-

Documentation for SpatialPy 1.2.0

+

Documentation for SpatialPy 1.2.1

SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems embedded in Lagrangian reference frame particle based fluid dynamics domain

This package is intended to replace the PyURDME software https://github.com/pyurdme/pyurdme and will feature both a NSM solver for RDME simulation on static domains and a sSSA-SDPD particle based fluid dynamics solver as described in the publication “A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection–diffusion–reaction problems” by Drawert, Jacob, Li, Yi, Petzold https://www.sciencedirect.com/science/article/pii/S0021999118307101

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From: Bryan Rumsey Date: Thu, 9 Feb 2023 16:14:41 -0500 Subject: [PATCH 3/6] Updated the copyright end year to 2023. --- COPYRIGHT | 2 +- setup.py | 2 +- spatialpy/__init__.py | 2 +- spatialpy/__version__.py | 4 ++-- spatialpy/core/__init__.py | 2 +- spatialpy/core/boundarycondition.py | 2 +- spatialpy/core/cleanup.py | 2 +- spatialpy/core/datafunction.py | 2 +- spatialpy/core/domain.py | 2 +- spatialpy/core/geometry.py | 2 +- spatialpy/core/initialcondition.py | 2 +- spatialpy/core/lattice.py | 2 +- spatialpy/core/model.py | 2 +- spatialpy/core/parameter.py | 2 +- spatialpy/core/reaction.py | 2 +- spatialpy/core/result.py | 2 +- spatialpy/core/spatialpyerror.py | 2 +- spatialpy/core/species.py | 2 +- spatialpy/core/timespan.py | 2 +- spatialpy/core/transformation.py | 2 +- spatialpy/core/visualization.py | 2 +- spatialpy/core/vtkreader.py | 2 +- spatialpy/solvers/__init__.py | 2 +- spatialpy/solvers/build_expression.py | 2 +- .../ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp | 2 +- .../ssa_sdpd-c-simulation-engine/include/count_cores.hpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/include/model.hpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/include/output.hpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp | 2 +- .../ssa_sdpd-c-simulation-engine/include/particle_system.hpp | 2 +- .../ssa_sdpd-c-simulation-engine/include/propensities.hpp | 2 +- .../ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp | 2 +- .../include/read_lammps_input_file.hpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp | 2 +- .../ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp | 2 +- .../ssa_sdpd-c-simulation-engine/propensity_file_template.cpp | 2 +- .../ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp | 2 +- .../solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/src/output.cpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp | 2 +- .../ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp | 2 +- .../src/read_lammps_input_file.cpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp | 2 +- .../c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp | 2 +- .../ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp | 2 +- spatialpy/solvers/solver.py | 2 +- spatialpy/stochss/__init__.py | 2 +- spatialpy/stochss/stochss_export.py | 2 +- test/ioperformance.py | 2 +- test/models/__init__.py | 2 +- test/models/cylinder_demo3D.py | 2 +- test/models/mincde.py | 2 +- test/models/mincde_5r.py | 2 +- test/run_integration_tests.py | 2 +- test/run_unit_tests.py | 2 +- test/test_mincde.py | 2 +- test/test_model.py | 2 +- test/test_solver.py | 2 +- test/test_threads.py | 2 +- test/unit_tests/test_parameter.py | 2 +- test/unit_tests/test_reaction.py | 2 +- test/unit_tests/test_species.py | 2 +- test/unit_tests/test_timespan.py | 2 +- 64 files changed, 65 insertions(+), 65 deletions(-) diff --git a/COPYRIGHT b/COPYRIGHT index 116227b0..13c52dc0 100644 --- a/COPYRIGHT +++ b/COPYRIGHT @@ -1,6 +1,6 @@ SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/setup.py b/setup.py index 32d8db35..b9676937 100644 --- a/setup.py +++ b/setup.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/__init__.py b/spatialpy/__init__.py index 8e541f81..0ff58136 100644 --- a/spatialpy/__init__.py +++ b/spatialpy/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/__version__.py b/spatialpy/__version__.py index bb83f022..31bd194c 100644 --- a/spatialpy/__version__.py +++ b/spatialpy/__version__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as @@ -29,4 +29,4 @@ __author__ = 'See AUTHORS' __email__ = 'bdrawert@unca.edu' __license__ = 'GPL-3.0-only' -__copyright__ = 'Copyright (C) 2019-2022' +__copyright__ = 'Copyright (C) 2019-2023' diff --git a/spatialpy/core/__init__.py b/spatialpy/core/__init__.py index af5e9d71..a9cff809 100644 --- a/spatialpy/core/__init__.py +++ b/spatialpy/core/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/boundarycondition.py b/spatialpy/core/boundarycondition.py index 8c833c2a..98204859 100644 --- a/spatialpy/core/boundarycondition.py +++ b/spatialpy/core/boundarycondition.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/cleanup.py b/spatialpy/core/cleanup.py index 6da34ccf..502b89ee 100644 --- a/spatialpy/core/cleanup.py +++ b/spatialpy/core/cleanup.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/datafunction.py b/spatialpy/core/datafunction.py index 5cfaff1b..a61bd7c6 100644 --- a/spatialpy/core/datafunction.py +++ b/spatialpy/core/datafunction.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/domain.py b/spatialpy/core/domain.py index 870022ee..0db0c0d3 100644 --- a/spatialpy/core/domain.py +++ b/spatialpy/core/domain.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/geometry.py b/spatialpy/core/geometry.py index 055418a2..4a0b482d 100644 --- a/spatialpy/core/geometry.py +++ b/spatialpy/core/geometry.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/initialcondition.py b/spatialpy/core/initialcondition.py index 94e35f32..4ebe5bdb 100644 --- a/spatialpy/core/initialcondition.py +++ b/spatialpy/core/initialcondition.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/lattice.py b/spatialpy/core/lattice.py index b9c5f5f6..0b1fa890 100644 --- a/spatialpy/core/lattice.py +++ b/spatialpy/core/lattice.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/model.py b/spatialpy/core/model.py index f5fe3687..6bf033c8 100644 --- a/spatialpy/core/model.py +++ b/spatialpy/core/model.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/parameter.py b/spatialpy/core/parameter.py index d3e9904f..0a588314 100644 --- a/spatialpy/core/parameter.py +++ b/spatialpy/core/parameter.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/reaction.py b/spatialpy/core/reaction.py index 7d5f5dff..678d98c1 100644 --- a/spatialpy/core/reaction.py +++ b/spatialpy/core/reaction.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/result.py b/spatialpy/core/result.py index 1753a1d9..10357b39 100644 --- a/spatialpy/core/result.py +++ b/spatialpy/core/result.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/spatialpyerror.py b/spatialpy/core/spatialpyerror.py index 51f89815..a0cccb69 100644 --- a/spatialpy/core/spatialpyerror.py +++ b/spatialpy/core/spatialpyerror.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/species.py b/spatialpy/core/species.py index e7533750..c85255d4 100644 --- a/spatialpy/core/species.py +++ b/spatialpy/core/species.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/timespan.py b/spatialpy/core/timespan.py index f8b7cfed..d32ea1ee 100644 --- a/spatialpy/core/timespan.py +++ b/spatialpy/core/timespan.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/transformation.py b/spatialpy/core/transformation.py index ebd86579..e2a90af0 100644 --- a/spatialpy/core/transformation.py +++ b/spatialpy/core/transformation.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/visualization.py b/spatialpy/core/visualization.py index b69abc9b..523a058c 100644 --- a/spatialpy/core/visualization.py +++ b/spatialpy/core/visualization.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/vtkreader.py b/spatialpy/core/vtkreader.py index 99e5f1a7..fe402091 100644 --- a/spatialpy/core/vtkreader.py +++ b/spatialpy/core/vtkreader.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/__init__.py b/spatialpy/solvers/__init__.py index fd7a442b..a6a2bb10 100644 --- a/spatialpy/solvers/__init__.py +++ b/spatialpy/solvers/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/build_expression.py b/spatialpy/solvers/build_expression.py index 573a1ea8..8e27a735 100644 --- a/spatialpy/solvers/build_expression.py +++ b/spatialpy/solvers/build_expression.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp index be4b090e..89de6dce 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp index 4d410ab7..758bc14b 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp index 5109c107..facefba5 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp index 356137c7..ed652abf 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp index ed237085..7066333c 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle_system.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle_system.hpp index 50de5b4a..54a3d141 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle_system.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle_system.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/propensities.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/propensities.hpp index c9135e60..7543dcd5 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/propensities.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/propensities.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp index 4c029d99..64c0868d 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp index cfd9001e..9865d0b4 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp index d6811f05..ba4cf09b 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp index 8481863e..556cbb55 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp index 8b1e80e7..a1cddb1e 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp index 3ba38a5a..f38015bb 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp index 03123125..430c01b8 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp index 346b505e..5d745007 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp index a37b75e1..4ebaef43 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp index 4efd1b28..c2555ea0 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp index 254ee855..2f7d9be3 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp index 6a4ed8ee..4fcb7b8f 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp index f8bc80ee..7597f80d 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp index 351b97b3..6c704144 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp index 0c6227ca..3645f16d 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py index c884a6f8..094884d0 100644 --- a/spatialpy/solvers/solver.py +++ b/spatialpy/solvers/solver.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/stochss/__init__.py b/spatialpy/stochss/__init__.py index 5449def2..be5b9eea 100644 --- a/spatialpy/stochss/__init__.py +++ b/spatialpy/stochss/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/stochss/stochss_export.py b/spatialpy/stochss/stochss_export.py index 5d7d586d..eaff6be4 100644 --- a/spatialpy/stochss/stochss_export.py +++ b/spatialpy/stochss/stochss_export.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/ioperformance.py b/test/ioperformance.py index bef0b459..9cf8cf9b 100644 --- a/test/ioperformance.py +++ b/test/ioperformance.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/models/__init__.py b/test/models/__init__.py index 5449def2..be5b9eea 100644 --- a/test/models/__init__.py +++ b/test/models/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/models/cylinder_demo3D.py b/test/models/cylinder_demo3D.py index 2e5835b4..e358649a 100644 --- a/test/models/cylinder_demo3D.py +++ b/test/models/cylinder_demo3D.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/models/mincde.py b/test/models/mincde.py index c11f66a5..ca17e866 100644 --- a/test/models/mincde.py +++ b/test/models/mincde.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/models/mincde_5r.py b/test/models/mincde_5r.py index 6f945ed3..8525b213 100644 --- a/test/models/mincde_5r.py +++ b/test/models/mincde_5r.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/run_integration_tests.py b/test/run_integration_tests.py index b84d845f..ed430f1f 100644 --- a/test/run_integration_tests.py +++ b/test/run_integration_tests.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/run_unit_tests.py b/test/run_unit_tests.py index d54c1fff..f1eb8932 100755 --- a/test/run_unit_tests.py +++ b/test/run_unit_tests.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/test_mincde.py b/test/test_mincde.py index 13ad6641..13d2482f 100644 --- a/test/test_mincde.py +++ b/test/test_mincde.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/test_model.py b/test/test_model.py index d0ab2afd..7b11cc09 100644 --- a/test/test_model.py +++ b/test/test_model.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/test_solver.py b/test/test_solver.py index 38e76c02..01a72455 100644 --- a/test/test_solver.py +++ b/test/test_solver.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/test_threads.py b/test/test_threads.py index 81224e6a..79f06bf3 100644 --- a/test/test_threads.py +++ b/test/test_threads.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/unit_tests/test_parameter.py b/test/unit_tests/test_parameter.py index 04ebcee6..f4d57786 100644 --- a/test/unit_tests/test_parameter.py +++ b/test/unit_tests/test_parameter.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/unit_tests/test_reaction.py b/test/unit_tests/test_reaction.py index 3220fb22..2e7cbe8a 100644 --- a/test/unit_tests/test_reaction.py +++ b/test/unit_tests/test_reaction.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/unit_tests/test_species.py b/test/unit_tests/test_species.py index af62456e..5af1c7e2 100644 --- a/test/unit_tests/test_species.py +++ b/test/unit_tests/test_species.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/unit_tests/test_timespan.py b/test/unit_tests/test_timespan.py index 87e3bc5d..35283672 100644 --- a/test/unit_tests/test_timespan.py +++ b/test/unit_tests/test_timespan.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as From 8814450c507f0c6779415d2fbcf568acb4e17b89 Mon Sep 17 00:00:00 2001 From: Brian Drawert Date: Tue, 14 Feb 2023 15:07:42 -0800 Subject: [PATCH 4/6] timeout works, but does not include compile time in limit --- spatialpy/solvers/solver.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py index c884a6f8..d1591728 100644 --- a/spatialpy/solvers/solver.py +++ b/spatialpy/solvers/solver.py @@ -27,7 +27,7 @@ import numpy -from spatialpy.core.spatialpyerror import ModelError, SimulationError, SimulationTimeout +from spatialpy.core.spatialpyerror import ModelError, SimulationError def _read_from_stdout(stdout ,verbose=True): try: @@ -536,7 +536,6 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, :returns: A SpatialPy Result object containing spatial and time series data from simulation. :rtype: spatialpy.Result.Result | list(spatialpy.Result.Result) - :raises SimulationTimeout: Simulation exceeded timeout. :raises SimulationError: Simulation execution failed. """ from spatialpy.core.result import Result # pylint: disable=import-outside-toplevel @@ -587,7 +586,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, result.timeout = True # send signal to the process group os.killpg(process.pid, signal.SIGINT) - raise SimulationTimeout("SpatialPy solver timeout exceded.") from err + except OSError as err: print(f"Error, execution of solver raised an exception: {err}") print(f"cmd = {solver_cmd}") From 20542963247ef0af8d1fbc70213428dda0457b8c Mon Sep 17 00:00:00 2001 From: Brian Drawert Date: Tue, 14 Feb 2023 15:11:56 -0800 Subject: [PATCH 5/6] Fixes #253, timeout only counts execution time, compile time is ignored. --- spatialpy/solvers/solver.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py index c884a6f8..5b2e9a46 100644 --- a/spatialpy/solvers/solver.py +++ b/spatialpy/solvers/solver.py @@ -27,7 +27,7 @@ import numpy -from spatialpy.core.spatialpyerror import ModelError, SimulationError, SimulationTimeout +from spatialpy.core.spatialpyerror import ModelError, SimulationError def _read_from_stdout(stdout ,verbose=True): try: @@ -536,7 +536,6 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, :returns: A SpatialPy Result object containing spatial and time series data from simulation. :rtype: spatialpy.Result.Result | list(spatialpy.Result.Result) - :raises SimulationTimeout: Simulation exceeded timeout. :raises SimulationError: Simulation execution failed. """ from spatialpy.core.result import Result # pylint: disable=import-outside-toplevel @@ -587,7 +586,6 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, result.timeout = True # send signal to the process group os.killpg(process.pid, signal.SIGINT) - raise SimulationTimeout("SpatialPy solver timeout exceded.") from err except OSError as err: print(f"Error, execution of solver raised an exception: {err}") print(f"cmd = {solver_cmd}") From 667097a43bd7bf2e869dc6f309d079d4dfa8bcdb Mon Sep 17 00:00:00 2001 From: Brian Drawert Date: Wed, 15 Feb 2023 15:38:17 -0800 Subject: [PATCH 6/6] Fixes #348 --- spatialpy/core/result.py | 13 +++++++++++++ spatialpy/solvers/solver.py | 14 ++++++-------- 2 files changed, 19 insertions(+), 8 deletions(-) diff --git a/spatialpy/core/result.py b/spatialpy/core/result.py index 1753a1d9..9b83348e 100644 --- a/spatialpy/core/result.py +++ b/spatialpy/core/result.py @@ -156,6 +156,19 @@ def __init__(self, model=None, result_dir=None): self.timeout = False self.official_vtk = False self.result_dir = result_dir + self.listOfResultObjects = [self] + + def __len__(self): + return len(self.listOfResultObjects) + + def __getitem__(self, index): + return self.listOfResultObjects[index] + + def __setitem__(self, index, item): + self.listOfResultObjects[index] = item + + def append(self, item): + self.listOfResultObjects.append(item) def __eq__(self, other): if isinstance(other, Result) and self.result_dir and other.result_dir: diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py index d1591728..e6ee3115 100644 --- a/spatialpy/solvers/solver.py +++ b/spatialpy/solvers/solver.py @@ -534,13 +534,11 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, :type verbose: bool :returns: A SpatialPy Result object containing spatial and time series data from simulation. - :rtype: spatialpy.Result.Result | list(spatialpy.Result.Result) + :rtype: spatialpy.Result.Result :raises SimulationError: Simulation execution failed. """ from spatialpy.core.result import Result # pylint: disable=import-outside-toplevel - if number_of_trajectories > 1: - result_list = [] # Check if compiled, call compile() if not. if not self.is_compiled: self.compile(debug=debug, profile=profile) @@ -601,9 +599,9 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, result.success = True if profile: self.__read_profile_info(result) - if number_of_trajectories > 1: - result_list.append(result) - else: - return result + if run_ndx == 0: + first_result = result + elif number_of_trajectories > 1: + first_result.append(result) - return result_list + return first_result