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2 changes: 2 additions & 0 deletions AUTHORS
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Expand Up @@ -21,3 +21,5 @@ Ethan Green
Josh Cooper
Matthew Dippel
Joshua Fisher-Caudill
Ben Blamey

2 changes: 1 addition & 1 deletion COPYRIGHT
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GillesPy2 is a Python 3 package for stochastic simulation of biochemical systems.
Copyright (C) 2019-2023 GillesPy2 developers.
Copyright (C) 2019-2024 GillesPy2 developers.

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
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<h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/cleanup.html
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<h1>Source code for gillespy2.core.cleanup</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/events.html
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<h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.functiondefinition</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/gillespyError.html
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<h1>Source code for gillespy2.core.gillespyError</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.gillespySolver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/jsonify.html
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<h1>Source code for gillespy2.core.jsonify</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.liveGraphing</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.model</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.parameter</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.raterule</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.reaction</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.results</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.core.sortableobject</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/species.html
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<h1>Source code for gillespy2.core.species</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/timespan.html
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<h1>Source code for gillespy2.core.timespan</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.build.build_engine</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.build.expression</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.build.make</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.build.template_gen</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.c_decoder</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.c_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.ode_c_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.ssa_c_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.cpp.tau_leaping_c_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.numpy.CLE_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.numpy.ode_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.numpy.ssa_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.numpy.tau_hybrid_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.numpy.tau_leaping_solver</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.stochkit.stochkit_solvers</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.utilities.Tau</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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<h1>Source code for gillespy2.solvers.utilities.cpp_support_test</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
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