Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

1.14.2 release #354

Merged
merged 53 commits into from
Jan 20, 2025
Merged

1.14.2 release #354

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
53 commits
Select commit Hold shift + click to select a range
ef60e6e
for github workflow ubuntu unit tests adjust from gcc version 11 to v…
elmbeech Jan 3, 2025
2cb6347
enable reload setting xml file.
elmbeech Jan 4, 2025
76e3584
update Makefile-default with episode-sample project.
elmbeech Jan 12, 2025
34d817f
add episode sample project.
elmbeech Jan 12, 2025
1a51f20
adjust to physicell formatting convention.
elmbeech Jan 12, 2025
8972473
add github workflow yml entries for the episode sample project.
elmbeech Jan 12, 2025
656fe08
fix event trigger in asym div ex
drbergman Jan 14, 2025
f9772dc
re-round template project cycle durations
drbergman Jan 14, 2025
56e93bc
Merge branch 'patch1141_unittest_ubuntu_gcc_v12' into patch1141_episode
elmbeech Jan 14, 2025
413ef48
Merge branch 'patch1141_reload_settingxml' into patch1141_episode
elmbeech Jan 14, 2025
ccabc3e
requested changes for pull request 349.
elmbeech Jan 14, 2025
589cc31
replace the current Makefile with the updated Makefile-default
elmbeech Jan 14, 2025
8de6be4
get mkdir command working on windows too.
elmbeech Jan 14, 2025
a18505e
get mkdir command working on windows too.
elmbeech Jan 14, 2025
14a9678
minor formatting changes.
elmbeech Jan 15, 2025
71045b9
refactor to simplify edits
drbergman Jan 15, 2025
8b554f9
Merge pull request #1 from drbergman/refactor-eb-code
elmbeech Jan 15, 2025
1c11943
restructure episode main.cpp
elmbeech Jan 15, 2025
e4fe6ac
typo bugfix.
elmbeech Jan 15, 2025
de8fc59
update output folder name.
elmbeech Jan 15, 2025
cc0d719
do not compare episode svgs in test suite
drbergman Jan 15, 2025
9fd6d9b
adjust output folder naming scheme
elmbeech Jan 15, 2025
f584ffb
Merge pull request #2 from drbergman/fix-episode-tests
elmbeech Jan 15, 2025
2e2be4b
marginal formatting change.
elmbeech Jan 16, 2025
cc9f8b8
rename the generate_cell_types function back to create_cell_types bec…
elmbeech Jan 16, 2025
cd0e24f
minor formatting changes.
elmbeech Jan 16, 2025
99245d3
minor formatting change.
elmbeech Jan 16, 2025
2bd87e2
minor formatting change.
elmbeech Jan 16, 2025
795f5b3
change form std::string to char* settingxml to be compatible with the…
elmbeech Jan 16, 2025
16bab19
add const in front of char* to be compatible with ISO C++
elmbeech Jan 17, 2025
7f90dd5
script to download latest Studio
rheiland Jan 18, 2025
6d44ee4
update setting.xml to the latest studio release v2.41.3
elmbeech Jan 19, 2025
1801121
preparing for 1.14.2 release
MathCancer Jan 20, 2025
481d019
Merge pull request #350 from drbergman/fix-asym-div-save-event-trigger
MathCancer Jan 20, 2025
d81b4f5
Merge pull request #351 from drbergman/reround-sample-project-cycle-d…
MathCancer Jan 20, 2025
060c9b6
Merge pull request #353 from rheiland/get_studio
MathCancer Jan 20, 2025
89c09ee
Update README.md
MathCancer Jan 20, 2025
a3bdeea
Merge branch 'development' of https://github.com/MathCancer/PhysiCell…
MathCancer Jan 20, 2025
cffa248
Merge pull request #349 from elmbeech/patch1141_episode
MathCancer Jan 20, 2025
55680a2
Update README.md
MathCancer Jan 20, 2025
f8db27f
Update README.md
MathCancer Jan 20, 2025
b3aa67a
Update .gitignore
MathCancer Jan 20, 2025
d4662bb
Update PhysiCell_signal_behavior.cpp
MathCancer Jan 20, 2025
facaa56
Update README.md
MathCancer Jan 20, 2025
7580d11
Update PhysiCell_signal_behavior.cpp
MathCancer Jan 20, 2025
c2cce92
Merge branch 'development' of https://github.com/MathCancer/PhysiCell…
MathCancer Jan 20, 2025
ef51402
bug fixes
MathCancer Jan 20, 2025
56f784c
Update README.md
MathCancer Jan 20, 2025
afa0625
Update README.md
MathCancer Jan 20, 2025
aa62294
prep for 1.14.2 release
MathCancer Jan 20, 2025
28c1bc9
Merge branch 'development' of https://github.com/MathCancer/PhysiCell…
MathCancer Jan 20, 2025
0709497
update copyright years in main code
MathCancer Jan 20, 2025
cbf625e
prepare for 1.14.2 release (changes.md)
MathCancer Jan 20, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 7 additions & 2 deletions .github/workflows/build_binaries.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ jobs:
{short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
{short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
{short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
{short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
]

runs-on: ubuntu-latest
Expand All @@ -32,7 +33,7 @@ jobs:
make ${{ matrix.projects.project }}
make clean
${{ matrix.projects.extra_run }}
make static STATIC_OPENMP=/usr/lib/gcc/x86_64-linux-gnu/11/libgomp.a
make static STATIC_OPENMP=/usr/lib/gcc/x86_64-linux-gnu/12/libgomp.a

- name: Checking binary for ${{ matrix.projects.name }}
run: |
Expand Down Expand Up @@ -66,6 +67,7 @@ jobs:
{short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
{short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
{short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
{short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
]

runs-on: windows-latest
Expand Down Expand Up @@ -122,6 +124,7 @@ jobs:
{short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
{short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
{short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
{short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
]

runs-on: macos-13
Expand Down Expand Up @@ -171,6 +174,7 @@ jobs:
{short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
{short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
{short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
{short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
]

runs-on: macos-14
Expand Down Expand Up @@ -220,6 +224,7 @@ jobs:
{short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
{short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
{short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
{short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
]

runs-on: macos-13
Expand Down Expand Up @@ -266,4 +271,4 @@ jobs:
upload_url: ${{ github.event.release.upload_url }}
asset_name: ${{ matrix.projects.short_name }}-macos.tar.gz
asset_path: ${{ github.workspace }}/${{ matrix.projects.short_name }}-macos.tar.gz
asset_content_type: application/gzip
asset_content_type: application/gzip
5 changes: 3 additions & 2 deletions .github/workflows/tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,8 @@ jobs:
{project: "interaction-sample", name: "PhysiCell interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
{project: "pred-prey-farmer", name: "PhysiCell prey predator", binary: "pred_prey", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
{project: "rules-sample", name: "PhysiCell rules sample", binary: "rules_sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
{project: "asymmetric-division-sample", name: "PhysiCell asymmetric division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""}
{project: "asymmetric-division-sample", name: "PhysiCell asymmetric division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
{project: "episode-sample", name: "PhysiCell Episode", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: ""},
]

name: Testing ${{ matrix.projects.name }} on ${{ matrix.os.name }}
Expand Down Expand Up @@ -64,4 +65,4 @@ jobs:
- name: Check ${{ matrix.projects.name }} project simulation results
if: matrix.projects.output_folder != ''
run: |
python beta/test_diff_svg.py ${{ matrix.projects.output_folder }} tests/cases/output_${{ matrix.projects.project }}
python beta/test_diff_svg.py ${{ matrix.projects.output_folder }} tests/cases/output_${{ matrix.projects.project }}
2 changes: 2 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,3 +19,5 @@ project
studio_debug.log
user_projects/*
!user_projects/empty.txt
Studio.zip
/studio
2 changes: 1 addition & 1 deletion BioFVM/BioFVM.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_MultiCellDS.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_MultiCellDS.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_agent_container.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_agent_container.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_basic_agent.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_basic_agent.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_matlab.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_matlab.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_mesh.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_mesh.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
55 changes: 7 additions & 48 deletions BioFVM/BioFVM_microenvironment.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down Expand Up @@ -253,7 +253,7 @@ bool Microenvironment::get_substrate_dirichlet_activation( int substrate_index )
// TODO? fix confusing swapped usage of args
double Microenvironment::get_substrate_dirichlet_value( int substrate_index, int index )
{
return dirichlet_value_vectors[index][substrate_index];
return dirichlet_value_vectors[index][substrate_index];
}

// new functions for finer-grained control of Dirichlet conditions -- 1.7.0
Expand Down Expand Up @@ -487,7 +487,7 @@ void Microenvironment::add_density( std::string name , std::string units )

void Microenvironment::add_density( std::string name , std::string units, double diffusion_constant, double decay_rate )
{
// fix in PhysiCell preview November 2017
// check if density exist
if ( find_density_index( name ) != -1 )
{
std::cout << "ERROR: density named " << name << " already exists. You probably want your substrates all have unique names!" << std::endl;
Expand Down Expand Up @@ -1198,7 +1198,11 @@ void initialize_microenvironment( void )
}

// set the initial condition
set_microenvironment_initial_condition();
}

void set_microenvironment_initial_condition( void )
{
if (default_microenvironment_options.initial_condition_from_file_enabled)
{
if (default_microenvironment_options.initial_condition_file_type=="matlab")
Expand Down Expand Up @@ -1389,51 +1393,6 @@ void initialize_microenvironment( void )
}

}

/*
if( default_microenvironment_options.outer_Dirichlet_conditions == true )
{

for( unsigned int k=0 ; k < microenvironment.mesh.z_coordinates.size() ; k++ )
{
// set Dirichlet conditions along the 4 outer edges
for( unsigned int i=0 ; i < microenvironment.mesh.x_coordinates.size() ; i++ )
{
int J = microenvironment.mesh.y_coordinates.size()-1;
microenvironment.add_dirichlet_node( microenvironment.voxel_index(i,0,k) , default_microenvironment_options.Dirichlet_condition_vector );
microenvironment.add_dirichlet_node( microenvironment.voxel_index(i,J,k) , default_microenvironment_options.Dirichlet_condition_vector );
}
int I = microenvironment.mesh.x_coordinates.size()-1;
for( unsigned int j=1; j < microenvironment.mesh.y_coordinates.size()-1 ; j++ )
{
microenvironment.add_dirichlet_node( microenvironment.voxel_index(0,j,k) , default_microenvironment_options.Dirichlet_condition_vector );
microenvironment.add_dirichlet_node( microenvironment.voxel_index(I,j,k) , default_microenvironment_options.Dirichlet_condition_vector );
}
}
// if 3-D, also along the corresponding additional faces
if( default_microenvironment_options.simulate_2D == false )
{
int K = microenvironment.mesh.z_coordinates.size()-1;
for( unsigned int j=1 ; j < microenvironment.mesh.y_coordinates.size()-1 ; j++ )
{
for( unsigned int i=1; i < microenvironment.mesh.x_coordinates.size()-1 ; i++ )
{
microenvironment.add_dirichlet_node( microenvironment.voxel_index(i,j,0) , default_microenvironment_options.Dirichlet_condition_vector );
microenvironment.add_dirichlet_node( microenvironment.voxel_index(i,j,K) , default_microenvironment_options.Dirichlet_condition_vector );
}
}
}

}
*/

// April 2023: no longer necessary after flipping our approach and doing an "additive" instead of "subtractive" DCs handling. I.e., we assume DC activation is false by default; make true on-demand.

// // set the Dirichlet condition activation vector to match the microenvironment options
// for( int i=0 ; i < default_microenvironment_options.Dirichlet_activation_vector.size(); i++ )
// {
// microenvironment.set_substrate_dirichlet_activation( i , default_microenvironment_options.Dirichlet_activation_vector[i] );
// }

microenvironment.display_information(std::cout);
return;
Expand Down
5 changes: 3 additions & 2 deletions BioFVM/BioFVM_microenvironment.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down Expand Up @@ -362,7 +362,8 @@ class Microenvironment_Options
extern Microenvironment_Options default_microenvironment_options;
extern Microenvironment microenvironment;

void initialize_microenvironment( void );
void initialize_microenvironment( void );
void set_microenvironment_initial_condition( void );

void load_initial_conditions_from_matlab( std::string filename );
void load_initial_conditions_from_csv( std::string filename );
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_solvers.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_solvers.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
2 changes: 1 addition & 1 deletion BioFVM/BioFVM_utilities.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# Copyright (c) 2015-2025, Paul Macklin and the BioFVM Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down
Loading
Loading