synkit 1.6.2__tar.gz → 1.6.3__tar.gz

{synkit-1.6.2 → synkit-1.6.3}/.gitignore

@@ -16,12 +16,16 @@ venv/
 /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
@@ -29,7 +33,7 @@ venv/
 *.txt
 
 # Package resources and repository evidence retained despite the broad rules
-!LICENSES/*.txt
+!Experiment/CRN/LICENSES/*.txt
 !synkit/CRN/Benchmark/data/kegg_modules.json
 !Data/Conformance/stereomolgraph_graph_conformance.json
 !Data/Mech/polar.json
@@ -37,7 +41,7 @@ venv/
 !Data/Mech/stereo.json
 !Data/Schema/
 !Data/Schema/attribute_propagation_v1_5.json
-!/tools/python_file_size_baseline.json
+!/scripts/python_file_size_baseline.json
 !Test/Synthesis/Reactor/fixtures/small_rewrite_conformance.json
 
 # Lewis benchmark inputs and reviewed evidence
@@ -65,6 +69,10 @@ venv/
 !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/
@@ -99,7 +107,8 @@ venv/
 /crn/
 /debug/
 /dev/
-/paper/*
+# Manuscripts, evidence, figures, and local cleanup archives
+/paper/
 /sprint/
 /synkit/Graph/dev/
 
@@ -114,3 +123,6 @@ 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-1.6.2 → synkit-1.6.3}/pyproject.toml

@@ -1,37 +1,42 @@
 [build-system]
-requires = ["hatchling"]
+requires = ["hatchling>=1.27.0"]
 build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "1.6.2"
+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 = [
   "numpy>=2.2.0",
-  "scikit-learn>=1.4.0",
-  "pandas>=1.5.3",
+  "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",
@@ -66,6 +71,7 @@ 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"
@@ -75,12 +81,13 @@ 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"

{synkit-1.6.2 → synkit-1.6.3}/synkit/CRN/Benchmark/__init__.py

@@ -1,7 +1,6 @@
 """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:
+The package includes:
 
 - **A validation set** (:mod:`~synkit.CRN.Benchmark.networks`,
   :mod:`~synkit.CRN.Benchmark.validate`) — literature and regression networks
@@ -11,7 +10,7 @@ results in the paper can be regenerated by a reader:
 - **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
+  modules processed from pathway retrieval through
   conservation laws, persistence and flux realizability.
 
 .. rubric:: Example

{synkit-1.6.2 → synkit-1.6.3}/synkit/CRN/Benchmark/kegg.py

@@ -504,11 +504,10 @@ def check_glycolysis_flux(
         reaction="label",
     )
     checker.build_petri_net_from_flow()
-    realizable, certificate = checker.is_realizable(max_states=max_states)
+    outcome = checker.realizability_result(max_states=max_states)
 
     return {
-        "realizable": bool(realizable),
-        "certificate": certificate,
+        **outcome.to_dict(),
         "flux": requested,
         "initial_marking": {"alpha-D-Glucose": initial_glucose},
     }

{synkit-1.6.2 → synkit-1.6.3}/synkit/CRN/Benchmark/scaling.py

@@ -1,12 +1,8 @@
 """Scaling benchmark for the :mod:`synkit.CRN` analysis stack.
 
-Measures wall-clock time of each analysis against network size, over families
-of synthetic networks whose size is a single parameter. The point is to show
-where the practical ceiling of each analysis lies, since the analyses have very
-different complexity: stoichiometric rank and conservation laws are polynomial,
-minimal semiflows and canonicalization are worst-case exponential in theory but
-tractable on the sparse networks chemistry produces, and minimal-siphon
-enumeration is the one that used to be the wall.
+Measures wall-clock time against network size for parameterized synthetic
+network families. The results locate practical runtime limits for the selected
+families; they do not establish asymptotic complexity.
 
 Network families
 ----------------
@@ -16,13 +12,13 @@ Network families
     linear metabolic pathway.
 ``reversible_chain``
     The same chain with every reaction reversed as well. Weakly reversible, so
-    every analysis has to do real work rather than bail out early.
+    exercises analyses that can terminate early on non-reversible networks.
 ``cycle``
     A closed chain ``S0 -> ... -> Sn -> S0``, which is weakly reversible and has
     a single conservation law.
 ``random_sparse``
     Random bimolecular reactions at a fixed reaction-to-species ratio. The
-    hardest of the four, and the closest to a rule-expanded network.
+    densest of the four benchmark families.
 
 .. rubric:: Example
 
@@ -39,6 +35,7 @@ from __future__ import annotations
 import random
 import time
 from dataclasses import dataclass
+from multiprocessing import get_all_start_methods, get_context
 from typing import Any, Callable, Dict, List, Optional, Sequence, Tuple
 
 from ..Petrinet.structure import find_siphons
@@ -305,6 +302,10 @@ class ScalingRecord:
     :param error:
         Exception text when the task raised.
     :type error: Optional[str]
+
+    :param timed_out:
+        Whether the task was terminated at the measurement budget.
+    :type timed_out: bool
     """
 
     family: str
@@ -315,6 +316,7 @@ class ScalingRecord:
     seconds: Optional[float] = None
     result: Any = None
     error: Optional[str] = None
+    timed_out: bool = False
 
     def to_dict(self) -> Dict[str, Any]:
         """Return the record as a serializable mapping.
@@ -331,19 +333,50 @@ class ScalingRecord:
             "seconds": self.seconds,
             "result": self.result,
             "error": self.error,
+            "timed_out": self.timed_out,
         }
 
 
+def _time_task_worker(
+    task: Callable[[SynCRN], Any],
+    crn: SynCRN,
+    repeats: int,
+    connection: Any,
+) -> None:
+    """Execute a timed task in a process that the parent can terminate.
+
+    :param task: Callable to time.
+    :type task: Callable[[SynCRN], Any]
+    :param crn: Network to pass to the task.
+    :type crn: SynCRN
+    :param repeats: Number of repeats.
+    :type repeats: int
+    :param connection: One-way multiprocessing connection.
+    :type connection: Any
+    """
+    best: Optional[float] = None
+    result: Any = None
+    try:
+        for _ in range(max(1, repeats)):
+            started = time.perf_counter()
+            result = task(crn)
+            elapsed = time.perf_counter() - started
+            best = elapsed if best is None else min(best, elapsed)
+        connection.send((best, result, None))
+    except Exception as exc:  # pragma: no cover - returned to parent
+        connection.send((None, None, f"{type(exc).__name__}: {exc}"))
+    finally:
+        connection.close()
+
+
 def _time_task(
     task: Callable[[SynCRN], Any],
     crn: SynCRN,
     *,
     repeats: int,
-) -> Tuple[Optional[float], Any, Optional[str]]:
-    """Time one task, reporting the best of ``repeats`` runs.
-
-    The best rather than the mean, because the slow runs measure the machine's
-    other work rather than the algorithm.
+    time_budget: Optional[float],
+) -> Tuple[Optional[float], Any, Optional[str], bool]:
+    """Time one task and report the minimum of ``repeats`` runs.
 
     :param task: Callable to time.
     :type task: Callable[[SynCRN], Any]
@@ -351,9 +384,34 @@ def _time_task(
     :type crn: SynCRN
     :param repeats: Number of repeats.
     :type repeats: int
-    :return: Tuple ``(seconds, result, error)``.
-    :rtype: Tuple[Optional[float], Any, Optional[str]]
+    :param time_budget: Hard wall-clock budget, or ``None`` for no limit.
+    :type time_budget: Optional[float]
+    :return: Tuple ``(seconds, result, error, timed_out)``.
+    :rtype: Tuple[Optional[float], Any, Optional[str], bool]
     """
+    if time_budget is not None:
+        start_method = "fork" if "fork" in get_all_start_methods() else "spawn"
+        context = get_context(start_method)
+        receiver, sender = context.Pipe(duplex=False)
+        process = context.Process(
+            target=_time_task_worker,
+            args=(task, crn, repeats, sender),
+        )
+        process.start()
+        sender.close()
+        process.join(max(0.0, time_budget))
+        if process.is_alive():
+            process.terminate()
+            process.join()
+            receiver.close()
+            return None, None, None, True
+        if receiver.poll():
+            seconds, result, error = receiver.recv()
+            receiver.close()
+            return seconds, result, error, False
+        receiver.close()
+        return None, None, f"worker exited with code {process.exitcode}", False
+
     best: Optional[float] = None
     result: Any = None
 
@@ -362,11 +420,11 @@ def _time_task(
         try:
             result = task(crn)
         except Exception as exc:  # pragma: no cover - reported, not raised
-            return None, None, f"{type(exc).__name__}: {exc}"
+            return None, None, f"{type(exc).__name__}: {exc}", False
         elapsed = time.perf_counter() - started
         best = elapsed if best is None else min(best, elapsed)
 
-    return best, result, None
+    return best, result, None, False
 
 
 def run_scaling_benchmark(
@@ -381,8 +439,8 @@ def run_scaling_benchmark(
 ) -> List[ScalingRecord]:
     """Time each analysis across network families and sizes.
 
-    Once a task exceeds ``time_budget`` on some size of a family, it is skipped
-    for every larger size of that family, so one slow analysis cannot make the
+    A task is terminated when it reaches ``time_budget`` and is skipped for
+    every larger size of that family, so one slow analysis cannot make the
     whole run open-ended.
 
     :param sizes:
@@ -445,8 +503,11 @@ def run_scaling_benchmark(
                 if (family, task) in exhausted:
                     continue
 
-                seconds, result, error = _time_task(
-                    TASKS[task], crn, repeats=repeats
+                seconds, result, error, timed_out = _time_task(
+                    TASKS[task],
+                    crn,
+                    repeats=repeats,
+                    time_budget=time_budget,
                 )
                 records.append(
                     ScalingRecord(
@@ -458,15 +519,13 @@ def run_scaling_benchmark(
                         seconds=seconds,
                         result=result,
                         error=error,
+                        timed_out=timed_out,
                     )
                 )
 
-                over_budget = (
-                    time_budget is not None
-                    and seconds is not None
-                    and seconds > time_budget
-                )
-                if error is not None or over_budget:
+                if error is not None:
+                    exhausted.add((family, task))
+                if timed_out:
                     exhausted.add((family, task))
 
     return records

{synkit-1.6.2 → synkit-1.6.3}/synkit/CRN/Benchmark/validate.py

@@ -3,10 +3,8 @@
 This is the reproducible form of the paper's validation table: every benchmark
 network is analysed, every asserted quantity is compared with the expected
 value, and every quantity is additionally recomputed by an independent route
-from :mod:`synkit.CRN.Benchmark.crosschecks`. A run that reports
-``all_passed`` therefore establishes two things at once — that the package
-reproduces the expected verdicts, and that it agrees with a second, disjoint
-computation of the same numbers.
+from :mod:`synkit.CRN.Benchmark.crosschecks`. ``all_passed`` requires agreement
+with both the expected verdicts and the independent computations.
 
 .. rubric:: Example
 

{synkit-1.6.2 → synkit-1.6.3}/synkit/CRN/IO/sbml.py

@@ -12,7 +12,7 @@ stoichiometry). No kinetic law is written, because a ``SynCRN`` carries none;
 structural analysis does not need one. Files that *do* carry kinetic laws are
 read fine — the laws are simply ignored.
 
-Two conversion choices are worth knowing:
+Conversion policies:
 
 - **Reversible reactions.** SBML marks a reaction ``reversible="true"``; a
   ``SynCRN`` reaction is always directed. On import, a reversible reaction is
@@ -564,6 +564,7 @@ def _read_species(
             "label": element.get("name") or sid,
             "smiles": annotation.get("smiles"),
             "sbml_id": sid,
+            "source_node_id": annotation.get("sourceNodeId", sid),
         }
 
     return species, dropped
@@ -799,7 +800,12 @@ def crn_from_sbml(
         reversible = _is_true(element.get("reversible"))
         annotation = _annotation_values(element, "reactionInfo")
 
-        extra: Dict[str, Any] = {"sbml_id": rid}
+        extra: Dict[str, Any] = {
+            "sbml_id": rid,
+            "source_node_id": annotation.get("sourceNodeId", rid),
+        }
+        if annotation.get("sourceKind"):
+            extra["source_kind"] = annotation["sourceKind"]
         if annotation.get("ruleRepr"):
             extra["rule_repr"] = annotation["ruleRepr"]
 

{synkit-1.6.2 → synkit-1.6.3}/synkit/CRN/Pathway/__init__.py

@@ -33,6 +33,9 @@ from .reachability import (
 from .realizability import (
     PathwayRealizability,
     RealizabilityConfig,
+    RealizabilityResult,
+    RealizabilitySearchLimit,
+    RealizabilityStatus,
     RealizabilitySummary,
     run_realizability_from_syncrn,
     syncrn_to_pr_inputs,
@@ -55,6 +58,9 @@ __all__ = [
     # realizability
     "PathwayRealizability",
     "RealizabilityConfig",
+    "RealizabilityResult",
+    "RealizabilitySearchLimit",
+    "RealizabilityStatus",
     "RealizabilitySummary",
     "run_realizability_from_syncrn",
     "syncrn_to_pr_inputs",