diff --git a/.github/workflows/run-full-tests.yml b/.github/workflows/run-full-tests.yml index 8157dee2..66c05326 100644 --- a/.github/workflows/run-full-tests.yml +++ b/.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 diff --git a/.github/workflows/run-integration-tests.yml b/.github/workflows/run-integration-tests.yml index a14a48d9..a9540639 100644 --- a/.github/workflows/run-integration-tests.yml +++ b/.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. diff --git a/.github/workflows/run-system-tests.yml b/.github/workflows/run-system-tests.yml index ddcb3ead..582e8e89 100644 --- a/.github/workflows/run-system-tests.yml +++ b/.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. diff --git a/.github/workflows/run-unit-tests.yml b/.github/workflows/run-unit-tests.yml index 26d8abbc..84b9dfba 100644 --- a/.github/workflows/run-unit-tests.yml +++ b/.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. diff --git a/AUTHORS b/AUTHORS index 8af1f04d..cca94b3a 100644 --- a/AUTHORS +++ b/AUTHORS @@ -21,3 +21,5 @@ Ethan Green Josh Cooper Matthew Dippel Joshua Fisher-Caudill +Ben Blamey + diff --git a/COPYRIGHT b/COPYRIGHT index 17de0aab..01d1cdb6 100644 --- a/COPYRIGHT +++ b/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 diff --git a/docs/build/html/_modules/gillespy2/core/assignmentrule.html b/docs/build/html/_modules/gillespy2/core/assignmentrule.html index 9763c27a..72a65fe8 100644 --- a/docs/build/html/_modules/gillespy2/core/assignmentrule.html +++ b/docs/build/html/_modules/gillespy2/core/assignmentrule.html @@ -103,7 +103,7 @@

Quick search

Source code for gillespy2.core.assignmentrule

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/cleanup.html b/docs/build/html/_modules/gillespy2/core/cleanup.html
index ecdb30f9..14d944f0 100644
--- a/docs/build/html/_modules/gillespy2/core/cleanup.html
+++ b/docs/build/html/_modules/gillespy2/core/cleanup.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.cleanup

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/events.html b/docs/build/html/_modules/gillespy2/core/events.html
index 7d592b7d..96f374f8 100644
--- a/docs/build/html/_modules/gillespy2/core/events.html
+++ b/docs/build/html/_modules/gillespy2/core/events.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.events

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/functiondefinition.html b/docs/build/html/_modules/gillespy2/core/functiondefinition.html
index d91c3e3c..00f69c11 100644
--- a/docs/build/html/_modules/gillespy2/core/functiondefinition.html
+++ b/docs/build/html/_modules/gillespy2/core/functiondefinition.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.core.functiondefinition

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/gillespyError.html b/docs/build/html/_modules/gillespy2/core/gillespyError.html
index ab70da16..84462819 100644
--- a/docs/build/html/_modules/gillespy2/core/gillespyError.html
+++ b/docs/build/html/_modules/gillespy2/core/gillespyError.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.gillespyError

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/gillespySolver.html b/docs/build/html/_modules/gillespy2/core/gillespySolver.html
index 69ecaded..71edff0e 100644
--- a/docs/build/html/_modules/gillespy2/core/gillespySolver.html
+++ b/docs/build/html/_modules/gillespy2/core/gillespySolver.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.gillespySolver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/jsonify.html b/docs/build/html/_modules/gillespy2/core/jsonify.html
index 834c332b..f238b9f1 100644
--- a/docs/build/html/_modules/gillespy2/core/jsonify.html
+++ b/docs/build/html/_modules/gillespy2/core/jsonify.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.jsonify

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/liveGraphing.html b/docs/build/html/_modules/gillespy2/core/liveGraphing.html
index 139cc607..8f662393 100644
--- a/docs/build/html/_modules/gillespy2/core/liveGraphing.html
+++ b/docs/build/html/_modules/gillespy2/core/liveGraphing.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.liveGraphing

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/model.html b/docs/build/html/_modules/gillespy2/core/model.html
index e6beb7f3..0273d918 100644
--- a/docs/build/html/_modules/gillespy2/core/model.html
+++ b/docs/build/html/_modules/gillespy2/core/model.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.core.model

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/parameter.html b/docs/build/html/_modules/gillespy2/core/parameter.html
index 28975fe5..acc57155 100644
--- a/docs/build/html/_modules/gillespy2/core/parameter.html
+++ b/docs/build/html/_modules/gillespy2/core/parameter.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.parameter

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/raterule.html b/docs/build/html/_modules/gillespy2/core/raterule.html
index 676a21dc..237701a1 100644
--- a/docs/build/html/_modules/gillespy2/core/raterule.html
+++ b/docs/build/html/_modules/gillespy2/core/raterule.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.raterule

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/reaction.html b/docs/build/html/_modules/gillespy2/core/reaction.html
index f2919173..018b7ab4 100644
--- a/docs/build/html/_modules/gillespy2/core/reaction.html
+++ b/docs/build/html/_modules/gillespy2/core/reaction.html
@@ -103,7 +103,7 @@ 

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Source code for gillespy2.core.reaction

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/results.html b/docs/build/html/_modules/gillespy2/core/results.html
index b26f6ca8..d33d3d7a 100644
--- a/docs/build/html/_modules/gillespy2/core/results.html
+++ b/docs/build/html/_modules/gillespy2/core/results.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.core.results

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/sortableobject.html b/docs/build/html/_modules/gillespy2/core/sortableobject.html
index 7a3e3aed..ca9aec3a 100644
--- a/docs/build/html/_modules/gillespy2/core/sortableobject.html
+++ b/docs/build/html/_modules/gillespy2/core/sortableobject.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.core.sortableobject

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/species.html b/docs/build/html/_modules/gillespy2/core/species.html
index 055cdcc5..27315901 100644
--- a/docs/build/html/_modules/gillespy2/core/species.html
+++ b/docs/build/html/_modules/gillespy2/core/species.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.core.species

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/core/timespan.html b/docs/build/html/_modules/gillespy2/core/timespan.html
index 5d8616e3..0750d7c9 100644
--- a/docs/build/html/_modules/gillespy2/core/timespan.html
+++ b/docs/build/html/_modules/gillespy2/core/timespan.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.core.timespan

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/build/build_engine.html b/docs/build/html/_modules/gillespy2/solvers/cpp/build/build_engine.html
index 239516f3..4774de50 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/build/build_engine.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/build/build_engine.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.build.build_engine

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/build/expression.html b/docs/build/html/_modules/gillespy2/solvers/cpp/build/expression.html
index 0214735a..26d38063 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/build/expression.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/build/expression.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.build.expression

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html b/docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html
index 883d5aa1..26558287 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.build.make

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html b/docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html
index d49c0447..1eb561bd 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.build.template_gen

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/c_decoder.html b/docs/build/html/_modules/gillespy2/solvers/cpp/c_decoder.html
index ef6642cb..4b64a6fd 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/c_decoder.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/c_decoder.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.c_decoder

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/c_solver.html b/docs/build/html/_modules/gillespy2/solvers/cpp/c_solver.html
index ee052746..f16fa19b 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/c_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/c_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.c_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/ode_c_solver.html b/docs/build/html/_modules/gillespy2/solvers/cpp/ode_c_solver.html
index 3719207f..7f27c555 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/ode_c_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/ode_c_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.ode_c_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/ssa_c_solver.html b/docs/build/html/_modules/gillespy2/solvers/cpp/ssa_c_solver.html
index 7e866796..bd321ef6 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/ssa_c_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/ssa_c_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.ssa_c_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/tau_leaping_c_solver.html b/docs/build/html/_modules/gillespy2/solvers/cpp/tau_leaping_c_solver.html
index 55139dfb..3813080f 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/tau_leaping_c_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/tau_leaping_c_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.cpp.tau_leaping_c_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html b/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
index 69b001c9..7ce016f8 100644
--- a/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.numpy.CLE_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/numpy/ode_solver.html b/docs/build/html/_modules/gillespy2/solvers/numpy/ode_solver.html
index bc534b4e..d5fb0f28 100644
--- a/docs/build/html/_modules/gillespy2/solvers/numpy/ode_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/numpy/ode_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.numpy.ode_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/numpy/ssa_solver.html b/docs/build/html/_modules/gillespy2/solvers/numpy/ssa_solver.html
index 38a51dc7..02da11a0 100644
--- a/docs/build/html/_modules/gillespy2/solvers/numpy/ssa_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/numpy/ssa_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.numpy.ssa_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/numpy/tau_hybrid_solver.html b/docs/build/html/_modules/gillespy2/solvers/numpy/tau_hybrid_solver.html
index 820db148..c76c9b60 100644
--- a/docs/build/html/_modules/gillespy2/solvers/numpy/tau_hybrid_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/numpy/tau_hybrid_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.numpy.tau_hybrid_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/numpy/tau_leaping_solver.html b/docs/build/html/_modules/gillespy2/solvers/numpy/tau_leaping_solver.html
index 5539ff09..0e06c8db 100644
--- a/docs/build/html/_modules/gillespy2/solvers/numpy/tau_leaping_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/numpy/tau_leaping_solver.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.numpy.tau_leaping_solver

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/stochkit/stochkit_solvers.html b/docs/build/html/_modules/gillespy2/solvers/stochkit/stochkit_solvers.html
index 4e6bcec4..992f1760 100644
--- a/docs/build/html/_modules/gillespy2/solvers/stochkit/stochkit_solvers.html
+++ b/docs/build/html/_modules/gillespy2/solvers/stochkit/stochkit_solvers.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.stochkit.stochkit_solvers

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/utilities/Tau.html b/docs/build/html/_modules/gillespy2/solvers/utilities/Tau.html
index 6677769e..4c4828c3 100644
--- a/docs/build/html/_modules/gillespy2/solvers/utilities/Tau.html
+++ b/docs/build/html/_modules/gillespy2/solvers/utilities/Tau.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.utilities.Tau

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/utilities/cpp_support_test.html b/docs/build/html/_modules/gillespy2/solvers/utilities/cpp_support_test.html
index 2184b06c..f54c1564 100644
--- a/docs/build/html/_modules/gillespy2/solvers/utilities/cpp_support_test.html
+++ b/docs/build/html/_modules/gillespy2/solvers/utilities/cpp_support_test.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.utilities.cpp_support_test

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/solvers/utilities/solverutils.html b/docs/build/html/_modules/gillespy2/solvers/utilities/solverutils.html
index 116e56b0..5b98c58d 100644
--- a/docs/build/html/_modules/gillespy2/solvers/utilities/solverutils.html
+++ b/docs/build/html/_modules/gillespy2/solvers/utilities/solverutils.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.solvers.utilities.solverutils

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/docs/build/html/_modules/gillespy2/stochss/StochSSexport.html b/docs/build/html/_modules/gillespy2/stochss/StochSSexport.html
index 04488adb..293dec89 100644
--- a/docs/build/html/_modules/gillespy2/stochss/StochSSexport.html
+++ b/docs/build/html/_modules/gillespy2/stochss/StochSSexport.html
@@ -103,7 +103,7 @@ 

Quick search

Source code for gillespy2.stochss.StochSSexport

 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/__init__.py b/gillespy2/__init__.py
index 0ebfafcf..f02dd71a 100644
--- a/gillespy2/__init__.py
+++ b/gillespy2/__init__.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/__version__.py b/gillespy2/__version__.py
index 68bbc8d8..2b08f31e 100644
--- a/gillespy2/__version__.py
+++ b/gillespy2/__version__.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/__init__.py b/gillespy2/core/__init__.py
index d635313f..b606a2c6 100644
--- a/gillespy2/core/__init__.py
+++ b/gillespy2/core/__init__.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/assignmentrule.py b/gillespy2/core/assignmentrule.py
index eb5373cc..74b14706 100644
--- a/gillespy2/core/assignmentrule.py
+++ b/gillespy2/core/assignmentrule.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/cleanup.py b/gillespy2/core/cleanup.py
index 0a21fd75..e3ab52c4 100644
--- a/gillespy2/core/cleanup.py
+++ b/gillespy2/core/cleanup.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/events.py b/gillespy2/core/events.py
index fc984a39..065f0c0a 100644
--- a/gillespy2/core/events.py
+++ b/gillespy2/core/events.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/functiondefinition.py b/gillespy2/core/functiondefinition.py
index a7151085..3ee2024a 100644
--- a/gillespy2/core/functiondefinition.py
+++ b/gillespy2/core/functiondefinition.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/gillespyError.py b/gillespy2/core/gillespyError.py
index 26f05558..51414b29 100644
--- a/gillespy2/core/gillespyError.py
+++ b/gillespy2/core/gillespyError.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/gillespySolver.py b/gillespy2/core/gillespySolver.py
index c6c0cdf3..db886e9c 100644
--- a/gillespy2/core/gillespySolver.py
+++ b/gillespy2/core/gillespySolver.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/jsonify.py b/gillespy2/core/jsonify.py
index ab5ffa09..5396c5a6 100644
--- a/gillespy2/core/jsonify.py
+++ b/gillespy2/core/jsonify.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/liveGraphing.py b/gillespy2/core/liveGraphing.py
index c086b479..96721d0b 100644
--- a/gillespy2/core/liveGraphing.py
+++ b/gillespy2/core/liveGraphing.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
diff --git a/gillespy2/core/model.py b/gillespy2/core/model.py
index 63da5224..1ff76dfb 100644
--- a/gillespy2/core/model.py
+++ b/gillespy2/core/model.py
@@ -1,5 +1,5 @@
 # GillesPy2 is a modeling toolkit for biochemical simulation.
-# 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
@@ -1664,8 +1664,8 @@ def to_string(self):
             doc = eTree.tostring(self.document)
             xmldoc = xml.dom.minidom.parseString(doc)
             ugly_xml = xmldoc.toprettyxml(indent='  ')
-            text_re = re.compile(">\n\s+([^<>\s].*?)\n\s+\g<1>\n\s+([^<>\s].*?)\n\s+\g<1>