NOTICE

BNGsim — THIRD-PARTY NOTICES
============================

BNGsim itself is licensed under the MIT License; see the LICENSE file in this
directory for the full text and the U.S. Government / Triad National Security
copyright notice (Los Alamos National Laboratory release O5098).

This NOTICE lists third-party software and data that BNGsim redistributes —
either vendored into the source tree or, in the case of SUNDIALS and
SuiteSparse, built from source and linked into the installed package (SUNDIALS
statically; SuiteSparse/KLU as bundled shared libraries). SuiteSparse/KLU is
bundled both into the binary wheels and, when a source (sdist) install finds no
system SuiteSparse, into that build's package directory. Each component is
redistributed under its own license, reproduced or referenced below; where
BNGsim has modified a component, that is stated.

Per-file provenance for the vendored model and test-data corpora — the exact
upstream path, pinned commit, and SHA-256 of each individual file — is
documented in benchmarks/models/README.md, benchmarks/models/sbml/README.md,
and the corpus manifests under parity_checks/ and harness/.


================================================================================
1. Vendored source code (third_party/)
================================================================================

--------------------------------------------------------------------------------
NFsim — network-free stochastic simulator
--------------------------------------------------------------------------------
Upstream:      https://github.com/RuleWorld/nfsim
Version:       branch `bngsim/vendor` at 8478a3c8 (based on origin/master 4c3da839)
License:       MIT — Copyright (c) 2016 Michael W. Sneddon, James R. Faeder,
               Thierry Emonet
In repository: third_party/nfsim/
License text:  third_party/nfsim/LICENSE.txt
Modified:      YES. BNGsim carries local patches to the vendored NFsim (raising
               exceptions instead of exit()/terminate, BNG-compatibility fixes,
               and library-only build trims). Every change is recorded in
               third_party/nfsim/VENDOR.json ("carry_queue").

--------------------------------------------------------------------------------
RuleMonkey — canonical rule/species graph library
--------------------------------------------------------------------------------
Upstream:      https://github.com/richardposner/RuleMonkey
Version:       fbdde54f
License:       MIT — Copyright (c) 2026 Bill Hlavacek
In repository: third_party/rulemonkey/
License text:  third_party/rulemonkey/LICENSE
Modified:      No source changes. The CLI, tests, and examples are pruned and one
               include path is normalized at build-configuration time
               (third_party/rulemonkey/VENDOR.json).

--------------------------------------------------------------------------------
MIR — lightweight JIT compiler (optional micro-JIT backend, default OFF)
--------------------------------------------------------------------------------
Upstream:      https://github.com/vnmakarov/mir
Version:       439a90a2
License:       MIT — Copyright (c) 2018-2024 Vladimir Makarov
In repository: third_party/mir/
License text:  third_party/mir/LICENSE
Modified:      No. The upstream tree is pruned to the translation units BNGsim
               builds (third_party/mir/VENDOR.json). The MIR backend is gated
               behind the BNGSIM_ENABLE_MIR CMake option and is OFF by default.

--------------------------------------------------------------------------------
ExprTk — C++ Mathematical Expression Toolkit Library
--------------------------------------------------------------------------------
Upstream:      https://github.com/ArashPartow/exprtk
Version:       66883f0d
License:       MIT — Copyright (c) 1999-2025 Arash Partow
In repository: third_party/exprtk/exprtk.hpp
License text:  third_party/exprtk/LICENSE (also stated in the exprtk.hpp header)
Modified:      No.


================================================================================
2. Build-time dependencies bundled in binary (wheel) distributions
================================================================================

--------------------------------------------------------------------------------
SUNDIALS — SUite of Nonlinear and DIfferential/ALgebraic equation Solvers
--------------------------------------------------------------------------------
Upstream:      https://github.com/LLNL/sundials
Version:       v7.2.1
License:       BSD-3-Clause — Copyright (c) 2002-2024, Lawrence Livermore National
               Security and Southern Methodist University
In repository: Not committed to source. Fetched at build time from the pinned
               official release archive (third_party/sundials/VENDOR.json, via
               CMake FetchContent) and statically linked into the compiled
               extension, so it is present in BNGsim's binary wheel distributions.
License text:  https://github.com/LLNL/sundials/blob/v7.2.1/LICENSE
               (BSD-3-Clause text reproduced in Section 5 below)
Modified:      No.

--------------------------------------------------------------------------------
SuiteSparse — KLU sparse direct solver and its ordering/support libraries
--------------------------------------------------------------------------------
Upstream:      https://github.com/DrTimothyAldenDavis/SuiteSparse
Version:       v7.8.3 (commit d3c4926d)
Components:    Only the KLU subset SUNDIALS' KLU linear-solver interface links is
               built and bundled, under two licenses:
                 - KLU, BTF ............. GNU LGPL-2.1-or-later
                       Copyright (C) 2004-2023, University of Florida
                       (Timothy A. Davis and Ekanathan Palamadai)
                 - AMD, COLAMD .......... BSD-3-Clause
                       AMD Copyright (c) 1996-2023, Timothy A. Davis,
                       Patrick R. Amestoy, and Iain S. Duff
                       COLAMD Copyright (c) 1998-2023, Timothy A. Davis
                 - SuiteSparse_config ... BSD-3-Clause
                       Copyright (c) 2012-2023, Timothy A. Davis
               Built with -DKLU_USE_CHOLMOD=OFF, so CHOLMOD/CAMD/CCOLAMD and any
               BLAS dependency are excluded; SUNDIALS' KLU interface does not
               need them.
In repository: Not committed to source. Built FROM SOURCE at the pinned tag at
               wheel-build time (ci/build_suitesparse.sh, ci/build_suitesparse.ps1)
               as SHARED libraries and bundled into the binary wheels by the
               wheel-repair step (auditwheel / delocate / delvewheel). Because the
               LGPL-2.1+ components (KLU, BTF) are dynamically linked and shipped
               as separate, replaceable shared libraries, their inclusion in an
               otherwise-MIT work is permitted by LGPL-2.1.
License text:  KLU/BTF: GNU LGPL v2.1 — reproduced in full in Section 5 below.
               AMD/COLAMD/SuiteSparse_config: BSD-3-Clause — reproduced in
               Section 5 below. Upstream per-package texts: AMD/Doc/License.txt,
               COLAMD/Doc/License.txt, BTF/Doc/License.txt, KLU/Doc/License.txt at
               the pinned tag (SuiteSparse_config carries a BSD-3-Clause SPDX
               header).
Modified:      No. The build configuration selects the subset; sources are
               byte-identical to upstream v7.8.3.


================================================================================
3. Vendored model and test-data corpora
================================================================================

These are redistributed data files (BNGL / SBML models and stochastic test
cases). Per-file provenance — upstream path, pinned commit, and SHA-256 — is in
benchmarks/models/README.md and the corpus manifests under parity_checks/ and
harness/.

--------------------------------------------------------------------------------
RuleHub — curated rule-based model repository
--------------------------------------------------------------------------------
Upstream:      https://github.com/RuleWorld/RuleHub
Version:       479d6d62
License:       MIT — Copyright (c) 2018 RuleWorld (no individual holder is named
               in the upstream LICENSE)
In repository: benchmarks/models/ (bngl/rulehub/ and curated role buckets),
               parity_checks/bng_parity/ (vendored per manifest.json)
License text:  MIT — reproduced in Section 5 below.
Modified:      Some vendored copies were comment-scrubbed (comments/formatting
               only; the reaction network is unchanged).

--------------------------------------------------------------------------------
BNGL-Models — BNGL model collection
--------------------------------------------------------------------------------
Upstream:      https://github.com/wshlavacek/BNGL-Models
Version:       81c90d8f
License:       CC-BY-4.0 — Copyright (c) 2026 Bill Hlavacek
               (https://creativecommons.org/licenses/by/4.0/)
In repository: benchmarks/models/ (curated role buckets),
               parity_checks/bng_parity/ (vendored per manifest.json)
Attribution (required by CC-BY-4.0):
                 Title:   BNGL-Models
                 Author:  Bill Hlavacek
                 Source:  https://github.com/wshlavacek/BNGL-Models
                 License: CC-BY-4.0
Modified:      YES — some vendored copies were comment-scrubbed (comments/
               formatting only; reaction networks unchanged). CC-BY-4.0 requires
               this indication that changes were made.

--------------------------------------------------------------------------------
BioNetGen model distribution (Models2)
--------------------------------------------------------------------------------
Upstream:      BioNetGen 2.9.3 distribution — https://github.com/RuleWorld/bionetgen
Version:       2.9.3
License:       MIT — Copyright (c) 2024 James R. Faeder
In repository: benchmarks/models/ (bngl/models2/ and some curated role buckets)
License text:  MIT — reproduced in Section 5 below.
Modified:      No.

--------------------------------------------------------------------------------
DSMTS — Discrete Stochastic Models Test Suite
--------------------------------------------------------------------------------
Upstream:      https://github.com/sbmlteam/sbml-test-suite
               (commit 473e119d, "3.4.0-36-g473e119dd")
Original
authors:       Thomas W. Evans, Colin S. Gillespie, Darren J. Wilkinson
License:       GNU LGPL-2.1-or-later — Copyright (C) 2004-2017 jointly by the
               California Institute of Technology, EMBL-EBI, University of
               Heidelberg, University of Tübingen, The Babraham Institute, and
               the University of Hertfordshire (see the vendored LICENSE.txt)
In repository: harness/sbml_test_suite/dsmts/cases/ (the 39 DSMTS-proper
               stochastic cases, 156 files; hashed in dsmts_manifest.json)
License text:  harness/sbml_test_suite/dsmts/LICENSE.txt (upstream terms and the
               DSMTS attribution) and harness/sbml_test_suite/dsmts/COPYING.txt
               (the full GNU LGPL v2.1)
Modified:      No — vendored byte-identical to upstream at the pinned commit.


================================================================================
4. Development and validation tools (NOT redistributed)
================================================================================

BNGsim was developed and validated against several external tools that are NOT
redistributed with it — RoadRunner, AMICI, COPASI, BioNetGen's BNG2.pl /
run_network, and the SBML semantic test suite. Using them as reference oracles
imposes no redistribution obligation, but they are gratefully acknowledged, with
citations, in ACKNOWLEDGMENTS.md.


================================================================================
5. Full license texts
================================================================================

--------------------------------------------------------------------------------
MIT License
--------------------------------------------------------------------------------
Applies to NFsim, RuleMonkey, MIR, ExprTk, RuleHub, and the BioNetGen Models2
distribution, each under its own copyright as listed in Sections 1 and 3.

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

--------------------------------------------------------------------------------
BSD 3-Clause License
--------------------------------------------------------------------------------
Applies to SUNDIALS (Copyright (c) 2002-2024, Lawrence Livermore National
Security and Southern Methodist University) and to the SuiteSparse components
AMD (Copyright (c) 1996-2023, Timothy A. Davis, Patrick R. Amestoy, and Iain S.
Duff), COLAMD (Copyright (c) 1998-2023, Timothy A. Davis), and
SuiteSparse_config (Copyright (c) 2012-2023, Timothy A. Davis). All rights
reserved by the respective copyright holders.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors
   may be used to endorse or promote products derived from this software without
   specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

--------------------------------------------------------------------------------
Creative Commons Attribution 4.0 International (CC-BY-4.0)
--------------------------------------------------------------------------------
Applies to BNGL-Models. Full legal code:
https://creativecommons.org/licenses/by/4.0/legalcode
Human-readable summary: https://creativecommons.org/licenses/by/4.0/
Attribution is provided in Section 3 above; changes made by BNGsim are noted.

--------------------------------------------------------------------------------
GNU Lesser General Public License, version 2.1
--------------------------------------------------------------------------------
Applies to:
  - the SuiteSparse components KLU and BTF (Section 2), built from source and
    bundled as shared libraries in the binary (wheel) distributions; and
  - the DSMTS test cases (Section 3).

Both are shipped such that the LGPL-2.1 components remain replaceable (KLU/BTF as
dynamically linked shared libraries; the DSMTS cases as verbatim data files). The
SBML Test Suite's own terms (including the DSMTS attribution) are vendored at
harness/sbml_test_suite/dsmts/LICENSE.txt. The full GNU LGPL v2.1 text follows.

                  GNU LESSER GENERAL PUBLIC LICENSE
                       Version 2.1, February 1999

 Copyright (C) 1991, 1999 Free Software Foundation, Inc.
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 Everyone is permitted to copy and distribute verbatim copies
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    that part of it is a work based on the Library, and explaining
    where to find the accompanying uncombined form of the same work.

  8. You may not copy, modify, sublicense, link with, or distribute
the Library except as expressly provided under this License.  Any
attempt otherwise to copy, modify, sublicense, link with, or
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rights under this License.  However, parties who have received copies,
or rights, from you under this License will not have their licenses
terminated so long as such parties remain in full compliance.

  9. You are not required to accept this License, since you have not
signed it.  However, nothing else grants you permission to modify or
distribute the Library or its derivative works.  These actions are
prohibited by law if you do not accept this License.  Therefore, by
modifying or distributing the Library (or any work based on the
Library), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Library or works based on it.

  10. Each time you redistribute the Library (or any work based on the
Library), the recipient automatically receives a license from the
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You are not responsible for enforcing compliance by third parties with
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^L
  11. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
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If any portion of this section is held invalid or unenforceable under
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It is not the purpose of this section to induce you to infringe any
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to distribute software through any other system and a licensee cannot
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This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.

  12. If the distribution and/or use of the Library is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Library under this License
may add an explicit geographical distribution limitation excluding those
countries, so that distribution is permitted only in or among
countries not thus excluded.  In such case, this License incorporates
the limitation as if written in the body of this License.

  13. The Free Software Foundation may publish revised and/or new
versions of the Lesser General Public License from time to time.
Such new versions will be similar in spirit to the present version,
but may differ in detail to address new problems or concerns.

Each version is given a distinguishing version number.  If the Library
specifies a version number of this License which applies to it and
"any later version", you have the option of following the terms and
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the Free Software Foundation.  If the Library does not specify a
license version number, you may choose any version ever published by
the Free Software Foundation.
^L
  14. If you wish to incorporate parts of the Library into other free
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write to the author to ask for permission.  For software which is
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                            NO WARRANTY

  15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
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LIBRARY IS WITH YOU.  SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

  16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
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                     END OF TERMS AND CONDITIONS
^L
           How to Apply These Terms to Your New Libraries

  If you develop a new library, and you want it to be of the greatest
possible use to the public, we recommend making it free software that
everyone can redistribute and change.  You can do so by permitting
redistribution under these terms (or, alternatively, under the terms
of the ordinary General Public License).

  To apply these terms, attach the following notices to the library.
It is safest to attach them to the start of each source file to most
effectively convey the exclusion of warranty; and each file should
have at least the "copyright" line and a pointer to where the full
notice is found.


    <one line to give the library's name and a brief idea of what it
does.>
    Copyright (C) <year>  <name of author>

    This library is free software; you can redistribute it and/or
    modify it under the terms of the GNU Lesser General Public
    License as published by the Free Software Foundation; either
    version 2.1 of the License, or (at your option) any later version.

    This library is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
    Lesser General Public License for more details.

    You should have received a copy of the GNU Lesser General Public
    License along with this library; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA

Also add information on how to contact you by electronic and paper
mail.

You should also get your employer (if you work as a programmer) or
your school, if any, to sign a "copyright disclaimer" for the library,
if necessary.  Here is a sample; alter the names:

  Yoyodyne, Inc., hereby disclaims all copyright interest in the
  library `Frob' (a library for tweaking knobs) written by James
  Random Hacker.

  <signature of Ty Coon>, 1 April 1990
  Ty Coon, President of Vice

That's all there is to it!