bngsim 0.11.32__tar.gz

bngsim-0.11.32/.clang-format

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+BasedOnStyle: LLVM
+IndentWidth: 4
+ColumnLimit: 100

bngsim-0.11.32/.github/workflows/release.yml

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+name: release
+
+# Build release artifacts (wheels + sdist) and publish via PyPI Trusted
+# Publishing (OIDC — no API tokens).
+#
+#   - Manual run (workflow_dispatch): choose `testpypi` (rehearsal) or `pypi`.
+#   - Tag push (v*): publishes to PyPI.
+#
+# Scope: Linux (manylinux x86_64) + macOS arm64 + sdist. Intel-macOS / Windows
+# wheels can be added later; platforms without a wheel fall back to the sdist.
+#
+# The publish job runs in the `pypi` / `testpypi` GitHub Environment so it matches
+# the trusted-publisher configuration on (Test)PyPI.
+
+on:
+  workflow_dispatch:
+    inputs:
+      target:
+        description: "Publish target"
+        type: choice
+        options: [testpypi, pypi]
+        default: testpypi
+  push:
+    tags: ["v*"]
+
+concurrency:
+  group: release-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  wheels:
+    name: wheels · ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest        # manylinux x86_64
+          - os: macos-14             # macOS arm64 (Apple Silicon)
+            macos_target: "11.0"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v4.1.0
+        env:
+          MACOSX_DEPLOYMENT_TARGET: ${{ matrix.macos_target }}
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        run: pipx run build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist-sdist
+          path: ./dist/*.tar.gz
+          if-no-files-found: error
+
+  publish:
+    needs: [wheels, sdist]
+    runs-on: ubuntu-latest
+    # `pypi` for a tag push or an explicit dispatch target of pypi; else `testpypi`.
+    environment: ${{ (github.event_name == 'push' || inputs.target == 'pypi') && 'pypi' || 'testpypi' }}
+    permissions:
+      id-token: write        # OIDC token for Trusted Publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          pattern: dist-*
+          merge-multiple: true
+      - name: List collected distributions
+        run: ls -la dist
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist
+          repository-url: ${{ (github.event_name == 'push' || inputs.target == 'pypi') && 'https://upload.pypi.org/legacy/' || 'https://test.pypi.org/legacy/' }}

bngsim-0.11.32/.github/workflows/wheels.yml

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+name: wheels
+
+# Build binary wheels (Linux / macOS / Windows) + an sdist with cibuildwheel,
+# and upload them as CI artifacts. No PyPI publishing — that's a separate step.
+# Wheels bundle SuiteSparse/KLU (see [tool.cibuildwheel] in pyproject.toml).
+
+on:
+  workflow_dispatch: {}
+  push:
+    branches: [main]
+    paths:
+      - "pyproject.toml"
+      - "CMakeLists.txt"
+      - "src/**"
+      - "include/**"
+      - "third_party/**"
+      - "python/bngsim/**"
+      - "ci/**"
+      - ".github/workflows/wheels.yml"
+
+concurrency:
+  group: wheels-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  wheels:
+    name: wheels · ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    # Windows KLU (vcpkg AMD/COLAMD/BTF + dlsym) still WIP → non-blocking.
+    continue-on-error: ${{ matrix.os == 'windows-latest' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest          # manylinux x86_64
+          - os: macos-13               # macOS x86_64 (Intel)
+            macos_target: "10.15"      # from-source SuiteSparse -> broad target
+          - os: macos-14               # macOS arm64 (Apple Silicon)
+            macos_target: "11.0"       # arm64 floor; from-source SuiteSparse
+          - os: windows-latest         # Windows x86_64
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v4.1.0
+        env:
+          MACOSX_DEPLOYMENT_TARGET: ${{ matrix.macos_target }}
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  sdist:
+    name: sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        run: pipx run build --sdist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: ./dist/*.tar.gz
+          if-no-files-found: error

bngsim-0.11.32/.gitignore

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+# Sphinx build output
+docs/_build/

bngsim-0.11.32/.pre-commit-config.yaml

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+default_install_hook_types: [pre-commit, pre-push]
+default_stages: [pre-commit]
+fail_fast: false
+
+# Standalone bngsim/ config. In the upstream development monorepo the active
+# config lives at that repo's root (with every path bngsim/-prefixed); this file
+# is the de-prefixed sibling that travels with `git subtree split -P bngsim` so
+# the extracted repo lints/tests itself with no path fixups.
+
+# Globally excluded paths (apply to every hook below):
+#   - third_party/  vendored NFsim/SUNDIALS/exprtk/mir/rulemonkey source;
+#                   upstream-byte-faithful, do not reformat / EOL-fix
+#   - dev/          scratch notes, plans, ADRs — informal markdown
+exclude: ^(third_party|dev)/
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      # Hygiene hooks are scoped to *source* file types only.
+      # Test data (.bngl, .net, .ant, .xml, .gdat, .cdat, .csv, .json,
+      # …) must NOT be touched: many are byte-mirrored from upstream
+      # sources (BioModels SBML, BNG2.pl-generated .net) and are
+      # consumed by parsers that may be sensitive to whitespace/EOL.
+      - id: check-yaml
+        files: \.(yaml|yml)$
+      - id: end-of-file-fixer
+        files: ^.*\.(py|cpp|hpp|cc|cxx|hh|hxx|c|h|md|toml|cfg|ini|yaml|yml)$
+      - id: trailing-whitespace
+        files: ^.*\.(py|cpp|hpp|cc|cxx|hh|hxx|c|h|md|toml|cfg|ini|yaml|yml)$
+      - id: check-merge-conflict
+      - id: check-added-large-files
+        # Committed spec manifests (parity_checks/*/ *_jobs.json) run ~0.6 MB;
+        # the multi-MB SBML/SED-ML corpora are gitignored, so 1 MB still
+        # catches accidental binary commits.
+        args: ['--maxkb=1024']
+        # bng_parity golden.json is committed reference data (per-job seed=1
+        # checksums + fingerprints over the full 895-job corpus, ~1.7 MB at full
+        # coverage) — the same category as jobs.json above, just denser. The
+        # fingerprints are not thinnable without weakening the consumer check,
+        # so this one file is exempted from the 1 MB cap.
+        exclude: ^parity_checks/bng_parity/golden/golden\.json$
+      - id: mixed-line-ending
+        files: ^.*\.(py|cpp|hpp|cc|cxx|hh|hxx|c|h|md|toml|cfg|ini|yaml|yml)$
+      - id: debug-statements
+        files: ^.*\.py$
+      - id: detect-private-key
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.0
+    hooks:
+      # Lint + format gate the entire tree. Per-file ignores for E501
+      # (long lines) in benchmarks/harness/scripts live in
+      # pyproject.toml [tool.ruff.lint.per-file-ignores]; the dev/ tree
+      # (scratch notes) is gitignored.
+      - id: ruff
+        args: [--fix]
+        files: ^.*\.py$
+      - id: ruff-format
+        files: ^.*\.py$
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v17.0.6
+    hooks:
+      - id: clang-format
+        files: ^(src|include)/.*\.(c|cc|cpp|cxx|h|hh|hpp|hxx)$
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.13.0
+    hooks:
+      - id: mypy
+        files: ^python/bngsim/.*\.py$
+        args: [--ignore-missing-imports, --follow-imports=silent]
+        additional_dependencies: [numpy]
+
+  - repo: local
+    hooks:
+      - id: pytest
+        name: pytest (bngsim)
+        entry: bash -c '.venv/bin/pytest -q python/tests'
+        language: system
+        pass_filenames: false
+        files: ^.
+        stages: [pre-push]
+
+      # ─── Manual-stage local-CI hooks ─────────────────────────────────
+      # The wheel matrix is validated locally on each target platform.
+      # See scripts/LOCAL_CI.md. These hooks do NOT run on commit or
+      # push — invoke explicitly:
+      #
+      #   pre-commit run --hook-stage manual local-ci-wheel   --all-files
+      #   pre-commit run --hook-stage manual local-ci-matrix  --all-files
+      #   pre-commit run --hook-stage manual local-ci-linux   --all-files
+      - id: local-ci-wheel
+        name: local CI — wheel build + smoke (uv, current Python)
+        entry: uv run python scripts/local_ci.py wheel
+        language: system
+        pass_filenames: false
+        stages: [manual]
+      - id: local-ci-matrix
+        name: local CI — wheel matrix cp310-cp313 (uv, native arch)
+        entry: uv run python scripts/local_ci.py matrix
+        language: system
+        pass_filenames: false
+        stages: [manual]
+      - id: local-ci-linux
+        name: local CI — manylinux2014 wheel + smoke (Docker)
+        entry: bash scripts/local_ci_linux_docker.sh
+        language: system
+        pass_filenames: false
+        stages: [manual]
+      # Tripwire: verifies that third_party/nfsim/ matches what
+      # vendor + the patch series under scripts/nfsim_vendor_patches/
+      # would produce. Catches the silent-direct-edit class of regression.
+      # Requires /tmp/nfsim-vendor-candidate to exist at the vendor tip;
+      # build it via the recipe in scripts/NFSIM_VENDORING.md.
+      - id: local-ci-vendor-verify
+        name: local CI — verify vendored NFsim matches carry queue
+        entry: python3 scripts/vendor_nfsim.py --verify-clean
+        language: system
+        pass_filenames: false
+        stages: [manual]
+      - id: local-ci-vendor-verify-strict
+        name: local CI — vendor verify + patch-series reproducibility
+        entry: python3 scripts/vendor_nfsim.py --verify-clean --strict
+        language: system
+        pass_filenames: false
+        stages: [manual]

bngsim-0.11.32/.readthedocs.yaml

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+# Read the Docs build configuration.
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+#
+# This file assumes `bngsim/` is the repository root (the public-release
+# layout). If instead the docs are built from a repo where bngsim lives in a
+# subdirectory, move this file to that repo's root and prefix the paths below
+# with `bngsim/` (e.g. `sphinx.configuration: bngsim/docs/conf.py`).
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+  # bngsim is a compiled C++/pybind11 extension. autodoc imports the package,
+  # so the extension is built here. SUNDIALS is fetched+compiled by CMake.
+  apt_packages:
+    - cmake
+    - ninja-build
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    # Build+install bngsim so autodoc reads real signatures/docstrings.
+    # If the compile ever exceeds the RTD build limit, drop this entry: conf.py
+    # falls back to mocking `bngsim._bngsim_core`, and Sphinx documents the
+    # pure-Python wrappers without compiling the kernel.
+    - method: pip
+      path: .

bngsim-0.11.32/ACKNOWLEDGMENTS.md

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+# Acknowledgments
+
+BNGsim was developed and validated using a large body of excellent
+open-source software from the systems-biology and scientific-Python
+communities. Most of these tools are **not** redistributed with BNGsim. They
+were used as reference implementations, parity oracles, library dependencies,
+data corpora, or standards. We
+gratefully acknowledge their authors and cite their work below.
+
+> Third-party software and data that BNGsim redistributes (vendored code
+> and model/test-data corpora, with their license terms) are listed separately in
+> [`NOTICE`](NOTICE).
+
+## Reference simulators and cross-validation oracles
+
+BNGsim's numerical results were cross-validated against these simulation engines:
+
+- **libRoadRunner** — the primary ODE and SSA parity oracle.
+  - Somogyi ET, Bouteiller J-M, Glazier JA, König M, Medley JK, Swat MH,
+    Sauro HM. libRoadRunner: a high performance SBML simulation and analysis
+    library. *Bioinformatics.* 2015;31(20):3315–3321.
+    doi:10.1093/bioinformatics/btv363
+  - Welsh C, Xu J, Smith L, König M, Choi K, Sauro HM. libRoadRunner 2.0: a
+    high-performance SBML simulation and analysis library. *Bioinformatics.*
+    2023;39(1):btac770. doi:10.1093/bioinformatics/btac770
+- **AMICI** — the reference for BNGsim's forward-sensitivity and gradient work.
+  - Fröhlich F, Weindl D, Schälte Y, Pathirana D, Paszkowski Ł, Lines GT,
+    Stapor P, Hasenauer J. AMICI: high-performance sensitivity analysis for
+    large ordinary differential equation models. *Bioinformatics.*
+    2021;37(20):3676–3677. doi:10.1093/bioinformatics/btab227
+- **COPASI** — an independent third oracle (variable-volume, rate-rule, and
+  stochastic cross-checks).
+  - Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L,
+    Mendes P, Kummer U. COPASI—a COmplex PAthway SImulator. *Bioinformatics.*
+    2006;22(24):3067–3074. doi:10.1093/bioinformatics/btl485
+- **BioNetGen** (`BNG2.pl`, `run_network`, Network3) — used to generate reaction
+  networks and reference trajectories, and as a rule-based ODE/SSA oracle.
+  - Harris LA, Hogg JS, Tapia J-J, Sekar JAP, Gupta S, Korsunsky I, Arora A,
+    Barua D, Sheehan RP, Faeder JR. BioNetGen 2.2: advances in rule-based
+    modeling. *Bioinformatics.* 2016;32(21):3366–3368.
+    doi:10.1093/bioinformatics/btw469
+  - Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. BioNetGen: software for
+    rule-based modeling of signal transduction based on the interactions of
+    molecular domains. *Bioinformatics.* 2004;20(17):3289–3291.
+    doi:10.1093/bioinformatics/bth378
+- **NFsim** — the network-free stochastic oracle (also vendored into BNGsim; see
+  [`NOTICE`](NOTICE)).
+  - Sneddon MW, Faeder JR, Emonet T. Efficient modeling, simulation and
+    coarse-graining of biological complexity with NFsim. *Nat Methods.*
+    2011;8(2):177–183. doi:10.1038/nmeth.1546
+
+## Vendored simulation engines
+
+BNGsim embeds these rule-based engines (license terms in [`NOTICE`](NOTICE)):
+
+- **NFsim** — network-free simulation (cited above).
+- **RuleMonkey** — the canonical rule/species-graph library and stochastic
+  simulator. BNGsim vendors the current C++ version; the original simulator is
+  described in:
+  - Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG.
+    RuleMonkey: software for stochastic simulation of rule-based models.
+    *BMC Bioinformatics.* 2010;11:404. doi:10.1186/1471-2105-11-404
+
+## Model-description standards and formats
+
+BNGsim reads and/or writes these community standards:
+
+- **SBML** (Systems Biology Markup Language) — core model interchange format.
+  - Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al. The
+    systems biology markup language (SBML): a medium for representation and
+    exchange of biochemical network models. *Bioinformatics.*
+    2003;19(4):524–531. doi:10.1093/bioinformatics/btg015
+  - Keating SM, Waltemath D, König M, et al. SBML Level 3: an extensible format
+    for the exchange and reuse of biological models. *Mol Syst Biol.*
+    2020;16(8):e9110. doi:10.15252/msb.20199110
+- **SED-ML** (Simulation Experiment Description Markup Language) — read/write of
+  simulation descriptions; also the format of the SED-ML protocol files BNGsim
+  consumes from BioModels (via the `sys-bio/temp-biomodels` mirror).
+  - Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK,
+    Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N. Reproducible
+    computational biology experiments with SED-ML — the Simulation Experiment
+    Description Markup Language. *BMC Syst Biol.* 2011;5:198.
+    doi:10.1186/1752-0509-5-198
+- **COMBINE archive / OMEX** — pack/unpack of SBML + SED-ML + manifest.
+  - Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M,
+    Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM,
+    Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N. COMBINE
+    archive and OMEX format: one file to share all information to reproduce a
+    modeling project. *BMC Bioinformatics.* 2014;15:369.
+    doi:10.1186/s12859-014-0369-z
+- **Antimony** — read/write via the Antimony library.
+  - Smith LP, Bergmann FT, Chandran D, Sauro HM. Antimony: a modular model
+    definition language. *Bioinformatics.* 2009;25(18):2452–2454.
+    doi:10.1093/bioinformatics/btp401
+- **BNGL** and the BNG `.net` format (BioNetGen, cited above), **Content
+  MathML**, and **KiSAO** (the Kinetic Simulation Algorithm Ontology, used to
+  tag SED-ML algorithms) are also handled.
+
+## Numerical and infrastructure libraries
+
+- **SUNDIALS** — the CVODES and KINSOL solvers underpin BNGsim's ODE
+  integration, forward sensitivities, and steady-state solves (bundled in
+  binary wheels).
+  - Hindmarsh AC, Brown PN, Grant KE, Lee SL, Serban R, Shumaker DE,
+    Woodward CS. SUNDIALS: Suite of nonlinear and differential/algebraic
+    equation solvers. *ACM Trans Math Softw.* 2005;31(3):363–396.
+    doi:10.1145/1089014.1089020
+- **SuiteSparse / KLU** — sparse direct solver for the sparse-Jacobian path.
+  - Davis TA, Palamadai Natarajan E. Algorithm 907: KLU, a direct sparse solver
+    for circuit simulation problems. *ACM Trans Math Softw.*
+    2010;37(3):Article 36. doi:10.1145/1824801.1824814
+- **LAPACK** — dense linear algebra used by the numerical backends.
+  - Anderson E, Bai Z, Bischof C, et al. LAPACK Users' Guide. 3rd ed.
+    Philadelphia: SIAM; 1999. doi:10.1137/1.9780898719604
+- **libSBML** — the SBML read/write API.
+  - Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: an API library for
+    SBML. *Bioinformatics.* 2008;24(6):880–881.
+    doi:10.1093/bioinformatics/btn051
+- **NumPy** — array programming throughout BNGsim.
+  - Harris CR, Millman KJ, van der Walt SJ, et al. Array programming with NumPy.
+    *Nature.* 2020;585(7825):357–362. doi:10.1038/s41586-020-2649-2
+- **SciPy** — scientific-computing routines (used in the test, benchmark, and
+  parity suites).
+  - Virtanen P, Gommers R, Oliphant TE, et al. SciPy 1.0: fundamental algorithms
+    for scientific computing in Python. *Nat Methods.* 2020;17(3):261–272.
+    doi:10.1038/s41592-019-0686-2
+- **SymPy** — symbolic differentiation for code-generated sensitivities and
+  Jacobians.
+  - Meurer A, Smith CP, Paprocki M, et al. SymPy: symbolic computing in Python.
+    *PeerJ Comput Sci.* 2017;3:e103. doi:10.7717/peerj-cs.103
+- **pandas** — the `Result.to_dataframe()` export.
+  - McKinney W. Data structures for statistical computing in Python. In:
+    *Proceedings of the 9th Python in Science Conference (SciPy).* 2010:56–61.
+    doi:10.25080/Majora-92bf1922-00a
+- **ExprTk** (Arash Partow; https://github.com/ArashPartow/exprtk) — the
+  vendored C++ math-expression evaluator; **MIR** (Vladimir Makarov;
+  https://github.com/vnmakarov/mir) — the optional micro-JIT backend; and
+  **pybind11** (Wenzel Jakob, Jason Rhinelander, Dean Moldovan;
+  https://github.com/pybind/pybind11) — the C++/Python binding layer. These are
+  software projects without an associated paper.
+
+## Optional feature backends and interoperability
+
+- **JAX** — the differentiable RHS/Jacobian bridge.
+  - Bradbury J, Frostig R, Hawkins P, Johnson MJ, Katariya Y, Leary C,
+    Maclaurin D, Necula G, Paszke A, VanderPlas J, Wanderman-Milne S, Zhang Q.
+    JAX: composable transformations of Python+NumPy programs. 2018.
+    http://github.com/jax-ml/jax
+- **Diffrax** — the JAX-based differentiable ODE solver backend.
+  - Kidger P. On Neural Differential Equations. PhD thesis, University of
+    Oxford; 2021. arXiv:2202.02435
+- **xarray** — labeled N-D arrays for the `Result.to_xarray()` / netCDF export.
+  - Hoyer S, Hamman J. xarray: N-D labeled Arrays and Datasets in Python.
+    *J Open Res Softw.* 2017;5(1):10. doi:10.5334/jors.148
+- **h5py** — HDF5 archival of results (Andrew Collette and contributors;
+  https://www.h5py.org).
+- **Vivarium** — the `bngsim.vivarium` process wrapper for multiscale modeling.
+  - Agmon E, Spangler RK, Skalnik CJ, Poole W, Peirce SM, Morrison JH,
+    Covert MW. Vivarium: an interface and engine for integrative multiscale
+    modeling in computational biology. *Bioinformatics.* 2022;38(7):1972–1979.
+    doi:10.1093/bioinformatics/btac049
+- **PyBNF (PyBioNetFit)** — the parameter-fitting front end that drives BNGsim,
+  and the source of several example models.
+  - Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM, Posner RG,
+    Hlavacek WS. PyBioNetFit and the Biological Property Specification Language.
+    *iScience.* 2019;19:1012–1036. doi:10.1016/j.isci.2019.08.045
+
+## Test suites and model corpora
+
+BNGsim's correctness is checked against, and its benchmarks draw from, these
+community corpora (vendored corpora and their licenses are in [`NOTICE`](NOTICE)):
+
+- **SBML Semantic Test Suite** — the SBML Team's conformance suite
+  (https://github.com/sbmlteam/sbml-test-suite).
+- **DSMTS (Discrete Stochastic Models Test Suite)** — vendored for hermetic
+  stochastic testing.
+  - Evans TW, Gillespie CS, Wilkinson DJ. The SBML discrete stochastic models
+    test suite. *Bioinformatics.* 2008;24(2):285–286.
+    doi:10.1093/bioinformatics/btm566
+- **BioModels Database** — the curated ODE model corpus (with its SED-ML
+  protocols) used for ODE benchmarking.
+  - Malik-Sheriff RS, Glont M, Nguyen TVN, et al. BioModels—15 years of sharing
+    computational models in life science. *Nucleic Acids Res.*
+    2020;48(D1):D407–D415. doi:10.1093/nar/gkz1055
+- **RuleHub** (RuleWorld; https://github.com/RuleWorld/RuleHub), **BNGL-Models**
+  (https://github.com/wshlavacek/BNGL-Models), and the **BioNetGen model
+  distribution** (Models2) — vendored BNGL model corpora (see [`NOTICE`](NOTICE)).
+
+## Algorithms
+
+- **Gillespie's Stochastic Simulation Algorithm (direct method)** — the basis of
+  BNGsim's exact SSA.
+  - Gillespie DT. Exact stochastic simulation of coupled chemical reactions.
+    *J Phys Chem.* 1977;81(25):2340–2361. doi:10.1021/j100540a008
+- **Extrande** — a thinning sampler used as an independent test oracle for the
+  rate-rule-under-SSA hybrid path.
+  - Voliotis M, Thomas P, Grima R, Bowsher CG. Stochastic simulation of
+    biomolecular networks in dynamic environments. *PLoS Comput Biol.*
+    2016;12(6):e1004923. doi:10.1371/journal.pcbi.1004923
+
+## Build, test, and documentation tooling
+
+BNGsim is built with **scikit-build-core**, **CMake**, **Ninja**, and
+**pybind11** (stubs via **pybind11-stubgen**); tested with **pytest** and linted
+with **ruff**, **mypy**, and **clang-format**; documented with **Sphinx**,
+**MyST-Parser**, and **Furo**. Benchmark and parity tooling additionally uses
+**matplotlib** and **bioservices**. We thank the maintainers of these projects.