN/Benchmark/data/kegg_modules.json`` contains records
+derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG), retrieved on
+the date recorded inside that file. KEGG is copyright Kanehisa Laboratories.
+
+This cache is not covered by SynKit's MIT licence. KEGG's current terms state
+that academic users may use the KEGG website and that non-academic use requires
+a commercial licence. See: https://www.kegg.jp/kegg/legal.html
+
+Release maintainers must confirm that their intended redistribution of this
+cache is authorized under the applicable KEGG terms. If it is not, the cache
+must be excluded from the release and users must retrieve the source records
+under their own authorized access.

synkit-1.6.3/PKG-INFO

@@ -0,0 +1,122 @@
+Metadata-Version: 2.4
+Name: synkit
+Version: 1.6.3
+Summary: Utility for reaction modeling using graph grammar
+Project-URL: homepage, https://github.com/TieuLongPhan/SynKit
+Project-URL: source, https://github.com/TieuLongPhan/SynKit
+Project-URL: issues, https://github.com/TieuLongPhan/SynKit/issues
+Project-URL: documentation, https://tieulongphan.github.io/SynKit/
+Author-email: Tieu Long Phan <tieu@bioinf.uni-leipzig.de>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Requires-Dist: joblib>=1.2.0
+Requires-Dist: matplotlib>=3.9
+Requires-Dist: networkx>=3.3
+Requires-Dist: numpy>=2.2.0
+Requires-Dist: pandas>=2.2.2
+Requires-Dist: pillow
+Requires-Dist: rdkit>=2025.3.1
+Requires-Dist: regex>=2024.11.6
+Requires-Dist: requests>=2.32.3
+Requires-Dist: scikit-learn>=1.4.2
+Requires-Dist: scipy>=1.14.0
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: tqdm
+Provides-Extra: all
+Requires-Dist: pulp; extra == 'all'
+Requires-Dist: sympy>=1.13.1; extra == 'all'
+Requires-Dist: torch>=2.2.0; extra == 'all'
+Provides-Extra: docs
+Requires-Dist: graphviz; extra == 'docs'
+Requires-Dist: myst-parser; extra == 'docs'
+Requires-Dist: pydata-sphinx-theme; extra == 'docs'
+Requires-Dist: sphinx-copybutton; extra == 'docs'
+Requires-Dist: sphinx-design; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme; extra == 'docs'
+Requires-Dist: sphinx-togglebutton; extra == 'docs'
+Requires-Dist: sphinx>=6.0; extra == 'docs'
+Requires-Dist: sphinxcontrib-bibtex; extra == 'docs'
+Provides-Extra: milp
+Requires-Dist: pulp; extra == 'milp'
+Provides-Extra: test
+Requires-Dist: flake8; extra == 'test'
+Requires-Dist: psutil<8,>=5.9; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+# SynKit
+
+[![PyPI version](https://img.shields.io/pypi/v/synkit.svg)](https://pypi.org/project/synkit/)
+[![License](https://img.shields.io/github/license/tieulongphan/synkit.svg)](https://github.com/tieulongphan/synkit/blob/main/LICENSE)
+[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.15269901.svg)](https://doi.org/10.5281/zenodo.15269901)
+[![CI](https://github.com/tieulongphan/synkit/actions/workflows/test-and-lint.yml/badge.svg?branch=main)](https://github.com/tieulongphan/synkit/actions/workflows/test-and-lint.yml)
+
+**Graph-native reaction informatics and executable electron-flow models**
+
+SynKit is a Python toolkit for atom mapping, chemical graph transformations,
+reaction rules, stereochemistry, and chemical reaction networks. It also
+represents Lewis-labelled graphs and verifies user-supplied electron-flow
+mechanisms. It does not predict the kinetically or thermodynamically preferred
+mechanism.
+
+![SynKit graphical abstract](https://raw.githubusercontent.com/TieuLongPhan/SynKit/main/Data/Figure/synkit_graphical_abstract.svg)
+
+## Installation
+
+Requires Python 3.11 or later.
+
+```bash
+python -m pip install synkit
+```
+
+See [Getting Started](doc/getting_started.rst) for examples, optional
+dependencies, and Docker installation.
+
+## Documentation
+
+- [Documentation](https://tieulongphan.github.io/SynKit/)
+- [API reference](https://tieulongphan.github.io/SynKit/api/index.html)
+- [Issue tracker](https://github.com/TieuLongPhan/SynKit/issues)
+- [Changelog](doc/changelog.rst)
+
+## Publications
+
+- [Lewis-labeled graphs: curly arrows and fishhooks as executable electron
+  transfers](https://arxiv.org/abs/2607.26088), submitted (2026).
+- [SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and
+  Analysis](https://pubs.acs.org/doi/full/10.1021/acs.jcim.5c02123), *Journal
+  of Chemical Information and Modeling* (2025).
+
+## Contributing
+
+Contributions and bug reports are welcome. Create a branch from the current
+mainline, make a focused change, and run the repository checks before opening
+a pull request:
+
+```bash
+git switch -c feature/short-description
+bash scripts/lint.sh
+bash scripts/pytest.sh
+```
+
+Questions can be sent to [tieu@bioinf.uni-leipzig.de](mailto:tieu@bioinf.uni-leipzig.de).
+
+## Contributors
+
+- [Tieu-Long Phan](https://tieulongphan.github.io/)
+- [Klaus Weinbauer](https://github.com/klausweinbauer)
+- [Phuoc-Chung Nguyen Van](https://github.com/phuocchung123)
+- [Tuyet-Minh Phan](https://github.com/tuyetminhphan)
+
+## License
+
+SynKit is distributed under the MIT License. See [LICENSE](LICENSE).
+
+## Acknowledgments
+
+This project received funding from the European Union’s Horizon Europe
+Doctoral Network programme under Marie Skłodowska-Curie grant agreement
+No. 101072930 ([TACsy](https://tacsy.eu/)).

synkit-1.6.3/README.md

@@ -0,0 +1,73 @@
+# SynKit
+
+[![PyPI version](https://img.shields.io/pypi/v/synkit.svg)](https://pypi.org/project/synkit/)
+[![License](https://img.shields.io/github/license/tieulongphan/synkit.svg)](https://github.com/tieulongphan/synkit/blob/main/LICENSE)
+[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.15269901.svg)](https://doi.org/10.5281/zenodo.15269901)
+[![CI](https://github.com/tieulongphan/synkit/actions/workflows/test-and-lint.yml/badge.svg?branch=main)](https://github.com/tieulongphan/synkit/actions/workflows/test-and-lint.yml)
+
+**Graph-native reaction informatics and executable electron-flow models**
+
+SynKit is a Python toolkit for atom mapping, chemical graph transformations,
+reaction rules, stereochemistry, and chemical reaction networks. It also
+represents Lewis-labelled graphs and verifies user-supplied electron-flow
+mechanisms. It does not predict the kinetically or thermodynamically preferred
+mechanism.
+
+![SynKit graphical abstract](https://raw.githubusercontent.com/TieuLongPhan/SynKit/main/Data/Figure/synkit_graphical_abstract.svg)
+
+## Installation
+
+Requires Python 3.11 or later.
+
+```bash
+python -m pip install synkit
+```
+
+See [Getting Started](doc/getting_started.rst) for examples, optional
+dependencies, and Docker installation.
+
+## Documentation
+
+- [Documentation](https://tieulongphan.github.io/SynKit/)
+- [API reference](https://tieulongphan.github.io/SynKit/api/index.html)
+- [Issue tracker](https://github.com/TieuLongPhan/SynKit/issues)
+- [Changelog](doc/changelog.rst)
+
+## Publications
+
+- [Lewis-labeled graphs: curly arrows and fishhooks as executable electron
+  transfers](https://arxiv.org/abs/2607.26088), submitted (2026).
+- [SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and
+  Analysis](https://pubs.acs.org/doi/full/10.1021/acs.jcim.5c02123), *Journal
+  of Chemical Information and Modeling* (2025).
+
+## Contributing
+
+Contributions and bug reports are welcome. Create a branch from the current
+mainline, make a focused change, and run the repository checks before opening
+a pull request:
+
+```bash
+git switch -c feature/short-description
+bash scripts/lint.sh
+bash scripts/pytest.sh
+```
+
+Questions can be sent to [tieu@bioinf.uni-leipzig.de](mailto:tieu@bioinf.uni-leipzig.de).
+
+## Contributors
+
+- [Tieu-Long Phan](https://tieulongphan.github.io/)
+- [Klaus Weinbauer](https://github.com/klausweinbauer)
+- [Phuoc-Chung Nguyen Van](https://github.com/phuocchung123)
+- [Tuyet-Minh Phan](https://github.com/tuyetminhphan)
+
+## License
+
+SynKit is distributed under the MIT License. See [LICENSE](LICENSE).
+
+## Acknowledgments
+
+This project received funding from the European Union’s Horizon Europe
+Doctoral Network programme under Marie Skłodowska-Curie grant agreement
+No. 101072930 ([TACsy](https://tacsy.eu/)).

{synkit-1.6.2b1 → synkit-1.6.3}/pyproject.toml

@@ -1,36 +1,42 @@
 [build-system]
-requires = ["hatchling"]
+requires = ["hatchling>=1.27.0"]
 build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "1.6.2b1"
+version = "1.6.3"
 description = "Utility for reaction modeling using graph grammar"
 readme = "README.md"
 requires-python = ">=3.11"
-license = { text = "MIT" }
+license = "MIT"
 license-files = ["LICENSE", "synkit/Graph/Stereo/LICENSES/*"]
 authors = [
   { name = "Tieu Long Phan", email = "tieu@bioinf.uni-leipzig.de" }
 ]
 classifiers = [
   "Programming Language :: Python :: 3",
-  "License :: OSI Approved :: MIT License",
   "Operating System :: OS Independent",
 ]
 dependencies = [
-  "scikit-learn>=1.4.0",
-  "pandas>=1.5.3",
+  "numpy>=2.2.0",
+  "scikit-learn>=1.4.2",
+  "pandas>=2.2.2",
   "rdkit>=2025.3.1",
   "networkx>=3.3",
   "scipy>=1.14.0",
   "seaborn>=0.13.2",
   "requests>=2.32.3",
   "regex>=2024.11.6",
+  "joblib>=1.2.0",
+  "matplotlib>=3.9",
+  "pillow",
+  "tqdm",
 ]
 
 [project.optional-dependencies]
-all = ["numpy>=2.2.0", "torch>=2.2.0", "sympy>=1.13.1"]
+test = ["flake8", "pytest", "psutil>=5.9,<8"]
+milp = ["pulp"]
+all = ["torch>=2.2.0", "sympy>=1.13.1", "pulp"]
 docs = [
   # Core Sphinx
   "sphinx>=6.0",
@@ -65,22 +71,26 @@ packages = ["synkit"]
 core-metadata-version = "2.4"
 
 [tool.hatch.build.targets.wheel.force-include]
+"synkit/Chem/Mapper/exact/native/native_distance.cpp" = "synkit/Chem/Mapper/exact/native/native_distance.cpp"
 "synkit/Data/aldol.json.gz" = "synkit/Data/aldol.json.gz"
 "synkit/Data/paracetamol.json.gz" = "synkit/Data/paracetamol.json.gz"
+"synkit/CRN/Benchmark/data/kegg_modules.json" = "synkit/CRN/Benchmark/data/kegg_modules.json"
 
 [tool.hatch.build.targets.sdist]
 core-metadata-version = "2.4"
 include = [
   "/synkit",
   "/LICENSE",
-  "/LICENSES",
+  "/Experiment/CRN/LICENSES",
   "/README.md",
   "/pyproject.toml",
 ]
 
 [tool.hatch.build.targets.sdist.force-include]
+"synkit/Chem/Mapper/exact/native/native_distance.cpp" = "synkit/Chem/Mapper/exact/native/native_distance.cpp"
 "synkit/Data/aldol.json.gz" = "synkit/Data/aldol.json.gz"
 "synkit/Data/paracetamol.json.gz" = "synkit/Data/paracetamol.json.gz"
+"synkit/CRN/Benchmark/data/kegg_modules.json" = "synkit/CRN/Benchmark/data/kegg_modules.json"
 
 [tool.coverage.run]
 source = ["synkit"]

synkit-1.6.3/synkit/CRN/Benchmark/__init__.py

@@ -0,0 +1,104 @@
+"""Benchmark, validation and case-study material for :mod:`synkit.CRN`.
+
+The package includes:
+
+- **A validation set** (:mod:`~synkit.CRN.Benchmark.networks`,
+  :mod:`~synkit.CRN.Benchmark.validate`) — literature and regression networks
+  with the structural verdicts they must reproduce, each quantity additionally
+  recomputed by an independent route from
+  :mod:`~synkit.CRN.Benchmark.crosschecks`.
+- **A scaling benchmark** (:mod:`~synkit.CRN.Benchmark.scaling`) — wall-clock
+  timings of the analysis stack against network size.
+- **A metabolic case study** (:mod:`~synkit.CRN.Benchmark.kegg`) — cached KEGG
+  modules processed from pathway retrieval through
+  conservation laws, persistence and flux realizability.
+
+.. rubric:: Example
+
+.. code-block:: python
+
+    from synkit.CRN.Benchmark import run_validation, validation_table
+
+    print(validation_table(run_validation()))
+"""
+
+from __future__ import annotations
+
+from .networks import (
+    BENCHMARK_NETWORKS,
+    BenchmarkNetwork,
+    get_network,
+    network_names,
+)
+from .crosschecks import (
+    brute_force_siphons,
+    check_conservation_laws,
+    check_semiflows,
+    deficiency_by_rank_identity,
+    persistence_by_brute_force,
+    rank_by_svd,
+)
+from .scaling import (
+    NETWORK_FAMILIES,
+    ScalingRecord,
+    TASKS,
+    generate_network,
+    run_scaling_benchmark,
+    scaling_table,
+)
+from .kegg import (
+    CASE_STUDY_MODULES,
+    GLYCOLYSIS_FLUX,
+    KeggModuleAnalysis,
+    analyze_kegg_module,
+    build_kegg_crn,
+    check_glycolysis_flux,
+    kegg_case_study_report,
+    load_kegg_cache,
+    module_ids,
+)
+from .validate import (
+    NetworkValidation,
+    ValidationReport,
+    run_validation,
+    validate_network,
+    validation_table,
+)
+
+__all__ = [
+    # networks
+    "BENCHMARK_NETWORKS",
+    "BenchmarkNetwork",
+    "get_network",
+    "network_names",
+    # independent cross-checks
+    "brute_force_siphons",
+    "check_conservation_laws",
+    "check_semiflows",
+    "deficiency_by_rank_identity",
+    "persistence_by_brute_force",
+    "rank_by_svd",
+    # scaling benchmark
+    "NETWORK_FAMILIES",
+    "ScalingRecord",
+    "TASKS",
+    "generate_network",
+    "run_scaling_benchmark",
+    "scaling_table",
+    # KEGG case study
+    "CASE_STUDY_MODULES",
+    "GLYCOLYSIS_FLUX",
+    "KeggModuleAnalysis",
+    "analyze_kegg_module",
+    "build_kegg_crn",
+    "check_glycolysis_flux",
+    "kegg_case_study_report",
+    "load_kegg_cache",
+    "module_ids",
+    # validation
+    "NetworkValidation",
+    "ValidationReport",
+    "run_validation",
+    "validate_network",
+    "validation_table",
+]