Merge pull request #961 from StochSS/fix_regex_strings

Fix regex strings

.github/workflows/run-full-tests.yml

@@ -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

.github/workflows/run-integration-tests.yml

@@ -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.

.github/workflows/run-system-tests.yml

@@ -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.

.github/workflows/run-unit-tests.yml

@@ -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.

AUTHORS

@@ -21,3 +21,5 @@ Ethan Green
 Josh Cooper
 Matthew Dippel
 Joshua Fisher-Caudill
+Ben Blamey
+

COPYRIGHT

@@ -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

docs/build/html/_modules/gillespy2/core/assignmentrule.html

@@ -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>

docs/build/html/_modules/gillespy2/core/cleanup.html

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

docs/build/html/_modules/gillespy2/core/events.html

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

docs/build/html/_modules/gillespy2/core/functiondefinition.html

@@ -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>

docs/build/html/_modules/gillespy2/core/gillespyError.html

@@ -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>

docs/build/html/_modules/gillespy2/core/gillespySolver.html

@@ -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>

docs/build/html/_modules/gillespy2/core/jsonify.html

@@ -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>

docs/build/html/_modules/gillespy2/core/liveGraphing.html

@@ -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>

docs/build/html/_modules/gillespy2/core/model.html

@@ -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>

docs/build/html/_modules/gillespy2/core/parameter.html

@@ -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>

docs/build/html/_modules/gillespy2/core/raterule.html

@@ -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>

docs/build/html/_modules/gillespy2/core/reaction.html

@@ -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>

docs/build/html/_modules/gillespy2/core/results.html

@@ -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>

docs/build/html/_modules/gillespy2/core/sortableobject.html

@@ -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>

docs/build/html/_modules/gillespy2/core/species.html

@@ -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>

docs/build/html/_modules/gillespy2/core/timespan.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/build/build_engine.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/build/expression.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/c_decoder.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/c_solver.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/ode_c_solver.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/ssa_c_solver.html

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

docs/build/html/_modules/gillespy2/solvers/cpp/tau_leaping_c_solver.html

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

docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html

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

docs/build/html/_modules/gillespy2/solvers/numpy/ode_solver.html

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

docs/build/html/_modules/gillespy2/solvers/numpy/ssa_solver.html

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

docs/build/html/_modules/gillespy2/solvers/numpy/tau_hybrid_solver.html

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

docs/build/html/_modules/gillespy2/solvers/numpy/tau_leaping_solver.html

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

docs/build/html/_modules/gillespy2/solvers/stochkit/stochkit_solvers.html

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