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 @@
# 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 @@ Quick search
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 @@ Quick search
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 @@ Quick search
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 @@ Quick search
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 @@ Quick search
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 @@ Quick search
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 @@ Quick search
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 @@ Quick search
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 @@ Quick search
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+", re.DOTALL)
- pretty_xml = text_re.sub(">\g<1>", ugly_xml)
+ text_re = re.compile(r">\n\s+([^<>\s].*?)\n\s+", re.DOTALL)
+ pretty_xml = text_re.sub(r">\g<1>", ugly_xml)
return pretty_xml
def __species_to_element(self, species):
diff --git a/gillespy2/core/parameter.py b/gillespy2/core/parameter.py
index 0608e649..c1845e68 100644
--- a/gillespy2/core/parameter.py
+++ b/gillespy2/core/parameter.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/raterule.py b/gillespy2/core/raterule.py
index 61fbce8f..7bfa075a 100644
--- a/gillespy2/core/raterule.py
+++ b/gillespy2/core/raterule.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/reaction.py b/gillespy2/core/reaction.py
index e4d21474..6a8759e3 100644
--- a/gillespy2/core/reaction.py
+++ b/gillespy2/core/reaction.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/results.py b/gillespy2/core/results.py
index 12b093ff..df3edd97 100644
--- a/gillespy2/core/results.py
+++ b/gillespy2/core/results.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
@@ -283,7 +283,7 @@ def build_from_solver_results(cls, solver, live_output_options):
return results
raise ValueError("number_of_trajectories must be non-negative and non-zero")
- def to_csv(self, path=".", nametag=None, stamp=None, postfix=".odf", verbose=False):
+ def to_csv(self, path=".", nametag=None, stamp=None, suffix=".odf", verbose=False):
"""
Outputs the Results to one or more .csv files in a new directory.
@@ -311,7 +311,7 @@ def to_csv(self, path=".", nametag=None, stamp=None, postfix=".odf", verbose=Fal
else:
identifier = nametag
- directory = os.path.join(path, f"{identifier}-{stamp}{postfix}")
+ directory = os.path.join(path, f"{identifier}-{stamp}{suffix}")
if verbose:
print(f"Writing data to: {directory}")
# multiple trajectories
diff --git a/gillespy2/core/sortableobject.py b/gillespy2/core/sortableobject.py
index 8b5002b5..28eb5357 100644
--- a/gillespy2/core/sortableobject.py
+++ b/gillespy2/core/sortableobject.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/species.py b/gillespy2/core/species.py
index e98af25f..4429c0f5 100644
--- a/gillespy2/core/species.py
+++ b/gillespy2/core/species.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/timespan.py b/gillespy2/core/timespan.py
index 07b74c0a..dda4d842 100644
--- a/gillespy2/core/timespan.py
+++ b/gillespy2/core/timespan.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/sbml/SBMLexport.py b/gillespy2/sbml/SBMLexport.py
index 1f777e18..2d70da0c 100644
--- a/gillespy2/sbml/SBMLexport.py
+++ b/gillespy2/sbml/SBMLexport.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/sbml/SBMLimport.py b/gillespy2/sbml/SBMLimport.py
index a3de936a..18bbf67b 100644
--- a/gillespy2/sbml/SBMLimport.py
+++ b/gillespy2/sbml/SBMLimport.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/sbml/__init__.py b/gillespy2/sbml/__init__.py
index 797e1168..4c14cfe3 100644
--- a/gillespy2/sbml/__init__.py
+++ b/gillespy2/sbml/__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/solvers/__init__.py b/gillespy2/solvers/__init__.py
index 36cf85ba..4deae4bf 100644
--- a/gillespy2/solvers/__init__.py
+++ b/gillespy2/solvers/__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/solvers/cpp/__init__.py b/gillespy2/solvers/cpp/__init__.py
index ce7eee6d..dadbd8c4 100644
--- a/gillespy2/solvers/cpp/__init__.py
+++ b/gillespy2/solvers/cpp/__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/solvers/cpp/build/SConstruct b/gillespy2/solvers/cpp/build/SConstruct
index 6f2b729f..f5b4eb65 100644
--- a/gillespy2/solvers/cpp/build/SConstruct
+++ b/gillespy2/solvers/cpp/build/SConstruct
@@ -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/solvers/cpp/build/__init__.py b/gillespy2/solvers/cpp/build/__init__.py
index 797e1168..4c14cfe3 100644
--- a/gillespy2/solvers/cpp/build/__init__.py
+++ b/gillespy2/solvers/cpp/build/__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/solvers/cpp/build/build_engine.py b/gillespy2/solvers/cpp/build/build_engine.py
index 05b5a3e3..fc698ee4 100644
--- a/gillespy2/solvers/cpp/build/build_engine.py
+++ b/gillespy2/solvers/cpp/build/build_engine.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/solvers/cpp/build/expression.py b/gillespy2/solvers/cpp/build/expression.py
index e7824830..b3d3be2f 100644
--- a/gillespy2/solvers/cpp/build/expression.py
+++ b/gillespy2/solvers/cpp/build/expression.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/solvers/cpp/build/make.py b/gillespy2/solvers/cpp/build/make.py
index 85fa218f..1a24bbbf 100644
--- a/gillespy2/solvers/cpp/build/make.py
+++ b/gillespy2/solvers/cpp/build/make.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/solvers/cpp/build/template_gen.py b/gillespy2/solvers/cpp/build/template_gen.py
index 929e2457..6529527e 100644
--- a/gillespy2/solvers/cpp/build/template_gen.py
+++ b/gillespy2/solvers/cpp/build/template_gen.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/solvers/cpp/c_base/SConscript b/gillespy2/solvers/cpp/c_base/SConscript
index ee8130af..cbce2a55 100644
--- a/gillespy2/solvers/cpp/c_base/SConscript
+++ b/gillespy2/solvers/cpp/c_base/SConscript
@@ -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/solvers/cpp/c_base/Sundials/SConscript b/gillespy2/solvers/cpp/c_base/Sundials/SConscript
index b9a1afbd..a291772f 100644
--- a/gillespy2/solvers/cpp/c_base/Sundials/SConscript
+++ b/gillespy2/solvers/cpp/c_base/Sundials/SConscript
@@ -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/solvers/cpp/c_base/Tau/SConscript b/gillespy2/solvers/cpp/c_base/Tau/SConscript
index b5271edb..3c38ee3a 100644
--- a/gillespy2/solvers/cpp/c_base/Tau/SConscript
+++ b/gillespy2/solvers/cpp/c_base/Tau/SConscript
@@ -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/solvers/cpp/c_base/Tau/tau.cpp b/gillespy2/solvers/cpp/c_base/Tau/tau.cpp
index eddf7666..fbdfd041 100644
--- a/gillespy2/solvers/cpp/c_base/Tau/tau.cpp
+++ b/gillespy2/solvers/cpp/c_base/Tau/tau.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/Tau/tau.h b/gillespy2/solvers/cpp/c_base/Tau/tau.h
index 644574c8..8b32f82b 100644
--- a/gillespy2/solvers/cpp/c_base/Tau/tau.h
+++ b/gillespy2/solvers/cpp/c_base/Tau/tau.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/arg_parser.cpp b/gillespy2/solvers/cpp/c_base/arg_parser.cpp
index 4cde153f..2244b243 100644
--- a/gillespy2/solvers/cpp/c_base/arg_parser.cpp
+++ b/gillespy2/solvers/cpp/c_base/arg_parser.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/arg_parser.h b/gillespy2/solvers/cpp/c_base/arg_parser.h
index 8b63d792..1a545119 100644
--- a/gillespy2/solvers/cpp/c_base/arg_parser.h
+++ b/gillespy2/solvers/cpp/c_base/arg_parser.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/model.cpp b/gillespy2/solvers/cpp/c_base/model.cpp
index 4c3403c8..2d338688 100644
--- a/gillespy2/solvers/cpp/c_base/model.cpp
+++ b/gillespy2/solvers/cpp/c_base/model.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/model.h b/gillespy2/solvers/cpp/c_base/model.h
index 9ce57a4c..91a813cd 100644
--- a/gillespy2/solvers/cpp/c_base/model.h
+++ b/gillespy2/solvers/cpp/c_base/model.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/ode_cpp_solver/ODESimulation.cpp b/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESimulation.cpp
index 5733a9c0..2c5b16ef 100644
--- a/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESimulation.cpp
+++ b/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESimulation.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/ode_cpp_solver/ODESolver.cpp b/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESolver.cpp
index 7ce77f8c..6685c91d 100644
--- a/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESolver.cpp
+++ b/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESolver.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/ode_cpp_solver/ODESolver.h b/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESolver.h
index 866572b6..d7547f62 100644
--- a/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESolver.h
+++ b/gillespy2/solvers/cpp/c_base/ode_cpp_solver/ODESolver.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/ode_cpp_solver/SConscript b/gillespy2/solvers/cpp/c_base/ode_cpp_solver/SConscript
index 8902f5e8..a7259378 100644
--- a/gillespy2/solvers/cpp/c_base/ode_cpp_solver/SConscript
+++ b/gillespy2/solvers/cpp/c_base/ode_cpp_solver/SConscript
@@ -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/solvers/cpp/c_base/ssa_cpp_solver/SConscript b/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SConscript
index 4e07d695..5f5f25c7 100644
--- a/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SConscript
+++ b/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SConscript
@@ -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/solvers/cpp/c_base/ssa_cpp_solver/SSASimulation.cpp b/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASimulation.cpp
index de22dc1d..2dcc68e8 100644
--- a/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASimulation.cpp
+++ b/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASimulation.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/ssa_cpp_solver/SSASolver.cpp b/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASolver.cpp
index 412bdd8f..dba16464 100644
--- a/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASolver.cpp
+++ b/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASolver.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/ssa_cpp_solver/SSASolver.h b/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASolver.h
index 35159413..43d8d980 100644
--- a/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASolver.h
+++ b/gillespy2/solvers/cpp/c_base/ssa_cpp_solver/SSASolver.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.cpp b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.cpp
index e423745c..eb791c57 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.cpp
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.h b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.h
index b42320a3..2cc760d1 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.h
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/SConscript b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/SConscript
index 89d56da1..3897e9c3 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/SConscript
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/SConscript
@@ -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/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSimulation.cpp b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSimulation.cpp
index da29c927..16a1e992 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSimulation.cpp
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSimulation.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.cpp b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.cpp
index 2790a498..e2e28725 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.cpp
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.h b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.h
index e2fad29b..f4f1dc91 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.h
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/hybrid_template.cpp b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/hybrid_template.cpp
index deaa92e1..0ab0e254 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/hybrid_template.cpp
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/hybrid_template.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/hybrid_template.h b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/hybrid_template.h
index 01df28e3..9e35be05 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/hybrid_template.h
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/hybrid_template.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.cpp b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.cpp
index 0a12a06c..c3d636ca 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.cpp
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.h b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.h
index 54737aa7..5f8f7708 100644
--- a/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.h
+++ b/gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_leaping_cpp_solver/SConscript b/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/SConscript
index 5c26e8a7..d5927de9 100644
--- a/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/SConscript
+++ b/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/SConscript
@@ -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/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSimulation.cpp b/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSimulation.cpp
index c1642c8d..741c522b 100644
--- a/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSimulation.cpp
+++ b/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSimulation.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSolver.cpp b/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSolver.cpp
index 9b157261..be06e153 100644
--- a/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSolver.cpp
+++ b/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSolver.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSolver.h b/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSolver.h
index 6e753ced..b7ae1330 100644
--- a/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSolver.h
+++ b/gillespy2/solvers/cpp/c_base/tau_leaping_cpp_solver/TauLeapingSolver.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/template/template.cpp b/gillespy2/solvers/cpp/c_base/template/template.cpp
index 00f09700..4586d550 100644
--- a/gillespy2/solvers/cpp/c_base/template/template.cpp
+++ b/gillespy2/solvers/cpp/c_base/template/template.cpp
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/template/template.h b/gillespy2/solvers/cpp/c_base/template/template.h
index 51fd2f41..3cc60945 100644
--- a/gillespy2/solvers/cpp/c_base/template/template.h
+++ b/gillespy2/solvers/cpp/c_base/template/template.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/template/template_defaults.h b/gillespy2/solvers/cpp/c_base/template/template_defaults.h
index 858e17c2..7ac4d51f 100644
--- a/gillespy2/solvers/cpp/c_base/template/template_defaults.h
+++ b/gillespy2/solvers/cpp/c_base/template/template_defaults.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/template/template_definitions.h b/gillespy2/solvers/cpp/c_base/template/template_definitions.h
index 96605ddd..fc042ec3 100644
--- a/gillespy2/solvers/cpp/c_base/template/template_definitions.h
+++ b/gillespy2/solvers/cpp/c_base/template/template_definitions.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_base/template/template_params.h b/gillespy2/solvers/cpp/c_base/template/template_params.h
index 178643aa..854b3fd2 100644
--- a/gillespy2/solvers/cpp/c_base/template/template_params.h
+++ b/gillespy2/solvers/cpp/c_base/template/template_params.h
@@ -1,6 +1,6 @@
/*
* 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/solvers/cpp/c_decoder.py b/gillespy2/solvers/cpp/c_decoder.py
index d418884b..d5e7856c 100644
--- a/gillespy2/solvers/cpp/c_decoder.py
+++ b/gillespy2/solvers/cpp/c_decoder.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/solvers/cpp/c_solver.py b/gillespy2/solvers/cpp/c_solver.py
index 5a1d5172..30d1b612 100644
--- a/gillespy2/solvers/cpp/c_solver.py
+++ b/gillespy2/solvers/cpp/c_solver.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/solvers/cpp/ode_c_solver.py b/gillespy2/solvers/cpp/ode_c_solver.py
index 9478f718..41549191 100644
--- a/gillespy2/solvers/cpp/ode_c_solver.py
+++ b/gillespy2/solvers/cpp/ode_c_solver.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/solvers/cpp/ssa_c_solver.py b/gillespy2/solvers/cpp/ssa_c_solver.py
index a4f8ee2a..098d2d38 100644
--- a/gillespy2/solvers/cpp/ssa_c_solver.py
+++ b/gillespy2/solvers/cpp/ssa_c_solver.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/solvers/cpp/tau_leaping_c_solver.py b/gillespy2/solvers/cpp/tau_leaping_c_solver.py
index 7b6148fd..47d10034 100644
--- a/gillespy2/solvers/cpp/tau_leaping_c_solver.py
+++ b/gillespy2/solvers/cpp/tau_leaping_c_solver.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/solvers/numpy/CLE_solver.py b/gillespy2/solvers/numpy/CLE_solver.py
index 73c7049c..13a84c14 100644
--- a/gillespy2/solvers/numpy/CLE_solver.py
+++ b/gillespy2/solvers/numpy/CLE_solver.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
@@ -59,7 +59,7 @@ def __init__(self, model=None, debug=False):
self.is_instantiated = True
def __get_reactions(self, step, curr_state, curr_time, save_time, propensities, reactions):
- """
+ r"""
Helper Function to get reactions fired from t to t+tau.
In the equation:
diff --git a/gillespy2/solvers/numpy/__init__.py b/gillespy2/solvers/numpy/__init__.py
index af7b5a2f..f4ae5cf4 100644
--- a/gillespy2/solvers/numpy/__init__.py
+++ b/gillespy2/solvers/numpy/__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/solvers/numpy/ode_solver.py b/gillespy2/solvers/numpy/ode_solver.py
index 7ba728a8..75eed12d 100644
--- a/gillespy2/solvers/numpy/ode_solver.py
+++ b/gillespy2/solvers/numpy/ode_solver.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/solvers/numpy/ssa_solver.py b/gillespy2/solvers/numpy/ssa_solver.py
index 5c885e1a..8a6bb6c5 100644
--- a/gillespy2/solvers/numpy/ssa_solver.py
+++ b/gillespy2/solvers/numpy/ssa_solver.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/solvers/numpy/tau_hybrid_solver.py b/gillespy2/solvers/numpy/tau_hybrid_solver.py
index 2972d428..470ddf58 100644
--- a/gillespy2/solvers/numpy/tau_hybrid_solver.py
+++ b/gillespy2/solvers/numpy/tau_hybrid_solver.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/solvers/numpy/tau_leaping_solver.py b/gillespy2/solvers/numpy/tau_leaping_solver.py
index d76e5784..555dbedb 100644
--- a/gillespy2/solvers/numpy/tau_leaping_solver.py
+++ b/gillespy2/solvers/numpy/tau_leaping_solver.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/solvers/utilities/Tau.py b/gillespy2/solvers/utilities/Tau.py
index 8eff8497..1fa9c3fe 100644
--- a/gillespy2/solvers/utilities/Tau.py
+++ b/gillespy2/solvers/utilities/Tau.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/solvers/utilities/__init__.py b/gillespy2/solvers/utilities/__init__.py
index 797e1168..4c14cfe3 100644
--- a/gillespy2/solvers/utilities/__init__.py
+++ b/gillespy2/solvers/utilities/__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/solvers/utilities/cpp_support_test.py b/gillespy2/solvers/utilities/cpp_support_test.py
index bbdb9623..04f08db5 100644
--- a/gillespy2/solvers/utilities/cpp_support_test.py
+++ b/gillespy2/solvers/utilities/cpp_support_test.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/solvers/utilities/solverutils.py b/gillespy2/solvers/utilities/solverutils.py
index a808ee91..659078c9 100644
--- a/gillespy2/solvers/utilities/solverutils.py
+++ b/gillespy2/solvers/utilities/solverutils.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/stochss/StochSSexport.py b/gillespy2/stochss/StochSSexport.py
index d56a276e..e3645a6b 100644
--- a/gillespy2/stochss/StochSSexport.py
+++ b/gillespy2/stochss/StochSSexport.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/stochss/__init__.py b/gillespy2/stochss/__init__.py
index 797e1168..4c14cfe3 100644
--- a/gillespy2/stochss/__init__.py
+++ b/gillespy2/stochss/__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/setup.py b/setup.py
index 7ea5c7e8..05e470d0 100644
--- a/setup.py
+++ b/setup.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/test/TestBattery.py b/test/TestBattery.py
index a07f4c0d..5332cf90 100644
--- a/test/TestBattery.py
+++ b/test/TestBattery.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/test/example_models.py b/test/example_models.py
index a317fe0d..0ea6845a 100644
--- a/test/example_models.py
+++ b/test/example_models.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/test/pause_model.py b/test/pause_model.py
index 7c5670a6..7396081e 100644
--- a/test/pause_model.py
+++ b/test/pause_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
diff --git a/test/profiling/__init__.py b/test/profiling/__init__.py
index 797e1168..4c14cfe3 100644
--- a/test/profiling/__init__.py
+++ b/test/profiling/__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/test/profiling/c_profiler.py b/test/profiling/c_profiler.py
index 5768633b..8cbfc68c 100644
--- a/test/profiling/c_profiler.py
+++ b/test/profiling/c_profiler.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/test/profiling/performance_data.py b/test/profiling/performance_data.py
index d98589fd..dd5b3537 100644
--- a/test/profiling/performance_data.py
+++ b/test/profiling/performance_data.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/test/profiling/python_profiler.py b/test/profiling/python_profiler.py
index b36f524f..c9c40e8f 100644
--- a/test/profiling/python_profiler.py
+++ b/test/profiling/python_profiler.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/test/run_integration_tests.py b/test/run_integration_tests.py
index 0f7a3f25..015d5d60 100644
--- a/test/run_integration_tests.py
+++ b/test/run_integration_tests.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/test/run_system_tests.py b/test/run_system_tests.py
index 8f90e425..c7307ad1 100644
--- a/test/run_system_tests.py
+++ b/test/run_system_tests.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/test/run_unit_tests.py b/test/run_unit_tests.py
index 78290cbf..4aded3aa 100644
--- a/test/run_unit_tests.py
+++ b/test/run_unit_tests.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/test/test_SBML.py b/test/test_SBML.py
index b9c00743..b8fd6fea 100644
--- a/test/test_SBML.py
+++ b/test/test_SBML.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/test/test_StochML.py b/test/test_StochML.py
index b617bcec..f8fe42f8 100644
--- a/test/test_StochML.py
+++ b/test/test_StochML.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/test/test_all_solvers.py b/test/test_all_solvers.py
index 243b21d0..20febd67 100644
--- a/test/test_all_solvers.py
+++ b/test/test_all_solvers.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
@@ -147,14 +147,14 @@ def test_return_type_show_labels(self):
for solver in self.solvers:
self.assertTrue(isinstance(self.labeled_results[solver.name], Results))
self.assertTrue(isinstance(self.labeled_results[solver.name]['Sp'], np.ndarray))
- self.assertTrue(isinstance(self.labeled_results[solver.name]['Sp'][0], np.float))
+ self.assertTrue(isinstance(self.labeled_results[solver.name]['Sp'][0], float))
self.assertTrue(isinstance(self.labeled_results[solver.name][0], Trajectory))
self.assertTrue(isinstance(self.labeled_results_more_trajectories[solver.name], Results))
self.assertTrue(isinstance(self.labeled_results_more_trajectories[solver.name][0], Trajectory))
self.assertTrue(isinstance(self.labeled_results_more_trajectories[solver.name][0]['Sp'], np.ndarray))
- self.assertTrue(isinstance(self.labeled_results_more_trajectories[solver.name][0]['Sp'][0], np.float))
+ self.assertTrue(isinstance(self.labeled_results_more_trajectories[solver.name][0]['Sp'][0], float))
def test_sbml_feature_validation(self):
def create_test_model(parameter_values=None):
diff --git a/test/test_build_engine.py b/test/test_build_engine.py
index 81eb72c1..556c59d9 100644
--- a/test/test_build_engine.py
+++ b/test/test_build_engine.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/test/test_c_decode.py b/test/test_c_decode.py
index 6f655afe..736296cb 100644
--- a/test/test_c_decode.py
+++ b/test/test_c_decode.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/test/test_c_solver_perf.py b/test/test_c_solver_perf.py
index f41799f5..6be744e2 100644
--- a/test/test_c_solver_perf.py
+++ b/test/test_c_solver_perf.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/test/test_c_solvers.py b/test/test_c_solvers.py
index c0998c94..79aee67e 100644
--- a/test/test_c_solvers.py
+++ b/test/test_c_solvers.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/test/test_check_cpp_support.py b/test/test_check_cpp_support.py
index 803c0e12..c0167433 100644
--- a/test/test_check_cpp_support.py
+++ b/test/test_check_cpp_support.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/test/test_empty_model.py b/test/test_empty_model.py
index e7e8aa6b..c33377ce 100644
--- a/test/test_empty_model.py
+++ b/test/test_empty_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
diff --git a/test/test_example_models.py b/test/test_example_models.py
index f3eac315..98f636dd 100644
--- a/test/test_example_models.py
+++ b/test/test_example_models.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/test/test_hybrid_c_events.py b/test/test_hybrid_c_events.py
index bc165e3a..8745d8d5 100644
--- a/test/test_hybrid_c_events.py
+++ b/test/test_hybrid_c_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/test/test_hybrid_event_round.py b/test/test_hybrid_event_round.py
index 444333ef..6583e295 100644
--- a/test/test_hybrid_event_round.py
+++ b/test/test_hybrid_event_round.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/test/test_hybrid_negative_state.py b/test/test_hybrid_negative_state.py
index 75eef2e4..091032f8 100644
--- a/test/test_hybrid_negative_state.py
+++ b/test/test_hybrid_negative_state.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/test/test_hybrid_solver.py b/test/test_hybrid_solver.py
index 27761964..10096fcf 100644
--- a/test/test_hybrid_solver.py
+++ b/test/test_hybrid_solver.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
@@ -65,8 +65,8 @@ def test_add_assignment_rule(self):
model.add_species([species])
model.add_assignment_rule([rule])
results = model.run()
- self.assertEquals(results[species.name][0], 2)
- self.assertEquals(results[species.name][-1], 2)
+ self.assertEqual(results[species.name][0], 2)
+ self.assertEqual(results[species.name][-1], 2)
self.assertEqual(results[0].solver_name,'TauHybridSolver')
def test_add_function_definition(self):
diff --git a/test/test_hybrid_solver_opioid_model.py b/test/test_hybrid_solver_opioid_model.py
index 8ddd939e..17d8b48b 100644
--- a/test/test_hybrid_solver_opioid_model.py
+++ b/test/test_hybrid_solver_opioid_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
diff --git a/test/test_jsonify.py b/test/test_jsonify.py
index 9be488ae..e5e58b17 100644
--- a/test/test_jsonify.py
+++ b/test/test_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
@@ -79,7 +79,7 @@ def test_equality_of_named_results(self):
results_from = Results.from_json(results.to_json())
- self.assertEquals(results.to_json(), results_from.to_json())
+ self.assertEqual(results.to_json(), results_from.to_json())
def test_equality_of_named_results(self):
"""
@@ -178,7 +178,7 @@ def test_named_to_anon_accuracy(self):
model_2 = Model.from_json(model_1_json)
# Assert that the anonymized model_1 and the new model_2 are identical.
- self.assertEquals(
+ self.assertEqual(
model_1.to_anon().to_json(),
model_2.to_json()
)
@@ -187,7 +187,7 @@ def test_named_to_anon_accuracy(self):
model_2 = model_2.to_named()
# Assert that model_1 and model_2 are still the same.
- self.assertEquals(
+ self.assertEqual(
model_1.to_json(),
model_2.to_json()
)
@@ -205,7 +205,7 @@ def test_model_hash_whitespace_accuracy(self):
model_with_whitespace.add_species([X, Y])
# Up to this point the JSON hash of the two models should be the same.
- self.assertEquals(model_no_whitespace.get_json_hash(), model_with_whitespace.get_json_hash())
+ self.assertEqual(model_no_whitespace.get_json_hash(), model_with_whitespace.get_json_hash())
# Add a custom reaction to both models, differing the amount of whitespace in the
# propensity functions.
diff --git a/test/test_model.py b/test/test_model.py
index b2808e10..3d41d23f 100644
--- a/test/test_model.py
+++ b/test/test_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
diff --git a/test/test_notebooks.py b/test/test_notebooks.py
index 9de7c43e..c4705dc6 100644
--- a/test/test_notebooks.py
+++ b/test/test_notebooks.py
@@ -1,6 +1,6 @@
# 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/test/test_numpy_ssa_solver.py b/test/test_numpy_ssa_solver.py
index 29866039..81a6127e 100644
--- a/test/test_numpy_ssa_solver.py
+++ b/test/test_numpy_ssa_solver.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/test/test_ode_c_solver.py b/test/test_ode_c_solver.py
index d3a46301..192d677a 100644
--- a/test/test_ode_c_solver.py
+++ b/test/test_ode_c_solver.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/test/test_ode_solver.py b/test/test_ode_solver.py
index 14ddbb62..c1c92ae4 100644
--- a/test/test_ode_solver.py
+++ b/test/test_ode_solver.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/test/test_pause_resume.py b/test/test_pause_resume.py
index 01f03459..313f097d 100644
--- a/test/test_pause_resume.py
+++ b/test/test_pause_resume.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/test/test_propensity_parser.py b/test/test_propensity_parser.py
index ec4a7f41..cc939853 100644
--- a/test/test_propensity_parser.py
+++ b/test/test_propensity_parser.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/test/test_python_solver_perf.py b/test/test_python_solver_perf.py
index fab21f59..df7407bc 100644
--- a/test/test_python_solver_perf.py
+++ b/test/test_python_solver_perf.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/test/test_results.py b/test/test_results.py
index a2c37d2e..afd4dc7a 100644
--- a/test/test_results.py
+++ b/test/test_results.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
@@ -16,6 +16,7 @@
import unittest
import os
+import sys
import tempfile
from gillespy2.core import Model
from gillespy2.core.results import Results, Trajectory
@@ -109,8 +110,8 @@ def test_to_csv_single_result_no_data(self):
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(stamp = test_stamp, nametag = test_nametag, path=tempdir)
- test_path = tempdir+"/"+test_nametag+test_stamp
- assert not os.path.isdir(test_path)
+ test_path = tempdir+"/"+test_nametag+'-'+test_stamp
+ self.assertFalse(os.path.isdir(test_path))
def test_to_csv_single_result_directory_exists(self):
test_data = {'time':[0]}
@@ -120,8 +121,8 @@ def test_to_csv_single_result_directory_exists(self):
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(stamp = test_stamp, nametag = test_nametag, path=tempdir)
- test_path = tempdir+"/"+test_nametag+test_stamp
- assert os.path.isdir(test_path)
+ test_path = tempdir+"/"+test_nametag+'-'+test_stamp+".odf"
+ self.assertTrue(os.path.isdir(test_path))
def test_to_csv_single_result_file_exists(self):
test_data = {'time':[0]}
@@ -131,8 +132,9 @@ def test_to_csv_single_result_file_exists(self):
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(stamp = test_stamp, nametag = test_nametag, path=tempdir)
- test_path = tempdir+"/"+test_nametag+test_stamp+"/"+test_nametag+"0.csv"
- assert os.path.isfile(test_path)
+ test_path = tempdir+"/"+test_nametag+'-'+test_stamp+".odf/"+test_nametag+"0.csv"
+ sys.stderr.write('test_path='+test_path+"\n\n")
+ self.assertTrue( os.path.isfile(test_path), msg=f"test_path={test_path} is not a file. tempdir={tempdir} os.listdir()={os.listdir(tempdir)}")
def test_to_csv_single_result_no_stamp(self):
test_data = {'time':[0]}
@@ -141,7 +143,7 @@ def test_to_csv_single_result_no_stamp(self):
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(nametag=test_nametag, path=tempdir)
- assert len(os.listdir(tempdir)) != 0
+ self.assertNotEqual(len(os.listdir(tempdir)), 0)
def test_to_csv_single_result_no_nametag(self):
test_model = Model('test_model')
@@ -149,7 +151,7 @@ def test_to_csv_single_result_no_nametag(self):
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(nametag=test_nametag, path=tempdir)
- assert len(os.listdir(tempdir)) != 0
+ self.assertNotEqual(len(os.listdir(tempdir)), 0)
def test_to_csv_single_result_no_nametag(self):
test_model = Model('test_model')
@@ -160,7 +162,7 @@ def test_to_csv_single_result_no_nametag(self):
with tempfile.TemporaryDirectory() as tempdir:
result.to_csv(stamp=test_stamp, path=tempdir)
- assert len(os.listdir(tempdir)) != 0
+ self.assertNotEqual(len(os.listdir(tempdir)), 0)
def test_to_csv_single_result_no_path(self):
test_data = Trajectory({'time':[0]},model=Model('test_model'),solver_name='test_solver_name')
diff --git a/test/test_run_output.py b/test/test_run_output.py
index 57918012..c16bbc5e 100644
--- a/test/test_run_output.py
+++ b/test/test_run_output.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/test/test_simple_model.py b/test/test_simple_model.py
index 029c1208..49760c1f 100644
--- a/test/test_simple_model.py
+++ b/test/test_simple_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
diff --git a/test/test_ssa_c_solver.py b/test/test_ssa_c_solver.py
index f04daa15..e9d2b861 100644
--- a/test/test_ssa_c_solver.py
+++ b/test/test_ssa_c_solver.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/test/test_sys_init.py b/test/test_sys_init.py
index 11d88697..93d1310d 100644
--- a/test/test_sys_init.py
+++ b/test/test_sys_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/test/test_tau_leaping_c_solver.py b/test/test_tau_leaping_c_solver.py
index ab735009..077bc96f 100644
--- a/test/test_tau_leaping_c_solver.py
+++ b/test/test_tau_leaping_c_solver.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/test/test_tau_leaping_solver.py b/test/test_tau_leaping_solver.py
index aa8fa6ea..df761203 100644
--- a/test/test_tau_leaping_solver.py
+++ b/test/test_tau_leaping_solver.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/test/test_telegraph_model.py b/test/test_telegraph_model.py
index 1d302242..35c8dca6 100644
--- a/test/test_telegraph_model.py
+++ b/test/test_telegraph_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
diff --git a/test/test_variable_solvers.py b/test/test_variable_solvers.py
index 097f4956..f6c44a93 100644
--- a/test/test_variable_solvers.py
+++ b/test/test_variable_solvers.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/test/unit_tests/test_model.py b/test/unit_tests/test_model.py
index 0c777ba4..5b886e34 100644
--- a/test/unit_tests/test_model.py
+++ b/test/unit_tests/test_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
diff --git a/test/unit_tests/test_parameter.py b/test/unit_tests/test_parameter.py
index a23e6933..21878ce0 100644
--- a/test/unit_tests/test_parameter.py
+++ b/test/unit_tests/test_parameter.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/test/unit_tests/test_reaction.py b/test/unit_tests/test_reaction.py
index bacb176b..1f3ff095 100644
--- a/test/unit_tests/test_reaction.py
+++ b/test/unit_tests/test_reaction.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/test/unit_tests/test_species.py b/test/unit_tests/test_species.py
index 032ae1bf..eca3e1f7 100644
--- a/test/unit_tests/test_species.py
+++ b/test/unit_tests/test_species.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/test/unit_tests/test_timespan.py b/test/unit_tests/test_timespan.py
index 0fbd61ae..4cbce0bb 100644
--- a/test/unit_tests/test_timespan.py
+++ b/test/unit_tests/test_timespan.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