From 5c1693b96353242bde1c7ef6b55a5b375d210113 Mon Sep 17 00:00:00 2001 From: bue Date: Tue, 4 Jun 2024 21:40:27 -0400 Subject: [PATCH 1/7] changes to the cp command from make save and make load to allow user project config and custom_modules with a folder structure. --- Makefile | 8 ++++---- sample_projects/Makefile-default | 8 ++++---- sample_projects/biorobots/Makefile | 8 ++++---- sample_projects/cancer_biorobots/Makefile | 8 ++++---- sample_projects/cancer_immune/Makefile | 8 ++++---- sample_projects/celltypes3/Makefile | 8 ++++---- sample_projects/heterogeneity/Makefile | 8 ++++---- sample_projects/interactions/Makefile | 8 ++++---- sample_projects/mechano/Makefile | 8 ++++---- sample_projects/physimess/Makefile | 4 ++-- sample_projects/pred_prey_farmer/Makefile | 8 ++++---- sample_projects/rules_sample/Makefile | 8 ++++---- sample_projects/template/Makefile | 8 ++++---- sample_projects/virus_macrophage/Makefile | 8 ++++---- sample_projects/worm/Makefile | 8 ++++---- .../boolean/cancer_invasion/Makefile | 4 ++-- .../boolean/physiboss_cell_lines/Makefile | 4 ++-- .../boolean/template_BM/Makefile | 4 ++-- sample_projects_intracellular/boolean/tutorial/Makefile | 4 ++-- unit_tests/custom_DCs_2substrates/Makefile | 8 ++++---- unit_tests/custom_voxel_values/Makefile | 8 ++++---- 21 files changed, 74 insertions(+), 74 deletions(-) diff --git a/Makefile b/Makefile index 02b313890..eeeb17e61 100644 --- a/Makefile +++ b/Makefile @@ -493,15 +493,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default index 02b313890..eeeb17e61 100644 --- a/sample_projects/Makefile-default +++ b/sample_projects/Makefile-default @@ -493,15 +493,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/biorobots/Makefile b/sample_projects/biorobots/Makefile index 26314225c..c32d06509 100644 --- a/sample_projects/biorobots/Makefile +++ b/sample_projects/biorobots/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/cancer_biorobots/Makefile b/sample_projects/cancer_biorobots/Makefile index b74f8837a..44951983d 100644 --- a/sample_projects/cancer_biorobots/Makefile +++ b/sample_projects/cancer_biorobots/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/cancer_immune/Makefile b/sample_projects/cancer_immune/Makefile index 5cbb2ca8f..0ffc905e5 100644 --- a/sample_projects/cancer_immune/Makefile +++ b/sample_projects/cancer_immune/Makefile @@ -281,15 +281,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/celltypes3/Makefile b/sample_projects/celltypes3/Makefile index 29732af20..20cc9bdc5 100644 --- a/sample_projects/celltypes3/Makefile +++ b/sample_projects/celltypes3/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/heterogeneity/Makefile b/sample_projects/heterogeneity/Makefile index 93d055ea9..92272eaad 100644 --- a/sample_projects/heterogeneity/Makefile +++ b/sample_projects/heterogeneity/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/interactions/Makefile b/sample_projects/interactions/Makefile index c42fc9666..fe570ebca 100644 --- a/sample_projects/interactions/Makefile +++ b/sample_projects/interactions/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/mechano/Makefile b/sample_projects/mechano/Makefile index e90a9966f..eca7eadcf 100644 --- a/sample_projects/mechano/Makefile +++ b/sample_projects/mechano/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/physimess/Makefile b/sample_projects/physimess/Makefile index 0dcd2449c..0336713bc 100644 --- a/sample_projects/physimess/Makefile +++ b/sample_projects/physimess/Makefile @@ -303,8 +303,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/pred_prey_farmer/Makefile b/sample_projects/pred_prey_farmer/Makefile index 06ec2705e..13469412e 100644 --- a/sample_projects/pred_prey_farmer/Makefile +++ b/sample_projects/pred_prey_farmer/Makefile @@ -281,15 +281,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/rules_sample/Makefile b/sample_projects/rules_sample/Makefile index 6682b5c46..a0321f84a 100644 --- a/sample_projects/rules_sample/Makefile +++ b/sample_projects/rules_sample/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/template/Makefile b/sample_projects/template/Makefile index 6682b5c46..a0321f84a 100644 --- a/sample_projects/template/Makefile +++ b/sample_projects/template/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/virus_macrophage/Makefile b/sample_projects/virus_macrophage/Makefile index d8c8ad4e8..54f957e6b 100644 --- a/sample_projects/virus_macrophage/Makefile +++ b/sample_projects/virus_macrophage/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/worm/Makefile b/sample_projects/worm/Makefile index e953e28ad..bdef51da1 100644 --- a/sample_projects/worm/Makefile +++ b/sample_projects/worm/Makefile @@ -280,15 +280,15 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects_intracellular/boolean/cancer_invasion/Makefile b/sample_projects_intracellular/boolean/cancer_invasion/Makefile index 34e9ccba1..15814996e 100644 --- a/sample_projects_intracellular/boolean/cancer_invasion/Makefile +++ b/sample_projects_intracellular/boolean/cancer_invasion/Makefile @@ -323,8 +323,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile index b616fb2da..7a92d9a81 100644 --- a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile +++ b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile @@ -319,8 +319,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects_intracellular/boolean/template_BM/Makefile b/sample_projects_intracellular/boolean/template_BM/Makefile index 989398e41..18358c374 100644 --- a/sample_projects_intracellular/boolean/template_BM/Makefile +++ b/sample_projects_intracellular/boolean/template_BM/Makefile @@ -333,8 +333,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects_intracellular/boolean/tutorial/Makefile b/sample_projects_intracellular/boolean/tutorial/Makefile index 193ee09cb..029bb3fcd 100644 --- a/sample_projects_intracellular/boolean/tutorial/Makefile +++ b/sample_projects_intracellular/boolean/tutorial/Makefile @@ -324,8 +324,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/unit_tests/custom_DCs_2substrates/Makefile b/unit_tests/custom_DCs_2substrates/Makefile index faa887869..20a136071 100644 --- a/unit_tests/custom_DCs_2substrates/Makefile +++ b/unit_tests/custom_DCs_2substrates/Makefile @@ -281,16 +281,16 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules # useage: make load PROJ=your_project_name load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ # useage: make share PROJ=your_project_name share: diff --git a/unit_tests/custom_voxel_values/Makefile b/unit_tests/custom_voxel_values/Makefile index e27362f79..591879107 100644 --- a/unit_tests/custom_voxel_values/Makefile +++ b/unit_tests/custom_voxel_values/Makefile @@ -278,16 +278,16 @@ save: cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules # useage: make load PROJ=your_project_name load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ # useage: make share PROJ=your_project_name share: From 1bcc7683a38f258885f3beaad9f3ce247b9248e8 Mon Sep 17 00:00:00 2001 From: bue Date: Fri, 7 Jun 2024 11:36:53 -0400 Subject: [PATCH 2/7] the Makefile-default reset function is now compatible with the config and custom_modules deep folder structure. --- sample_projects/Makefile-default | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default index eeeb17e61..bb13d6989 100644 --- a/sample_projects/Makefile-default +++ b/sample_projects/Makefile-default @@ -387,16 +387,18 @@ PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp # cleanup reset: + make clean rm -f *.cpp PhysiCell_cell.o - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml touch ./config/empty.csv - rm ./config/*.csv clean: rm -f *.o From ec3ed6e51c2039a2fcbde35f73b04223f28f57d1 Mon Sep 17 00:00:00 2001 From: bue Date: Sun, 9 Jun 2024 08:38:47 -0400 Subject: [PATCH 3/7] updated Makefile reset function, so that the function is compatible with the config and custome_modules deep folder structure. --- Makefile | 22 ++++++------ sample_projects/Makefile-default | 6 ++-- sample_projects/biorobots/Makefile | 22 ++++++------ sample_projects/cancer_biorobots/Makefile | 22 ++++++------ sample_projects/cancer_immune/Makefile | 20 ++++++----- sample_projects/celltypes3/Makefile | 22 ++++++------ sample_projects/heterogeneity/Makefile | 22 ++++++------ sample_projects/interactions/Makefile | 22 ++++++------ sample_projects/mechano/Makefile | 22 ++++++------ sample_projects/physimess/Makefile | 23 ++++++------- sample_projects/pred_prey_farmer/Makefile | 22 ++++++------ sample_projects/rules_sample/Makefile | 22 ++++++------ sample_projects/template/Makefile | 22 ++++++------ sample_projects/virus_macrophage/Makefile | 22 ++++++------ sample_projects/worm/Makefile | 22 ++++++------ .../boolean/cancer_invasion/Makefile | 26 +++++++------- .../boolean/physiboss_cell_lines/Makefile | 26 +++++++------- .../boolean/template_BM/Makefile | 34 ++++++++++--------- .../boolean/tutorial/Makefile | 27 ++++++++------- .../fba/cancer_metabolism/Make-windows | 8 +++-- .../fba/cancer_metabolism/Makefile | 20 +++++------ .../fba/ecoli_acetic_switch/Makefile | 9 ++--- .../ode/ode_energy/Makefile | 24 ++++++------- unit_tests/custom_DCs_2substrates/Makefile | 22 ++++++------ unit_tests/custom_voxel_values/Makefile | 22 ++++++------ .../Makefile-unit-test-conservation | 20 ++++++----- 26 files changed, 279 insertions(+), 272 deletions(-) diff --git a/Makefile b/Makefile index eeeb17e61..b215d70c6 100644 --- a/Makefile +++ b/Makefile @@ -387,17 +387,17 @@ PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp # cleanup reset: - rm -f *.cpp PhysiCell_cell.o - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default index bb13d6989..b215d70c6 100644 --- a/sample_projects/Makefile-default +++ b/sample_projects/Makefile-default @@ -388,8 +388,7 @@ PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp reset: make clean - rm -f *.cpp PhysiCell_cell.o - touch ./core/PhysiCell_cell.cpp + rm -f *.cpp cp ./sample_projects/Makefile-default Makefile rm -fr ./custom_modules/* touch ./custom_modules/empty.txt @@ -398,8 +397,7 @@ reset: mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/biorobots/Makefile b/sample_projects/biorobots/Makefile index c32d06509..aad8aca30 100644 --- a/sample_projects/biorobots/Makefile +++ b/sample_projects/biorobots/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/cancer_biorobots/Makefile b/sample_projects/cancer_biorobots/Makefile index 44951983d..121d64fa7 100644 --- a/sample_projects/cancer_biorobots/Makefile +++ b/sample_projects/cancer_biorobots/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/cancer_immune/Makefile b/sample_projects/cancer_immune/Makefile index 0ffc905e5..a0487ec66 100644 --- a/sample_projects/cancer_immune/Makefile +++ b/sample_projects/cancer_immune/Makefile @@ -172,15 +172,17 @@ cancer_immune_3D.o: ./custom_modules/cancer_immune_3D.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/celltypes3/Makefile b/sample_projects/celltypes3/Makefile index 20cc9bdc5..3e1ab9ca9 100644 --- a/sample_projects/celltypes3/Makefile +++ b/sample_projects/celltypes3/Makefile @@ -171,17 +171,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/heterogeneity/Makefile b/sample_projects/heterogeneity/Makefile index 92272eaad..7a6caccf4 100644 --- a/sample_projects/heterogeneity/Makefile +++ b/sample_projects/heterogeneity/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/interactions/Makefile b/sample_projects/interactions/Makefile index fe570ebca..c2928a8a7 100644 --- a/sample_projects/interactions/Makefile +++ b/sample_projects/interactions/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/mechano/Makefile b/sample_projects/mechano/Makefile index eca7eadcf..739af2604 100644 --- a/sample_projects/mechano/Makefile +++ b/sample_projects/mechano/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/physimess/Makefile b/sample_projects/physimess/Makefile index 0336713bc..a52942317 100644 --- a/sample_projects/physimess/Makefile +++ b/sample_projects/physimess/Makefile @@ -189,18 +189,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/mymodel.xml *.csv - rm -fr ./config/Cell_Fibre_Mechanics ./config/Fibre_Crosslinks ./config/Fibre_Initialisation ./config/Neighbours_in_voxels ./config/Fibre_Degradation - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/pred_prey_farmer/Makefile b/sample_projects/pred_prey_farmer/Makefile index 13469412e..385c472a9 100644 --- a/sample_projects/pred_prey_farmer/Makefile +++ b/sample_projects/pred_prey_farmer/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/rules_sample/Makefile b/sample_projects/rules_sample/Makefile index a0321f84a..ba50bdd6a 100644 --- a/sample_projects/rules_sample/Makefile +++ b/sample_projects/rules_sample/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/template/Makefile b/sample_projects/template/Makefile index a0321f84a..ba50bdd6a 100644 --- a/sample_projects/template/Makefile +++ b/sample_projects/template/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/virus_macrophage/Makefile b/sample_projects/virus_macrophage/Makefile index 54f957e6b..38439b71f 100644 --- a/sample_projects/virus_macrophage/Makefile +++ b/sample_projects/virus_macrophage/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects/worm/Makefile b/sample_projects/worm/Makefile index bdef51da1..e403f5ef3 100644 --- a/sample_projects/worm/Makefile +++ b/sample_projects/worm/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/sample_projects_intracellular/boolean/cancer_invasion/Makefile b/sample_projects_intracellular/boolean/cancer_invasion/Makefile index 15814996e..b128ff261 100644 --- a/sample_projects_intracellular/boolean/cancer_invasion/Makefile +++ b/sample_projects_intracellular/boolean/cancer_invasion/Makefile @@ -220,24 +220,26 @@ custom.o: ./custom_modules/custom.cpp $(MaBoSS) # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - rm ALL_CITATIONS.txt - rm ./config/PhysiCell_settings_*.xml - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - rm -rf ./config/boolean_network/ ./config/cells.csv ./config/rules.csv ./config/init.tsv + make MaBoSS-clean + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: rm -fr addons/PhysiBoSS/MaBoSS-env-2.0 - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* - + data-cleanup: rm -f *.mat rm -f *.xml @@ -245,7 +247,7 @@ data-cleanup: rm -rf ./output mkdir ./output touch ./output/empty.txt - + # archival checkpoint: diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile index 7a92d9a81..808e92fed 100644 --- a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile +++ b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile @@ -217,31 +217,33 @@ custom.o: ./custom_modules/custom.cpp $(MaBoSS) # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - rm -rf ./config/model_*.bnd ./config/model.cfg ./config/cells.csv + make MaBoSS-clean + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: rm -fr addons/PhysiBoSS/MaBoSS-env-2.0 - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* - + data-cleanup: rm -f *.mat rm -f *.xml rm -f *.svg rm -f ./output/* touch ./output/empty.txt - + # archival checkpoint: diff --git a/sample_projects_intracellular/boolean/template_BM/Makefile b/sample_projects_intracellular/boolean/template_BM/Makefile index 18358c374..be1f223d6 100644 --- a/sample_projects_intracellular/boolean/template_BM/Makefile +++ b/sample_projects_intracellular/boolean/template_BM/Makefile @@ -217,40 +217,42 @@ custom.o: ./custom_modules/custom.cpp $(MaBoSS) # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - rm -fr ./config/cells.csv ./config/cell_rules.csv + make MaBoSS-clean + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: rm -fr addons/PhysiBoSS/MaBoSS-env-2.0 - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* - + data-cleanup: rm -rf ./output mkdir ./output touch ./output/empty.txt - + # archival - + checkpoint: zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* - + zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* cp latest.zip $$(date +%b_%d_%Y_%H%M).zip cp latest.zip VERSION_$(VERSION).zip mv *.zip archives/ - + tar: tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* cp latest.tar $$(date +%b_%d_%Y_%H%M).tar @@ -260,7 +262,7 @@ tar: unzip: cp ./archives/latest.zip . unzip latest.zip - + untar: cp ./archives/latest.tar . tar -xzf latest.tar diff --git a/sample_projects_intracellular/boolean/tutorial/Makefile b/sample_projects_intracellular/boolean/tutorial/Makefile index 029bb3fcd..82b8584ea 100644 --- a/sample_projects_intracellular/boolean/tutorial/Makefile +++ b/sample_projects_intracellular/boolean/tutorial/Makefile @@ -220,25 +220,26 @@ custom.o: ./custom_modules/custom.cpp $(MaBoSS) # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - rm -rf ./config/simple_tnf/ - rm -fr ./config/cell_cycle/ - rm -fr ./config/differentiation/ + make MaBoSS-clean + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: rm -fr addons/PhysiBoSS/MaBoSS-env-2.0 - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* - + data-cleanup: rm -f *.mat rm -f *.xml @@ -246,7 +247,7 @@ data-cleanup: rm -rf ./output mkdir ./output touch ./output/empty.txt - + # archival checkpoint: diff --git a/sample_projects_intracellular/fba/cancer_metabolism/Make-windows b/sample_projects_intracellular/fba/cancer_metabolism/Make-windows index 245bbe2a2..2bfe1511b 100644 --- a/sample_projects_intracellular/fba/cancer_metabolism/Make-windows +++ b/sample_projects_intracellular/fba/cancer_metabolism/Make-windows @@ -198,14 +198,16 @@ cancer_metabolism.o: ./custom_modules/cancer_metabolism.cpp # cleanup reset: + make clean rm -f *.cpp cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* + rm -fr ./custom_modules/* touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings_default.xml ./config/PhysiCell_settings.xml - touch ./config/empty.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/fba/cancer_metabolism/Makefile b/sample_projects_intracellular/fba/cancer_metabolism/Makefile index 1ed8367ee..b99e2a010 100755 --- a/sample_projects_intracellular/fba/cancer_metabolism/Makefile +++ b/sample_projects_intracellular/fba/cancer_metabolism/Makefile @@ -203,16 +203,16 @@ cancer_metabolism.o: ./custom_modules/cancer_metabolism.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm ./config/*.csv + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile b/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile index 0e85b19ef..600c3d152 100644 --- a/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile +++ b/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile @@ -251,15 +251,16 @@ ecoli_acetic_switch.o: ./custom_modules/ecoli_acetic_switch.cpp # cleanup reset: + make clean rm -f *.cpp cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* + rm -fr ./custom_modules/* touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/ode/ode_energy/Makefile b/sample_projects_intracellular/ode/ode_energy/Makefile index 42168464c..0e5ad52c0 100644 --- a/sample_projects_intracellular/ode/ode_energy/Makefile +++ b/sample_projects_intracellular/ode/ode_energy/Makefile @@ -227,20 +227,16 @@ data-cleanup: touch ./output/empty.txt reset: - rm -f *.cpp PhysiCell_cell.o - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm ./config/*.csv - rm ./config/*.m - rm ./config/*.cps - rm ./config/Toy_Metabolic_Model.xml - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml FOLDER := output FRAMERATE := 24 diff --git a/unit_tests/custom_DCs_2substrates/Makefile b/unit_tests/custom_DCs_2substrates/Makefile index 20a136071..404195a0b 100644 --- a/unit_tests/custom_DCs_2substrates/Makefile +++ b/unit_tests/custom_DCs_2substrates/Makefile @@ -174,17 +174,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/unit_tests/custom_voxel_values/Makefile b/unit_tests/custom_voxel_values/Makefile index 591879107..4d374df4a 100644 --- a/unit_tests/custom_voxel_values/Makefile +++ b/unit_tests/custom_voxel_values/Makefile @@ -171,17 +171,17 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* diff --git a/unit_tests/substrate_internalization/Makefile-unit-test-conservation b/unit_tests/substrate_internalization/Makefile-unit-test-conservation index d5c82fae8..7e6471b39 100644 --- a/unit_tests/substrate_internalization/Makefile-unit-test-conservation +++ b/unit_tests/substrate_internalization/Makefile-unit-test-conservation @@ -140,15 +140,17 @@ custom-unit-substrate-conservation.o: ./custom_modules/custom-unit-substrate-con # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings_default.xml ./config/PhysiCell_settings.xml - touch ./config/empty.txt - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + mv ./config/PhysiCell_settings-backup.xml . + rm -fr ./config/* + mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* From 364101ef40ef9881ec40c024e62affff53a6dd93 Mon Sep 17 00:00:00 2001 From: bue Date: Sun, 9 Jun 2024 09:04:38 -0400 Subject: [PATCH 4/7] updated Makefile checkpoint function, so that the function is compatible with the config and custome_modules deep folder structure. --- Makefile | 2 +- sample_projects/Makefile-default | 2 +- sample_projects/biorobots/Makefile | 2 +- sample_projects/cancer_biorobots/Makefile | 2 +- sample_projects/cancer_immune/Makefile | 2 +- sample_projects/celltypes3/Makefile | 2 +- sample_projects/heterogeneity/Makefile | 2 +- sample_projects/interactions/Makefile | 2 +- sample_projects/mechano/Makefile | 2 +- sample_projects/physimess/Makefile | 2 +- sample_projects/pred_prey_farmer/Makefile | 2 +- sample_projects/rules_sample/Makefile | 2 +- sample_projects/template/Makefile | 2 +- sample_projects/virus_macrophage/Makefile | 2 +- sample_projects/worm/Makefile | 2 +- sample_projects_intracellular/boolean/cancer_invasion/Makefile | 2 +- .../boolean/physiboss_cell_lines/Makefile | 2 +- sample_projects_intracellular/boolean/template_BM/Makefile | 2 +- sample_projects_intracellular/boolean/tutorial/Makefile | 2 +- sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile | 2 +- sample_projects_intracellular/ode/ode_energy/Makefile | 2 +- unit_tests/custom_DCs_2substrates/Makefile | 2 +- unit_tests/custom_voxel_values/Makefile | 2 +- 23 files changed, 23 insertions(+), 23 deletions(-) diff --git a/Makefile b/Makefile index b215d70c6..0d165b113 100644 --- a/Makefile +++ b/Makefile @@ -410,7 +410,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default index b215d70c6..0d165b113 100644 --- a/sample_projects/Makefile-default +++ b/sample_projects/Makefile-default @@ -410,7 +410,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/biorobots/Makefile b/sample_projects/biorobots/Makefile index aad8aca30..1b3d78112 100644 --- a/sample_projects/biorobots/Makefile +++ b/sample_projects/biorobots/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/cancer_biorobots/Makefile b/sample_projects/cancer_biorobots/Makefile index 121d64fa7..ca0651a80 100644 --- a/sample_projects/cancer_biorobots/Makefile +++ b/sample_projects/cancer_biorobots/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/cancer_immune/Makefile b/sample_projects/cancer_immune/Makefile index a0487ec66..559d60154 100644 --- a/sample_projects/cancer_immune/Makefile +++ b/sample_projects/cancer_immune/Makefile @@ -195,7 +195,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/celltypes3/Makefile b/sample_projects/celltypes3/Makefile index 3e1ab9ca9..2c6f8135f 100644 --- a/sample_projects/celltypes3/Makefile +++ b/sample_projects/celltypes3/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/heterogeneity/Makefile b/sample_projects/heterogeneity/Makefile index 7a6caccf4..52489b5ea 100644 --- a/sample_projects/heterogeneity/Makefile +++ b/sample_projects/heterogeneity/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/interactions/Makefile b/sample_projects/interactions/Makefile index c2928a8a7..407458422 100644 --- a/sample_projects/interactions/Makefile +++ b/sample_projects/interactions/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/mechano/Makefile b/sample_projects/mechano/Makefile index 739af2604..d093ef3c0 100644 --- a/sample_projects/mechano/Makefile +++ b/sample_projects/mechano/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/physimess/Makefile b/sample_projects/physimess/Makefile index a52942317..36a62a9c0 100644 --- a/sample_projects/physimess/Makefile +++ b/sample_projects/physimess/Makefile @@ -212,7 +212,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/pred_prey_farmer/Makefile b/sample_projects/pred_prey_farmer/Makefile index 385c472a9..a61bd4ee8 100644 --- a/sample_projects/pred_prey_farmer/Makefile +++ b/sample_projects/pred_prey_farmer/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/rules_sample/Makefile b/sample_projects/rules_sample/Makefile index ba50bdd6a..09fc2d131 100644 --- a/sample_projects/rules_sample/Makefile +++ b/sample_projects/rules_sample/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/template/Makefile b/sample_projects/template/Makefile index ba50bdd6a..09fc2d131 100644 --- a/sample_projects/template/Makefile +++ b/sample_projects/template/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/virus_macrophage/Makefile b/sample_projects/virus_macrophage/Makefile index 38439b71f..0a373c1ec 100644 --- a/sample_projects/virus_macrophage/Makefile +++ b/sample_projects/virus_macrophage/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects/worm/Makefile b/sample_projects/worm/Makefile index e403f5ef3..a0f1a9942 100644 --- a/sample_projects/worm/Makefile +++ b/sample_projects/worm/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects_intracellular/boolean/cancer_invasion/Makefile b/sample_projects_intracellular/boolean/cancer_invasion/Makefile index b128ff261..2eebc0b5a 100644 --- a/sample_projects_intracellular/boolean/cancer_invasion/Makefile +++ b/sample_projects_intracellular/boolean/cancer_invasion/Makefile @@ -251,7 +251,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile index 933b043d0..5d2ec9b2d 100644 --- a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile +++ b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile @@ -247,7 +247,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects_intracellular/boolean/template_BM/Makefile b/sample_projects_intracellular/boolean/template_BM/Makefile index be1f223d6..35c3ddae5 100644 --- a/sample_projects_intracellular/boolean/template_BM/Makefile +++ b/sample_projects_intracellular/boolean/template_BM/Makefile @@ -245,7 +245,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects_intracellular/boolean/tutorial/Makefile b/sample_projects_intracellular/boolean/tutorial/Makefile index 82b8584ea..a6c782fda 100644 --- a/sample_projects_intracellular/boolean/tutorial/Makefile +++ b/sample_projects_intracellular/boolean/tutorial/Makefile @@ -251,7 +251,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile b/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile index 600c3d152..549b35c08 100644 --- a/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile +++ b/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile @@ -276,7 +276,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects_intracellular/ode/ode_energy/Makefile b/sample_projects_intracellular/ode/ode_energy/Makefile index 0e5ad52c0..3e660b2dd 100644 --- a/sample_projects_intracellular/ode/ode_energy/Makefile +++ b/sample_projects_intracellular/ode/ode_energy/Makefile @@ -248,7 +248,7 @@ movie: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/unit_tests/custom_DCs_2substrates/Makefile b/unit_tests/custom_DCs_2substrates/Makefile index 404195a0b..e3a7cbcfd 100644 --- a/unit_tests/custom_DCs_2substrates/Makefile +++ b/unit_tests/custom_DCs_2substrates/Makefile @@ -197,7 +197,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/unit_tests/custom_voxel_values/Makefile b/unit_tests/custom_voxel_values/Makefile index 4d374df4a..a9c8d2e6f 100644 --- a/unit_tests/custom_voxel_values/Makefile +++ b/unit_tests/custom_voxel_values/Makefile @@ -194,7 +194,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* From 74d3b12cc33f31fe2c5c160f6ca8baaf7bf1cbe2 Mon Sep 17 00:00:00 2001 From: bue Date: Sun, 9 Jun 2024 12:38:16 -0400 Subject: [PATCH 5/7] the Makefile reset function now uses sample_projects/PhysiCell_settings.xml-default instead of config/PhysiCell_settings-backup.xml to restore initial condition. --- Makefile | 3 +- sample_projects/Makefile-default | 3 +- .../PhysiCell_settings.xml-default | 271 ++++++++++++++++++ sample_projects/biorobots/Makefile | 3 +- sample_projects/cancer_biorobots/Makefile | 3 +- sample_projects/cancer_immune/Makefile | 3 +- sample_projects/celltypes3/Makefile | 3 +- sample_projects/heterogeneity/Makefile | 3 +- sample_projects/interactions/Makefile | 3 +- sample_projects/mechano/Makefile | 3 +- sample_projects/physimess/Makefile | 3 +- sample_projects/pred_prey_farmer/Makefile | 3 +- sample_projects/rules_sample/Makefile | 3 +- sample_projects/template/Makefile | 3 +- sample_projects/virus_macrophage/Makefile | 3 +- sample_projects/worm/Makefile | 3 +- .../boolean/cancer_invasion/Makefile | 3 +- .../boolean/physiboss_cell_lines/Makefile | 3 +- .../boolean/template_BM/Makefile | 3 +- .../boolean/tutorial/Makefile | 3 +- .../fba/cancer_metabolism/Make-windows | 3 +- .../fba/cancer_metabolism/Makefile | 3 +- .../fba/ecoli_acetic_switch/Makefile | 3 +- .../ode/ode_energy/Makefile | 3 +- unit_tests/custom_DCs_2substrates/Makefile | 3 +- unit_tests/custom_voxel_values/Makefile | 3 +- .../Makefile-unit-test-conservation | 3 +- 27 files changed, 297 insertions(+), 52 deletions(-) create mode 100644 sample_projects/PhysiCell_settings.xml-default diff --git a/Makefile b/Makefile index 0d165b113..f39df416b 100644 --- a/Makefile +++ b/Makefile @@ -394,9 +394,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default index 0d165b113..f39df416b 100644 --- a/sample_projects/Makefile-default +++ b/sample_projects/Makefile-default @@ -394,9 +394,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/PhysiCell_settings.xml-default b/sample_projects/PhysiCell_settings.xml-default new file mode 100644 index 000000000..d35c44fc7 --- /dev/null +++ b/sample_projects/PhysiCell_settings.xml-default @@ -0,0 +1,271 @@ + + + + -500 + 500 + -500 + 500 + -10 + 10 + 20 + 20 + 20 + true + + + + 14400 + min + micron + 0.01 + 0.1 + 6 + + + + 6 + + + + output + + 60 + true + + + 60 + true + + + false + + + + + false + true + + + + + + 100000.0 + 0.1 + + 38 + 0 + + 38 + 10 + 10 + 38 + 0 + 0 + + + + + 10 + .1 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + + + + + 10 + 0.1 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + + + + true + true + + ./config/initial.mat + + + ./config/dirichlet.mat + + + + + + + + + + 0.000 + + + + + 5.31667e-05 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 2.80E-03 + + 0 + 86400 + + + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 + + + + + 2494 + 0.75 + 540 + 0.05 + 0.0045 + 0.0055 + 0 + 0 + 2.0 + + + 0.4 + 10.0 + 1.25 + + 1 + + + 1.8 + 15.12 + + 4.0 + 10.0 + 0.01 + 0.0 + 0.0 + + + 1 + 1 + .5 + + false + true + + false + oxygen + 1 + + + false + false + + 0.0 + 0.0 + 0.0 + + + + + + + 0 + 1 + 10 + 0 + + + 0.0 + 1 + 0.0 + 0.0 + + + 0.0 + 1 + 0.0 + 0.0 + + + + 0 + + 0 + 0 + + + 0 + 0 + + 1 + + 0 + 0 + + + + + 0 + 0 + + + + + 1.0 + + + + + + + ./config + cells.csv + + + + + + + ./config + cell_rules_v2.csv + + + + + + + + 0 + 0 + + \ No newline at end of file diff --git a/sample_projects/biorobots/Makefile b/sample_projects/biorobots/Makefile index 1b3d78112..bd317b45f 100644 --- a/sample_projects/biorobots/Makefile +++ b/sample_projects/biorobots/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/cancer_biorobots/Makefile b/sample_projects/cancer_biorobots/Makefile index ca0651a80..22f09728e 100644 --- a/sample_projects/cancer_biorobots/Makefile +++ b/sample_projects/cancer_biorobots/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/cancer_immune/Makefile b/sample_projects/cancer_immune/Makefile index 559d60154..76f62fafb 100644 --- a/sample_projects/cancer_immune/Makefile +++ b/sample_projects/cancer_immune/Makefile @@ -179,9 +179,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/celltypes3/Makefile b/sample_projects/celltypes3/Makefile index 2c6f8135f..9183e68fd 100644 --- a/sample_projects/celltypes3/Makefile +++ b/sample_projects/celltypes3/Makefile @@ -178,9 +178,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/heterogeneity/Makefile b/sample_projects/heterogeneity/Makefile index 52489b5ea..8d4ef892d 100644 --- a/sample_projects/heterogeneity/Makefile +++ b/sample_projects/heterogeneity/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/interactions/Makefile b/sample_projects/interactions/Makefile index 407458422..89c99f000 100644 --- a/sample_projects/interactions/Makefile +++ b/sample_projects/interactions/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/mechano/Makefile b/sample_projects/mechano/Makefile index d093ef3c0..d2886fcc3 100644 --- a/sample_projects/mechano/Makefile +++ b/sample_projects/mechano/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/physimess/Makefile b/sample_projects/physimess/Makefile index 36a62a9c0..cb5e9682e 100644 --- a/sample_projects/physimess/Makefile +++ b/sample_projects/physimess/Makefile @@ -196,9 +196,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/pred_prey_farmer/Makefile b/sample_projects/pred_prey_farmer/Makefile index a61bd4ee8..5b1bc054a 100644 --- a/sample_projects/pred_prey_farmer/Makefile +++ b/sample_projects/pred_prey_farmer/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/rules_sample/Makefile b/sample_projects/rules_sample/Makefile index 09fc2d131..00f7f519e 100644 --- a/sample_projects/rules_sample/Makefile +++ b/sample_projects/rules_sample/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/template/Makefile b/sample_projects/template/Makefile index 09fc2d131..00f7f519e 100644 --- a/sample_projects/template/Makefile +++ b/sample_projects/template/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/virus_macrophage/Makefile b/sample_projects/virus_macrophage/Makefile index 0a373c1ec..c0cae0ce9 100644 --- a/sample_projects/virus_macrophage/Makefile +++ b/sample_projects/virus_macrophage/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects/worm/Makefile b/sample_projects/worm/Makefile index a0f1a9942..c10ee3c5f 100644 --- a/sample_projects/worm/Makefile +++ b/sample_projects/worm/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/boolean/cancer_invasion/Makefile b/sample_projects_intracellular/boolean/cancer_invasion/Makefile index 2eebc0b5a..2dc1b91ec 100644 --- a/sample_projects_intracellular/boolean/cancer_invasion/Makefile +++ b/sample_projects_intracellular/boolean/cancer_invasion/Makefile @@ -228,9 +228,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile index 5d2ec9b2d..27a53f044 100644 --- a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile +++ b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile @@ -225,9 +225,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: diff --git a/sample_projects_intracellular/boolean/template_BM/Makefile b/sample_projects_intracellular/boolean/template_BM/Makefile index 35c3ddae5..1a4d9f8fd 100644 --- a/sample_projects_intracellular/boolean/template_BM/Makefile +++ b/sample_projects_intracellular/boolean/template_BM/Makefile @@ -225,9 +225,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: diff --git a/sample_projects_intracellular/boolean/tutorial/Makefile b/sample_projects_intracellular/boolean/tutorial/Makefile index a6c782fda..8ec84d21c 100644 --- a/sample_projects_intracellular/boolean/tutorial/Makefile +++ b/sample_projects_intracellular/boolean/tutorial/Makefile @@ -228,9 +228,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: diff --git a/sample_projects_intracellular/fba/cancer_metabolism/Make-windows b/sample_projects_intracellular/fba/cancer_metabolism/Make-windows index 2bfe1511b..1854f4aa6 100644 --- a/sample_projects_intracellular/fba/cancer_metabolism/Make-windows +++ b/sample_projects_intracellular/fba/cancer_metabolism/Make-windows @@ -205,9 +205,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/fba/cancer_metabolism/Makefile b/sample_projects_intracellular/fba/cancer_metabolism/Makefile index b99e2a010..8a4fb6582 100755 --- a/sample_projects_intracellular/fba/cancer_metabolism/Makefile +++ b/sample_projects_intracellular/fba/cancer_metabolism/Makefile @@ -210,9 +210,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile b/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile index 549b35c08..61e0ca3a8 100644 --- a/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile +++ b/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile @@ -258,9 +258,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/ode/ode_energy/Makefile b/sample_projects_intracellular/ode/ode_energy/Makefile index 3e660b2dd..a541abc02 100644 --- a/sample_projects_intracellular/ode/ode_energy/Makefile +++ b/sample_projects_intracellular/ode/ode_energy/Makefile @@ -234,9 +234,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml FOLDER := output FRAMERATE := 24 diff --git a/unit_tests/custom_DCs_2substrates/Makefile b/unit_tests/custom_DCs_2substrates/Makefile index e3a7cbcfd..3a9ff48b9 100644 --- a/unit_tests/custom_DCs_2substrates/Makefile +++ b/unit_tests/custom_DCs_2substrates/Makefile @@ -181,9 +181,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/unit_tests/custom_voxel_values/Makefile b/unit_tests/custom_voxel_values/Makefile index a9c8d2e6f..9e5b4485f 100644 --- a/unit_tests/custom_voxel_values/Makefile +++ b/unit_tests/custom_voxel_values/Makefile @@ -178,9 +178,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/unit_tests/substrate_internalization/Makefile-unit-test-conservation b/unit_tests/substrate_internalization/Makefile-unit-test-conservation index 7e6471b39..87cac2f63 100644 --- a/unit_tests/substrate_internalization/Makefile-unit-test-conservation +++ b/unit_tests/substrate_internalization/Makefile-unit-test-conservation @@ -147,9 +147,8 @@ reset: touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - mv ./config/PhysiCell_settings-backup.xml . rm -fr ./config/* - mv PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o From ef5e72205a28e55a944d267b757634769b8ae935 Mon Sep 17 00:00:00 2001 From: bue Date: Sun, 9 Jun 2024 15:28:33 -0400 Subject: [PATCH 6/7] the Makefile save function sets the PROJ variable in the Makefile to the actual name the project was saved with. --- Makefile | 1 + sample_projects/Makefile-default | 1 + sample_projects/biorobots/Makefile | 1 + sample_projects/cancer_biorobots/Makefile | 1 + sample_projects/cancer_immune/Makefile | 1 + sample_projects/celltypes3/Makefile | 1 + sample_projects/heterogeneity/Makefile | 1 + sample_projects/interactions/Makefile | 1 + sample_projects/mechano/Makefile | 1 + sample_projects/physimess/Makefile | 1 + sample_projects/pred_prey_farmer/Makefile | 1 + sample_projects/rules_sample/Makefile | 1 + sample_projects/template/Makefile | 1 + sample_projects/virus_macrophage/Makefile | 1 + sample_projects/worm/Makefile | 1 + sample_projects_intracellular/boolean/cancer_invasion/Makefile | 1 + .../boolean/physiboss_cell_lines/Makefile | 1 + sample_projects_intracellular/boolean/template_BM/Makefile | 1 + sample_projects_intracellular/boolean/tutorial/Makefile | 1 + unit_tests/custom_DCs_2substrates/Makefile | 1 + unit_tests/custom_voxel_values/Makefile | 1 + 21 files changed, 21 insertions(+) diff --git a/Makefile b/Makefile index f39df416b..d30f59e84 100644 --- a/Makefile +++ b/Makefile @@ -491,6 +491,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default index f39df416b..d30f59e84 100644 --- a/sample_projects/Makefile-default +++ b/sample_projects/Makefile-default @@ -491,6 +491,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/biorobots/Makefile b/sample_projects/biorobots/Makefile index bd317b45f..71fcbffc7 100644 --- a/sample_projects/biorobots/Makefile +++ b/sample_projects/biorobots/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/cancer_biorobots/Makefile b/sample_projects/cancer_biorobots/Makefile index 22f09728e..92c765db4 100644 --- a/sample_projects/cancer_biorobots/Makefile +++ b/sample_projects/cancer_biorobots/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/cancer_immune/Makefile b/sample_projects/cancer_immune/Makefile index 76f62fafb..cd1fd14f9 100644 --- a/sample_projects/cancer_immune/Makefile +++ b/sample_projects/cancer_immune/Makefile @@ -281,6 +281,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/celltypes3/Makefile b/sample_projects/celltypes3/Makefile index 9183e68fd..3016ae7dc 100644 --- a/sample_projects/celltypes3/Makefile +++ b/sample_projects/celltypes3/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/heterogeneity/Makefile b/sample_projects/heterogeneity/Makefile index 8d4ef892d..8f7ae4898 100644 --- a/sample_projects/heterogeneity/Makefile +++ b/sample_projects/heterogeneity/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/interactions/Makefile b/sample_projects/interactions/Makefile index 89c99f000..17a1457ba 100644 --- a/sample_projects/interactions/Makefile +++ b/sample_projects/interactions/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/mechano/Makefile b/sample_projects/mechano/Makefile index d2886fcc3..b4e1dff70 100644 --- a/sample_projects/mechano/Makefile +++ b/sample_projects/mechano/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/physimess/Makefile b/sample_projects/physimess/Makefile index cb5e9682e..97dedd383 100644 --- a/sample_projects/physimess/Makefile +++ b/sample_projects/physimess/Makefile @@ -293,6 +293,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/pred_prey_farmer/Makefile b/sample_projects/pred_prey_farmer/Makefile index 5b1bc054a..3c72ce29a 100644 --- a/sample_projects/pred_prey_farmer/Makefile +++ b/sample_projects/pred_prey_farmer/Makefile @@ -279,6 +279,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/rules_sample/Makefile b/sample_projects/rules_sample/Makefile index 00f7f519e..1b0c06273 100644 --- a/sample_projects/rules_sample/Makefile +++ b/sample_projects/rules_sample/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/template/Makefile b/sample_projects/template/Makefile index 00f7f519e..1b0c06273 100644 --- a/sample_projects/template/Makefile +++ b/sample_projects/template/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/virus_macrophage/Makefile b/sample_projects/virus_macrophage/Makefile index c0cae0ce9..1b6567180 100644 --- a/sample_projects/virus_macrophage/Makefile +++ b/sample_projects/virus_macrophage/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/worm/Makefile b/sample_projects/worm/Makefile index c10ee3c5f..b6b809cc3 100644 --- a/sample_projects/worm/Makefile +++ b/sample_projects/worm/Makefile @@ -278,6 +278,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects_intracellular/boolean/cancer_invasion/Makefile b/sample_projects_intracellular/boolean/cancer_invasion/Makefile index 2dc1b91ec..9c792d065 100644 --- a/sample_projects_intracellular/boolean/cancer_invasion/Makefile +++ b/sample_projects_intracellular/boolean/cancer_invasion/Makefile @@ -316,6 +316,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile index 27a53f044..3e2d3d441 100644 --- a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile +++ b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile @@ -312,6 +312,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects_intracellular/boolean/template_BM/Makefile b/sample_projects_intracellular/boolean/template_BM/Makefile index 1a4d9f8fd..337bdd990 100644 --- a/sample_projects_intracellular/boolean/template_BM/Makefile +++ b/sample_projects_intracellular/boolean/template_BM/Makefile @@ -326,6 +326,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects_intracellular/boolean/tutorial/Makefile b/sample_projects_intracellular/boolean/tutorial/Makefile index 8ec84d21c..448d215f9 100644 --- a/sample_projects_intracellular/boolean/tutorial/Makefile +++ b/sample_projects_intracellular/boolean/tutorial/Makefile @@ -316,6 +316,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/unit_tests/custom_DCs_2substrates/Makefile b/unit_tests/custom_DCs_2substrates/Makefile index 3a9ff48b9..9cfd762c3 100644 --- a/unit_tests/custom_DCs_2substrates/Makefile +++ b/unit_tests/custom_DCs_2substrates/Makefile @@ -279,6 +279,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/unit_tests/custom_voxel_values/Makefile b/unit_tests/custom_voxel_values/Makefile index 9e5b4485f..2af033a38 100644 --- a/unit_tests/custom_voxel_values/Makefile +++ b/unit_tests/custom_voxel_values/Makefile @@ -276,6 +276,7 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules From e334eb63679265f93dde3ee66a6f7b274011d07e Mon Sep 17 00:00:00 2001 From: bue Date: Tue, 11 Jun 2024 10:54:10 -0400 Subject: [PATCH 7/7] Makefile save function sets the PROJ variable is now solved with awk instead of sed, to be hopefully compatible with all supported platforms and unix flavors. --- Makefile | 2 +- sample_projects/Makefile-default | 2 +- sample_projects/biorobots/Makefile | 2 +- sample_projects/cancer_biorobots/Makefile | 2 +- sample_projects/cancer_immune/Makefile | 2 +- sample_projects/celltypes3/Makefile | 2 +- sample_projects/heterogeneity/Makefile | 2 +- sample_projects/interactions/Makefile | 2 +- sample_projects/physimess/Makefile | 2 +- sample_projects/pred_prey_farmer/Makefile | 2 +- sample_projects/rules_sample/Makefile | 2 +- sample_projects/template/Makefile | 2 +- sample_projects/virus_macrophage/Makefile | 2 +- sample_projects/worm/Makefile | 2 +- sample_projects_intracellular/boolean/cancer_invasion/Makefile | 2 +- .../boolean/physiboss_cell_lines/Makefile | 2 +- sample_projects_intracellular/boolean/template_BM/Makefile | 2 +- sample_projects_intracellular/boolean/tutorial/Makefile | 2 +- unit_tests/custom_DCs_2substrates/Makefile | 2 +- unit_tests/custom_voxel_values/Makefile | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) diff --git a/Makefile b/Makefile index d30f59e84..455aae566 100644 --- a/Makefile +++ b/Makefile @@ -490,8 +490,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default index d30f59e84..455aae566 100644 --- a/sample_projects/Makefile-default +++ b/sample_projects/Makefile-default @@ -490,8 +490,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/biorobots/Makefile b/sample_projects/biorobots/Makefile index 71fcbffc7..ac4c97235 100644 --- a/sample_projects/biorobots/Makefile +++ b/sample_projects/biorobots/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/cancer_biorobots/Makefile b/sample_projects/cancer_biorobots/Makefile index 92c765db4..be43706c3 100644 --- a/sample_projects/cancer_biorobots/Makefile +++ b/sample_projects/cancer_biorobots/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/cancer_immune/Makefile b/sample_projects/cancer_immune/Makefile index cd1fd14f9..7c60292da 100644 --- a/sample_projects/cancer_immune/Makefile +++ b/sample_projects/cancer_immune/Makefile @@ -280,8 +280,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/celltypes3/Makefile b/sample_projects/celltypes3/Makefile index 3016ae7dc..a0862534f 100644 --- a/sample_projects/celltypes3/Makefile +++ b/sample_projects/celltypes3/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/heterogeneity/Makefile b/sample_projects/heterogeneity/Makefile index 8f7ae4898..12c6117b7 100644 --- a/sample_projects/heterogeneity/Makefile +++ b/sample_projects/heterogeneity/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/interactions/Makefile b/sample_projects/interactions/Makefile index 17a1457ba..84160b2e1 100644 --- a/sample_projects/interactions/Makefile +++ b/sample_projects/interactions/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/physimess/Makefile b/sample_projects/physimess/Makefile index 97dedd383..7adfd6924 100644 --- a/sample_projects/physimess/Makefile +++ b/sample_projects/physimess/Makefile @@ -292,8 +292,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/pred_prey_farmer/Makefile b/sample_projects/pred_prey_farmer/Makefile index 3c72ce29a..425fca742 100644 --- a/sample_projects/pred_prey_farmer/Makefile +++ b/sample_projects/pred_prey_farmer/Makefile @@ -278,8 +278,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/rules_sample/Makefile b/sample_projects/rules_sample/Makefile index 1b0c06273..ccb6bd44b 100644 --- a/sample_projects/rules_sample/Makefile +++ b/sample_projects/rules_sample/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/template/Makefile b/sample_projects/template/Makefile index 1b0c06273..ccb6bd44b 100644 --- a/sample_projects/template/Makefile +++ b/sample_projects/template/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/virus_macrophage/Makefile b/sample_projects/virus_macrophage/Makefile index 1b6567180..99febe95f 100644 --- a/sample_projects/virus_macrophage/Makefile +++ b/sample_projects/virus_macrophage/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects/worm/Makefile b/sample_projects/worm/Makefile index b6b809cc3..dce60c267 100644 --- a/sample_projects/worm/Makefile +++ b/sample_projects/worm/Makefile @@ -277,8 +277,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects_intracellular/boolean/cancer_invasion/Makefile b/sample_projects_intracellular/boolean/cancer_invasion/Makefile index 9c792d065..8c5b97cbe 100644 --- a/sample_projects_intracellular/boolean/cancer_invasion/Makefile +++ b/sample_projects_intracellular/boolean/cancer_invasion/Makefile @@ -315,8 +315,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile index 3e2d3d441..4f032ed35 100644 --- a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile +++ b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile @@ -311,8 +311,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects_intracellular/boolean/template_BM/Makefile b/sample_projects_intracellular/boolean/template_BM/Makefile index 337bdd990..f3ef2118c 100644 --- a/sample_projects_intracellular/boolean/template_BM/Makefile +++ b/sample_projects_intracellular/boolean/template_BM/Makefile @@ -325,8 +325,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/sample_projects_intracellular/boolean/tutorial/Makefile b/sample_projects_intracellular/boolean/tutorial/Makefile index 448d215f9..9ad2ec01a 100644 --- a/sample_projects_intracellular/boolean/tutorial/Makefile +++ b/sample_projects_intracellular/boolean/tutorial/Makefile @@ -315,8 +315,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/unit_tests/custom_DCs_2substrates/Makefile b/unit_tests/custom_DCs_2substrates/Makefile index 9cfd762c3..e1494f866 100644 --- a/unit_tests/custom_DCs_2substrates/Makefile +++ b/unit_tests/custom_DCs_2substrates/Makefile @@ -278,8 +278,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules diff --git a/unit_tests/custom_voxel_values/Makefile b/unit_tests/custom_voxel_values/Makefile index 2af033a38..d68adc2fb 100644 --- a/unit_tests/custom_voxel_values/Makefile +++ b/unit_tests/custom_voxel_values/Makefile @@ -275,8 +275,8 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) - sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules