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Fix regex strings #961

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merged 12 commits into from
Sep 19, 2024
Merged

Fix regex strings #961

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c5e3a56
Updated copyright and authors
briandrawert Aug 1, 2024
252d895
resolved conflicts
briandrawert Aug 1, 2024
30267b2
fixing unit test for suffix
briandrawert Aug 20, 2024
23297c5
updating test to use python 3.12
briandrawert Aug 20, 2024
4f039b5
Updating the rest of the test to Python 3.12
briandrawert Aug 20, 2024
99ab05d
updated test
briandrawert Aug 20, 2024
95892e6
Updating depricated code
briandrawert Aug 20, 2024
944b062
Updated tests
briandrawert Sep 12, 2024
21d46e0
added .odf to another spot
briandrawert Sep 19, 2024
78b5ee4
changed regex strings to raw strings
briandrawert Sep 19, 2024
d2314b9
Python doesn't like latex commands, need to make the comments a raw s…
briandrawert Sep 19, 2024
fb14813
assertEquals is not a valid function name
briandrawert Sep 19, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/run-full-tests.yml
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Expand Up @@ -10,7 +10,7 @@ jobs:
strategy:
matrix:
os: [ ubuntu-latest, macos-latest, windows-latest ]
python-versions: [ '3.7', '3.8', '3.9', '3.10' ]
python-versions: [ '3.10', '3.11', '3.12' ]

steps:
- name: Initialize environment
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2 changes: 1 addition & 1 deletion .github/workflows/run-integration-tests.yml
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Expand Up @@ -16,7 +16,7 @@ jobs:
- name: Install Python
uses: actions/setup-python@v2
with:
python-version: '3.7'
python-version: '3.12'

# see: https://github.com/actions/virtual-environments/pull/5729
# GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.
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2 changes: 1 addition & 1 deletion .github/workflows/run-system-tests.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:
- name: Install Python
uses: actions/setup-python@v2
with:
python-version: '3.7'
python-version: '3.12'

# see: https://github.com/actions/virtual-environments/pull/5729
# GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.
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2 changes: 1 addition & 1 deletion .github/workflows/run-unit-tests.yml
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Expand Up @@ -16,7 +16,7 @@ jobs:
- name: Install Python
uses: actions/setup-python@v2
with:
python-version: '3.7'
python-version: '3.12'

# see: https://github.com/actions/virtual-environments/pull/5729
# GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.
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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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@@ -1,5 +1,5 @@
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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/assignmentrule.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/functiondefinition.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/gillespySolver.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/liveGraphing.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/model.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/parameter.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/raterule.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/reaction.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/results.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/core/sortableobject.html
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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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Expand Up @@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>

<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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/build/build_engine.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/build/expression.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/c_decoder.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/c_solver.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/ode_c_solver.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/ssa_c_solver.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/cpp/tau_leaping_c_solver.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/numpy/ode_solver.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/numpy/ssa_solver.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/numpy/tau_leaping_solver.html
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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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2 changes: 1 addition & 1 deletion docs/build/html/_modules/gillespy2/solvers/stochkit/stochkit_solvers.html
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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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