synkit 1.6.1__tar.gz → 1.6.2__tar.gz

{synkit-1.6.1 → synkit-1.6.2}/.gitignore

@@ -1,108 +1,116 @@
-*.pyc
+# Python bytecode, environments, and tool caches
+**/__pycache__/
+*.py[cod]
+.coverage
+.mypy_cache/
+.pytest_cache/
+.ruff_cache/
+.tox/
+.venv/
+venv/
 *cachedir
-*.csv
-!Experiment/Lewis/Data/all.csv
-!Experiment/Lewis/Data/combinatorial_all.csv
-!Experiment/Lewis/mech_path/Data/reconstruction_audit/polar-failures.csv
-!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-failures.csv
-!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-arrow-review.csv
-*/catboost_info/*
+*/catboost_info/
 
+# Build and generated documentation output
+/build/
+/dist/
+/docs/
+*.egg-info/
 
-*.pkl.gz
+# Generated logs, reports, notebooks, and data files
+*.log
 *.pdf
-
-.coverage
-dev/*
-/debug/
-/Test/Conformance/
 *.rdf
-test_syn_reactor.py
-
-Data/Benchmark/*
-!Data/Benchmark/partial_expand/
-!Data/Benchmark/partial_expand/**
-Data/Benchmark/partial_expand/results/
-!Data/Benchmark/mech/
-Data/Benchmark/mech/*
-!Data/Benchmark/mech/README.md
-!Data/Benchmark/mech/polar-failures.csv
-!Data/Benchmark/mech/radical-failures.csv
-*.json.gz
-!Experiment/Lewis/Data/benchmark.json.gz
-# *.png
-
-run.sh
-docs/*
-run_rdcanon.py
-Data/Fragment/*
-test_partial.py
-Data/Benchmark/synthesis/*
-Data/USPTO/*
-crn/*
-test_run.py
-Data/Study/CRN/case_formose/*
-
-synkit/Graph/dev/*
 *.ipynb
+*.csv
 *.json
-# Stereo benchmark inputs are versioned for reproducible fresh-clone runs.
-# Generated reports stay Git-visible so completed results can be committed
-# explicitly, including reports created by the long raw stress stages.
-!Experiment/Stereo/Data/**/*.csv
-!Experiment/Stereo/Data/**/*.json
-!Data/Schema/
-!Data/Schema/attribute_propagation_v1_5.json
-!/tools/python_file_size_baseline.json
+*.json.gz
+*.pkl.gz
+*.txt
+
+# Package resources and repository evidence retained despite the broad rules
+!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
+!/tools/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
-# Canonical reviewed MechanismBench partitions are executable test data.
+!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/electrocyclic_machinery.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/perception_conformance_cases.json
 !Experiment/Stereo/Data/Perception/full_detection_report.json
-!Test/Synthesis/Reactor/fixtures/small_rewrite_conformance.json
-!Data/Conformance/stereomolgraph_graph_conformance.json
-!Data/Benchmark/Stereo/
-!Data/Benchmark/Stereo/**
-*.txt
-!LICENSES/*.txt
-*.log
-/dist/
-sprint/
-sprint/*
-test_syn.py
-.gitignore
-measure_candidate_stages.py
-run_valid_bug_cases.py
-paper/*
-# Nested standalone Git repository.
-/paper/og_paper/
+!Experiment/Stereo/Data/Perception/perception_conformance_cases.json
 
-# Fresh benchmark runs are reproducible and can be large. Retained reference
-# outputs live inside each experiment's Data directory.
-Experiment/Lewis/Runs/
+# 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. The portable
-# full-reaction batch payload is intentionally retained in Git.
-Experiment/Lewis/FLOWER/batches/
-Experiment/Lewis/FLOWER/full_reactions/
-Experiment/Lewis/FLOWER/replay-debug/
-Experiment/Lewis/FLOWER/replay-runs/
-Experiment/Lewis/FLOWER/replay-results*/
+# 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
 
-# Keep generated Python bytecode ignored after directory re-inclusions above.
-**/__pycache__/
-*.py[cod]
+# Resumable local benchmark state
+/Experiment/RBL/*checkpoint*.jsonl
+
+# Development and scratch paths
+/Test/Conformance/
+/crn/
+/debug/
+/dev/
+/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

{synkit-1.6.1 → synkit-1.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: synkit
-Version: 1.6.1
+Version: 1.6.2
 Summary: Utility for reaction modeling using graph grammar
 Project-URL: homepage, https://github.com/TieuLongPhan/SynKit
 Project-URL: source, https://github.com/TieuLongPhan/SynKit
@@ -14,6 +14,7 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.11
 Requires-Dist: networkx>=3.3
+Requires-Dist: numpy>=2.2.0
 Requires-Dist: pandas>=1.5.3
 Requires-Dist: rdkit>=2025.3.1
 Requires-Dist: regex>=2024.11.6
@@ -144,7 +145,7 @@ examples.
 ## Publications
 
 - [Lewis-labeled graphs: curly arrows and fishhooks as executable electron
-  transfers](https://arxiv.org/abs/2607.26088), arXiv:2607.26088 (2026).
+  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).

{synkit-1.6.1 → synkit-1.6.2}/README.md

@@ -105,7 +105,7 @@ examples.
 ## Publications
 
 - [Lewis-labeled graphs: curly arrows and fishhooks as executable electron
-  transfers](https://arxiv.org/abs/2607.26088), arXiv:2607.26088 (2026).
+  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).

{synkit-1.6.1 → synkit-1.6.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "1.6.1"
+version = "1.6.2"
 description = "Utility for reaction modeling using graph grammar"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -19,6 +19,7 @@ classifiers = [
   "Operating System :: OS Independent",
 ]
 dependencies = [
+  "numpy>=2.2.0",
   "scikit-learn>=1.4.0",
   "pandas>=1.5.3",
   "rdkit>=2025.3.1",
@@ -39,7 +40,7 @@ docs = [
   "pydata-sphinx-theme",
   "sphinx-rtd-theme",
 
-  # Your enabled extensions
+  # Sphinx extensions
   "sphinxcontrib-bibtex",
   "sphinx-design",
   "sphinx-copybutton",
@@ -49,8 +50,7 @@ docs = [
   # (still requires the system `dot` binary to render diagrams)
   "graphviz",
 
-  # Nice-to-have for markdown in docs if you ever add .md pages
-  # (safe even if unused)
+  # Markdown source support
   "myst-parser",
 ]
 
@@ -63,12 +63,15 @@ documentation = "https://tieulongphan.github.io/SynKit/"
 
 [tool.hatch.build.targets.wheel]
 packages = ["synkit"]
+core-metadata-version = "2.4"
 
 [tool.hatch.build.targets.wheel.force-include]
 "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",
@@ -80,3 +83,12 @@ include = [
 [tool.hatch.build.targets.sdist.force-include]
 "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"]
+
+[tool.coverage.report]
+fail_under = 70
+precision = 1
+show_missing = true

synkit-1.6.2/synkit/CRN/Benchmark/__init__.py

@@ -0,0 +1,105 @@
+"""Benchmark, validation and case-study material for :mod:`synkit.CRN`.
+
+Three things live here, all runnable and all shipped with the package so the
+results in the paper can be regenerated by a reader:
+
+- **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 pushed through the whole chain, from pathway retrieval to
+  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",
+]