PyPI - synkit - Versions diffs - 1.6.3__tar.gz → 1.7.0__tar.gz - Mend

synkit 1.6.3tar.gz → 1.7.0tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (923) hide show

synkit-1.7.0/.gitignore ADDED Viewed

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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/Synthesis/Reactor/cpp/CMakeLists.txt
+libsynkit_partial_*.so
+libsynkit_partial_*.dylib
+libsynkit_partial_*.dll
+libsynkit_partial_*.json
+!synkit/CRN/cpp/CMakeLists.txt
+!synkit/CRN/Construct/cpp/CMakeLists.txt
+!synkit/CRN/Construct/dpo_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
+!Experiment/CRN/environments/*.txt
+!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
+!Test/Synthesis/Reactor/fixtures/wildcard_conformance.json
+!Test/Synthesis/Reactor/fixtures/wildcard_real_examples.json
+!Test/Synthesis/Reactor/fixtures/wildcard_observed_examples.json
+!Test/Synthesis/Reactor/fixtures/wildcard_symbolic_example.json
+!Test/Synthesis/Reactor/fixtures/wildcard_aromatic_examples.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/
+# 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/Autocatalytic/
+# Third-party simulation code of Higgs and Blackmond (Zenodo), not redistributed.
+/Experiment/Autocatalytic/Homochiral/higgs2025/
+!/Experiment/__init__.py
+# Experiment READMEs are local documentation, including nested directories.
+/Experiment/**/[Rr][Ee][Aa][Dd][Mm][Ee]*

synkit-1.7.0/CMakeLists.txt ADDED Viewed

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+cmake_minimum_required(VERSION 3.20)
+project(synkit_native VERSION 1.7.0 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_BUILD_PARTIAL "Build typed partial-rule application" 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)
+  set(SYNKIT_PARTIAL_WHEEL ON CACHE BOOL "Install partial application 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()
+if(SYNKIT_BUILD_PARTIAL)
+  add_subdirectory(synkit/Synthesis/Reactor/cpp partial)
+endif()

synkit-1.7.0/Data/Figure/synkit_graphical_abstract.svg ADDED Viewed

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+<g id="mod-synth">
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+  <text x="521.15" y="688.94" text-anchor="end" font-size="21" fill="#5A5F63">Predict &amp; explore</text>
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+  <text x="407.00" y="466.00" text-anchor="end" font-size="21" fill="#5A5F63">Networks &amp; properties</text>
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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>
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+<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>
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synkit-1.7.0/Experiment/CRN/LICENSES/KEGG.txt ADDED Viewed

@@ -0,0 +1,15 @@
+KEGG-derived cache notice
+=========================
+The file ``Experiment/CRN/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-1.7.0/Experiment/CRN/__init__.py ADDED Viewed

@@ -0,0 +1,5 @@
+"""Chemical reaction network experiments.
+Experiments and shared fixtures live in studies; execution and checking helpers
+live in tools. Run the paper workload with run_all.py.
+"""

synkit-1.7.0/Experiment/CRN/data/biomodels_manifest.json ADDED Viewed

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+}

synkit 1.6.3__tar.gz → 1.7.0__tar.gz

synkit 1.6.3tar.gz → 1.7.0tar.gz