synkit 1.6.1b1__tar.gz → 1.6.2__tar.gz

synkit-1.6.2/.gitignore

@@ -0,0 +1,116 @@
+# 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/
+
+# Generated logs, reports, notebooks, and data files
+*.log
+*.pdf
+*.rdf
+*.ipynb
+*.csv
+*.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
+!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
+
+# 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/
+/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-1.6.2/PKG-INFO

@@ -0,0 +1,183 @@
+Metadata-Version: 2.4
+Name: synkit
+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
+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: MIT
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+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
+Requires-Dist: requests>=2.32.3
+Requires-Dist: scikit-learn>=1.4.0
+Requires-Dist: scipy>=1.14.0
+Requires-Dist: seaborn>=0.13.2
+Provides-Extra: all
+Requires-Dist: numpy>=2.2.0; 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'
+Description-Content-Type: text/markdown
+
+# SynKit
+
+[![PyPI version](https://img.shields.io/pypi/v/synkit.svg)](https://pypi.org/project/synkit/)
+[![Conda version](https://img.shields.io/conda/vn/tieulongphan/synkit.svg)](https://anaconda.org/tieulongphan/synkit)
+[![Docker Pulls](https://img.shields.io/docker/pulls/tieulongphan/synkit.svg)](https://hub.docker.com/r/tieulongphan/synkit)
+[![Docker Image Version](https://img.shields.io/docker/v/tieulongphan/synkit/latest?label=container)](https://hub.docker.com/r/tieulongphan/synkit)
+[![License](https://img.shields.io/github/license/tieulongphan/synkit.svg)](https://github.com/tieulongphan/synkit/blob/main/LICENSE)
+[![Release](https://img.shields.io/github/v/release/tieulongphan/synkit.svg)](https://github.com/tieulongphan/synkit/releases)
+[![Last Commit](https://img.shields.io/github/last-commit/tieulongphan/synkit.svg)](https://github.com/tieulongphan/synkit/commits)
+[![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)
+[![Stars](https://img.shields.io/github/stars/tieulongphan/synkit.svg?style=social&label=Star)](https://github.com/tieulongphan/synkit/stargazers)
+
+**Graph-native reaction informatics and executable electron-flow models**
+
+SynKit is a Python toolkit for atom-mapped reactions, chemical graph
+transformations, Lewis-labelled graphs, and explicitly supplied reaction
+mechanisms. It connects reaction representation, rule extraction, graph
+rewriting, stereochemistry, and mechanism verification through a common
+attributed-graph model.
+
+SynKit verifies mechanisms supplied by the user; it does not claim to predict
+the kinetically or thermodynamically preferred mechanism.
+
+![SynKit graphical abstract](https://raw.githubusercontent.com/TieuLongPhan/SynKit/main/Data/Figure/synkit_graphical_abstract.svg)
+
+## Highlights
+
+- Convert mapped reaction SMILES into ITS and reaction-centre graphs.
+- Extract and apply attributed graph-transformation rules.
+- Represent lone pairs, radicals, and separate sigma and pi occupancies with
+  Lewis-labelled graphs.
+- Execute curved-arrow and atomically coupled fishhook events.
+- Preserve tetrahedral, axial, and extended stereochemical information.
+- Build and analyse mechanism trajectory graphs and chemical reaction
+  networks.
+
+## Installation
+
+SynKit requires Python 3.11 or later.
+
+```bash
+python -m pip install synkit
+```
+
+Install the optional dependencies with:
+
+```bash
+python -m pip install "synkit[all]"
+```
+
+Alternatively, use the published container:
+
+```bash
+docker pull tieulongphan/synkit:latest
+docker run --rm tieulongphan/synkit:latest \
+  python -c "import synkit; print(synkit.__version__)"
+```
+
+## Quick start
+
+This self-contained example converts an atom-mapped substitution into an
+imaginary transition-state graph and reports its changed bonds:
+
+```python
+from synkit.IO import rsmi_to_its
+
+reaction = "[CH3:1][Br:2].[OH-:3]>>[CH3:1][OH:3].[Br-:2]"
+its = rsmi_to_its(reaction, core=False, format="tuple")
+
+changed_bonds = [
+    (source, target, data["order"])
+    for source, target, data in its.edges(data=True)
+    if data["order"][0] != data["order"][1]
+]
+print(changed_bonds)
+```
+
+The output records the broken C-Br bond as `(1.0, 0.0)` and the formed C-O
+bond as `(0.0, 1.0)`. Continue with the
+[graph](https://tieulongphan.github.io/SynKit/graph.html),
+[rule](https://tieulongphan.github.io/SynKit/rule.html), and
+[synthesis](https://tieulongphan.github.io/SynKit/synthesis.html) guides.
+
+## Supplied-mechanism verification
+
+SynKit can parse typed electron-flow annotations, replay their elementary
+steps, and return a verification certificate and mechanism trajectory graph.
+Canonical electron loci distinguish lone pairs, sigma bonds, pi bonds, and
+radical electrons. Curved arrows carry two electrons; fishhooks carry one;
+coupled radical events commit atomically from a common pre-state.
+
+See the
+[mechanism documentation](https://tieulongphan.github.io/SynKit/mechanism.html)
+for the supported interchange formats, verification policies, and complete
+examples.
+
+## 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/README.md

@@ -0,0 +1,143 @@
+# SynKit
+
+[![PyPI version](https://img.shields.io/pypi/v/synkit.svg)](https://pypi.org/project/synkit/)
+[![Conda version](https://img.shields.io/conda/vn/tieulongphan/synkit.svg)](https://anaconda.org/tieulongphan/synkit)
+[![Docker Pulls](https://img.shields.io/docker/pulls/tieulongphan/synkit.svg)](https://hub.docker.com/r/tieulongphan/synkit)
+[![Docker Image Version](https://img.shields.io/docker/v/tieulongphan/synkit/latest?label=container)](https://hub.docker.com/r/tieulongphan/synkit)
+[![License](https://img.shields.io/github/license/tieulongphan/synkit.svg)](https://github.com/tieulongphan/synkit/blob/main/LICENSE)
+[![Release](https://img.shields.io/github/v/release/tieulongphan/synkit.svg)](https://github.com/tieulongphan/synkit/releases)
+[![Last Commit](https://img.shields.io/github/last-commit/tieulongphan/synkit.svg)](https://github.com/tieulongphan/synkit/commits)
+[![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)
+[![Stars](https://img.shields.io/github/stars/tieulongphan/synkit.svg?style=social&label=Star)](https://github.com/tieulongphan/synkit/stargazers)
+
+**Graph-native reaction informatics and executable electron-flow models**
+
+SynKit is a Python toolkit for atom-mapped reactions, chemical graph
+transformations, Lewis-labelled graphs, and explicitly supplied reaction
+mechanisms. It connects reaction representation, rule extraction, graph
+rewriting, stereochemistry, and mechanism verification through a common
+attributed-graph model.
+
+SynKit verifies mechanisms supplied by the user; it does not claim to predict
+the kinetically or thermodynamically preferred mechanism.
+
+![SynKit graphical abstract](https://raw.githubusercontent.com/TieuLongPhan/SynKit/main/Data/Figure/synkit_graphical_abstract.svg)
+
+## Highlights
+
+- Convert mapped reaction SMILES into ITS and reaction-centre graphs.
+- Extract and apply attributed graph-transformation rules.
+- Represent lone pairs, radicals, and separate sigma and pi occupancies with
+  Lewis-labelled graphs.
+- Execute curved-arrow and atomically coupled fishhook events.
+- Preserve tetrahedral, axial, and extended stereochemical information.
+- Build and analyse mechanism trajectory graphs and chemical reaction
+  networks.
+
+## Installation
+
+SynKit requires Python 3.11 or later.
+
+```bash
+python -m pip install synkit
+```
+
+Install the optional dependencies with:
+
+```bash
+python -m pip install "synkit[all]"
+```
+
+Alternatively, use the published container:
+
+```bash
+docker pull tieulongphan/synkit:latest
+docker run --rm tieulongphan/synkit:latest \
+  python -c "import synkit; print(synkit.__version__)"
+```
+
+## Quick start
+
+This self-contained example converts an atom-mapped substitution into an
+imaginary transition-state graph and reports its changed bonds:
+
+```python
+from synkit.IO import rsmi_to_its
+
+reaction = "[CH3:1][Br:2].[OH-:3]>>[CH3:1][OH:3].[Br-:2]"
+its = rsmi_to_its(reaction, core=False, format="tuple")
+
+changed_bonds = [
+    (source, target, data["order"])
+    for source, target, data in its.edges(data=True)
+    if data["order"][0] != data["order"][1]
+]
+print(changed_bonds)
+```
+
+The output records the broken C-Br bond as `(1.0, 0.0)` and the formed C-O
+bond as `(0.0, 1.0)`. Continue with the
+[graph](https://tieulongphan.github.io/SynKit/graph.html),
+[rule](https://tieulongphan.github.io/SynKit/rule.html), and
+[synthesis](https://tieulongphan.github.io/SynKit/synthesis.html) guides.
+
+## Supplied-mechanism verification
+
+SynKit can parse typed electron-flow annotations, replay their elementary
+steps, and return a verification certificate and mechanism trajectory graph.
+Canonical electron loci distinguish lone pairs, sigma bonds, pi bonds, and
+radical electrons. Curved arrows carry two electrons; fishhooks carry one;
+coupled radical events commit atomically from a common pre-state.
+
+See the
+[mechanism documentation](https://tieulongphan.github.io/SynKit/mechanism.html)
+for the supported interchange formats, verification policies, and complete
+examples.
+
+## 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-1.6.1b1 → synkit-1.6.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "1.6.1b1"
+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",
+]