synkit 1.6.2b1__tar.gz → 1.6.5__tar.gz

synkit-1.6.5/.gitignore

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+# 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
+libsynkit_mapper_*.so
+libsynkit_mapper_*.dylib
+libsynkit_mapper_*.dll
+libsynkit_mapper_*.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
+!synkit/Chem/Mapper/solvers/native/cpp/CMakeLists.txt
+!synkit/Graph/Canon/cpp/CMakeLists.txt
+!synkit/CRN/cpp/CMakeLists.txt
+!synkit/Chem/Mapper/solvers/native/cpp/**/CMakeLists.txt
+!synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/LICENSE-2.0.txt
+
+# Package resources and repository evidence retained despite the broad rules
+!/CMakeLists.txt
+!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
+/Experiment/atom_map/
+/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/
+
+# Keep unreleased experiments local; publish only CRN and Lewis until release.
+/Experiment/*
+!/Experiment/CRN/
+!/Experiment/Lewis/
+!/Experiment/__init__.py
+
+# Experiment READMEs are local documentation, including nested directories.
+/Experiment/**/[Rr][Ee][Aa][Dd][Mm][Ee]*

synkit-1.6.5/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.20)
+project(synkit_native VERSION 1.6.5 LANGUAGES C CXX)
+
+option(SYNKIT_BUILD_MAPPER "Build the atom mapper and its solver backends" ON)
+option(SYNKIT_BUILD_CRN "Build exact chemical reaction network analysis" ON)
+option(SYNKIT_BUILD_CANON "Build graph and stereograph canonicalization" ON)
+option(SYNKIT_NATIVE_WHEEL "Install native libraries into their Python packages" OFF)
+
+if(SYNKIT_NATIVE_WHEEL)
+  set(SYNKIT_MAPPER_WHEEL ON CACHE BOOL "Install mapper into the wheel" FORCE)
+  set(SYNKIT_CANON_WHEEL ON CACHE BOOL "Install canonicalization into the wheel" FORCE)
+endif()
+
+enable_testing()
+if(SYNKIT_BUILD_MAPPER)
+  add_subdirectory(synkit/Chem/Mapper/solvers/native/cpp mapper)
+endif()
+if(SYNKIT_BUILD_CRN)
+  add_subdirectory(synkit/CRN/cpp crn)
+endif()
+if(SYNKIT_BUILD_CANON)
+  add_subdirectory(synkit/Graph/Canon/cpp canon)
+endif()

synkit-1.6.5/Data/Figure/synkit_graphical_abstract.svg

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+  <text x="521.15" y="658.94" text-anchor="end" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">Synthesis</text>
+  <text x="521.15" y="688.94" text-anchor="end" font-size="21" fill="#5A5F63">Predict &amp; explore</text>
+</g>
+<g id="mod-crn">
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+      <circle cx="28" cy="-22" r="6" fill="#FBFAF7" stroke="#B8860B" stroke-width="2.6"/>
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+      <path d="M -13 33 L -6 33 M 4 33 L 11 33 M -13 39 L -6 39 M 4 39 L 11 39" stroke="#B8860B" stroke-width="2.4" stroke-linecap="round" fill="none"/>
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+  <circle cx="534.59" cy="398.41" r="15" fill="#B8860B"/>
+  <text x="534.59" y="404.41" text-anchor="middle" font-size="16.5" font-weight="700" fill="#ffffff">6</text>
+  <text x="407.00" y="436.00" text-anchor="end" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">CRN</text>
+  <text x="407.00" y="466.00" text-anchor="end" font-size="21" fill="#5A5F63">Networks &amp; properties</text>
+</g>
+<g id="mod-vis">
+  <circle cx="609.15" cy="215.06" r="67" fill="#3D8FC4" fill-opacity="0.10"/>
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+      <path d="M 16 6 L 24 12" stroke="#3D8FC4" stroke-width="2.1" fill="none"/>
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+  <text x="521.15" y="213.06" text-anchor="end" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">Vis</text>
+  <text x="521.15" y="243.06" text-anchor="end" font-size="21" fill="#5A5F63">Molecule &amp; CRN views</text>
+</g>
+<line x1="380" y1="864" x2="1300" y2="864" stroke="#D9DBD6" stroke-width="1.6"/>
+<g font-size="21" text-anchor="middle">
+  <text x="840" y="896" fill="#5A5F63"><tspan fill="#0E5C63" font-weight="700">Open source · MIT</tspan><tspan fill="#D9DBD6">   ·   </tspan><tspan>pip install synkit</tspan><tspan fill="#D9DBD6">   ·   </tspan><tspan>github.com/TieuLongPhan/SynKit</tspan></text>
+</g>
+</svg>

synkit-1.6.5/Experiment/CRN/AGENTS.md

@@ -0,0 +1,13 @@
+# CRN experiment scope
+
+- Keep experiment drivers, benchmark inputs, timing harnesses, and result/report
+  tools here. Put regression test cases and assertions in `Test/CRN/`; do not
+  create a second test runner inside `Experiment/CRN`.
+- Reuse the public `synkit.CRN` APIs and shared benchmark inputs. Extend existing
+  studies and helpers before adding overlapping scripts or copied fixtures.
+- Keep inputs self-contained. Do not depend on manuscript directories, LaTeX
+  sources, or paper-specific helpers and filenames. Document rendering belongs
+  with the document that consumes the experiment reports.
+- Scientific outcome checks and report-completeness checks belong in study
+  reports. Keep generated outputs, native build artifacts, and downloaded XML
+  caches out of version control and package distributions.

synkit-1.6.5/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-1.6.5/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-1.6.5/Experiment/CRN/__init__.py

@@ -0,0 +1,6 @@
+"""Reproducible chemical reaction network studies and benchmarks.
+
+Study drivers live in :mod:`Experiment.CRN.studies`, fixtures and timing code
+in :mod:`Experiment.CRN.benchmarks`, and verification helpers in
+:mod:`Experiment.CRN.tools`. Run the studies with ``run_all.py``.
+"""

synkit-1.6.5/Experiment/CRN/benchmarks/__init__.py

@@ -0,0 +1,104 @@
+"""Benchmark, validation and case-study material for :mod:`synkit.CRN`.
+
+The package includes:
+
+- **A validation set** (:mod:`~Experiment.CRN.benchmarks.networks`,
+  :mod:`~Experiment.CRN.benchmarks.validate`) — literature and regression networks
+  with the structural verdicts they must reproduce, each quantity additionally
+  recomputed by an independent route from
+  :mod:`~Experiment.CRN.benchmarks.crosschecks`.
+- **A scaling benchmark** (:mod:`~Experiment.CRN.benchmarks.scaling`) — wall-clock
+  timings of the analysis stack against network size.
+- **A metabolic case study** (:mod:`~Experiment.CRN.benchmarks.kegg`) — cached KEGG
+  modules processed from pathway retrieval through
+  conservation laws, persistence and flux realizability.
+
+.. rubric:: Example
+
+.. code-block:: python
+
+    from Experiment.CRN.benchmarks 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",
+]