setup_new_proj.py

# 
# setup_new_proj.py - create a new PhysiCell Jupyter notebook project [for nanoHUB] by copying the contents of this 
#                     project and an existing PhysiCell project into the new project.
#
# Assumptions:
#   - the new project is a cloned, empty, public GitHub repo
#   - you have an existing PhysiCell project with files in specified locations: 
#       - config/PhysiCell_settings.xml 
#       - output/initial.xml)
# 
# Usage:
#   python setup_new_proj.py  <full-path-to-new-project>  <simple-project-name>  <full-path-to-PhysiCell-project>
#  e.g.:
#   python setup_new_proj.py  /Users/heiland/git/iu399_proj1  iu399_proj1  /Users/heiland/dev/PhysiCell_heterogeneity
#

import sys
import shutil
import os
import platform
import xml.etree.ElementTree as ET


num_args = len(sys.argv)
print('num_args=',num_args)
if (num_args < 4):
#    print("Usage: %s <full-path-to-new-project>  <simple-project-name>  <full-path-to-PhysiCell-project>")
    print("Usage: %s <full-path-to-new-project>  <full-path-to-PhysiCell-project> <tool name> [<makefile name> <main cpp>]")
#    print("Usage: %s <your repo name>")
    sys.exit(1)
#print('sys.argv[0] = ',sys.argv[0])
proj_fullpath = sys.argv[1]
if not proj_fullpath[-1].isalnum():
    proj_fullpath = proj_fullpath[0:-1]
print('proj_fullpath = ',proj_fullpath)

#proj_name = sys.argv[2]
proj_name = os.path.basename(proj_fullpath)
print('proj_name = ',proj_name)

physicell_fullpath= sys.argv[2]
print('physicell_fullpath = ',physicell_fullpath)

tool_name = sys.argv[3]
print('tool_name = ',tool_name)

make_file = "Makefile"
main_cpp_file = "main.cpp"
if (num_args > 4):
    make_file = sys.argv[4]
    main_cpp_file = sys.argv[5]

print("\n======  STEP 1: copy tool4nanobio to new project:\n")
to_file = os.path.join(proj_fullpath, ".travis.yml")        # (from_file, to_file)
shutil.copy(".travis.yml", to_file)

for elm in os.listdir('.'):
    print("---- elm (dir)= ",elm)
    try:
        if ('Example_GUI' in elm):  # avoid /.git, etc
            continue
        elif (elm[0] != '.'):  # avoid /.git, etc
            if os.path.isdir(elm):
                from_dir = elm
                to_dir = os.path.join(proj_fullpath, elm)
                print(from_dir, " --> ", to_dir)
                # shutil.copytree(elm, os.path.join(proj_fullpath, elm))        # (from_dir, to_dir)
                shutil.copytree(from_dir, to_dir)
            else:
                if (elm == sys.argv[0] or elm == "README.md"):
                    # print('------- skipping over ',elm)
                    continue
                from_file = elm
                to_file = os.path.join(proj_fullpath, elm)        # (from_file, to_file)
                print(from_file, " --> ", to_file)
                shutil.copy(from_file, to_file)
    except:
#        print("   can't copy ",elm," to ", proj_fullpath, " ... maybe you already did?")
        print("   can't copy ... maybe you already did?")

#------------------------------------
print("\n\n======  STEP 2: copy PhysiCell project's source (and data files) to new project's /src:\n")
# Copy (most of) your PhysiCell project to your project's /src directory
#os.chdir(os.path.join(proj_fullpath, 'src'))
proj_src_dir = os.path.join(proj_fullpath, 'src')
print("proj_src_dir = ",proj_src_dir)

dir_names = ["core", "BioFVM", "modules", "custom_modules"]
for dname in dir_names:
    from_dir = os.path.join(physicell_fullpath, dname)
    to_dir = os.path.join(proj_src_dir, dname)
    print(from_dir, " --> ", to_dir)
    try:
        shutil.copytree(from_dir, to_dir)
    except:
        print("   can't copy ... maybe you already did?")

#from_file = os.path.join(physicell_fullpath, "Makefile")
from_file = os.path.join(physicell_fullpath, make_file)
to_file = os.path.join(proj_src_dir, "Makefile")
print(from_file, " --> ", to_file, " plus, create 'myproj' and insert nanoHUB-specific targets.")
#shutil.copy(from_file, to_file)

with open(from_file,"r") as infile:
    with open(to_file,"w") as outfile:
        for line in infile:
            sline = line.split()
            if len(sline) > 0:
                if sline[0] == "PROGRAM_NAME":
                    # print('got PROGRAM_NAME')
                    newline = sline[0] + sline[1] + " myproj\n"
                    outfile.write(newline)
#                    outfile.write("\nUNAME := $(shell uname)\n")

#--------- new crap that Steve had me add during dev of pc4covid19 ------------------
                    # nanohub_extra_crap = "install: \n\t$(MODINIT); $(MODCMD); make all\n\tinstall --mode 0755 -D $(PROGRAM_NAME) $(BIN)/$(PROGRAM_NAME)\n\ndistclean: clean\n\trm -f $(BIN)/$(PROGRAM_NAME)\n\trm -rf $(BIN)/__pycache__\n\trm -rf ../.ipynb_checkpoints\n\n"
                    nanohub_extra_crap = 'osRelease = $(shell lsb_release -r | sed -e "s/Release:\W*//" -e "s/\..*//")\nifeq ($(osRelease),7)\n\thostName = $(shell hostname | sed -e "s:[-_].*::")$(osRelease)\nelse\n\thostName = $(shell hostname | sed -e "s:[-_].*::")\nendif\n\nifeq ($(hostName),nanohub7)\n\tBIN = ../bin\n\tMODINIT = . /etc/environ.sh\n\tMODCMD = use -e -r anaconda3-5.1\nelse\nifeq ($(hostName),rice7)\n\tBIN = ../bin/rice7\n\tMODINIT = . $(MODULESHOME)/init/sh\n\tMODCMD = module purge 2> /dev/null; module load gcc/7.3.0\nendif\nifeq ($(hostName),brown7)\n\tBIN = ../bin/brown7\n\tMODINIT = . $(MODULESHOME)/init/sh\n\tMODCMD = module purge 2> /dev/null; module load gcc/7.3.0\nendif\nendif\n'
                    outfile.write(nanohub_extra_crap)
# osRelease = $(shell lsb_release -r | sed -e "s/Release:\W*//" -e "s/\..*//")
# ifeq ($(osRelease),7)
#    hostName = $(shell hostname | sed -e "s:[-_].*::")$(osRelease)
# else
#    hostName = $(shell hostname | sed -e "s:[-_].*::")
# endif

# ifeq ($(hostName),nanohub7)
#    BIN = ../bin
# 	MODINIT = . /etc/environ.sh
#    MODCMD = use -e -r anaconda3-5.1
# else
# ifeq ($(hostName),rice7)
#    BIN = ../bin/rice7
# 	MODINIT = . $(MODULESHOME)/init/sh
#    MODCMD = module purge 2> /dev/null; module load gcc/7.3.0
# endif
# ifeq ($(hostName),brown7)
#    BIN = ../bin/brown7
# 	MODINIT = . $(MODULESHOME)/init/sh
#    MODCMD = module purge 2> /dev/null; module load gcc/7.3.0
# endif
# endif

                elif sline[0][0:6] == "CFLAGS":
                    newline = "# remove the -march arg to avoid SIGILL error on nanoHUB\n"
                    outfile.write(newline)
                    newline = "CFLAGS := -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11\n"
                    outfile.write(newline)
                elif sline[0] == "clean:":
                    # print('got ',sline[0])
#                    outfile.write(line)
#                    nanohub_targets = "# next 2 targets for nanoHUB\ninstall: \n\t. /etc/environ.sh; use -e -r anaconda3-5.1; make all\n\tcp $(PROGRAM_NAME) ../bin\n\ndistclean: clean\n\trm -f ../bin/$(PROGRAM_NAME)\n\n"
                    nanohub_targets = "# next 2 targets for nanoHUB\ninstall: \n\t$(MODINIT); $(MODCMD); make all\n\tinstall --mode 0755 -D $(PROGRAM_NAME) $(BIN)/$(PROGRAM_NAME)\n\ndistclean: clean\n\trm -f $(BIN)/$(PROGRAM_NAME)\n\trm -rf $(BIN)/__pycache__\n\trm -rf ../.ipynb_checkpoints\n\n"
                    outfile.write(nanohub_targets)
                    outfile.write("clean:\n")
                elif "rm -f $(PROGRAM_NAME)*" in line:  # don't want last "*" on nanoHUB
#                    outfile.write("\tifeq ($(OS),Windows_NT)\n")
#                    outfile.write("\t\trm -f $(PROGRAM_NAME)*\n")
#                    outfile.write("\telse\n")
#                    outfile.write("\t\trm -f $(PROGRAM_NAME)\n")
                    outfile.write("\trm -f $(PROGRAM_NAME)\n")  # what happens on Windows?
                else:
                    outfile.write(line)
            else:
                outfile.write(line)

#from_file = os.path.join(physicell_fullpath, "main.cpp")
#to_file = os.path.join(proj_src_dir, "main.cpp")
from_file = os.path.join(physicell_fullpath, main_cpp_file)
to_file = os.path.join(proj_src_dir, main_cpp_file)
print(from_file, " --> ", to_file)
shutil.copy(from_file, to_file)

from_file = os.path.join(physicell_fullpath, "VERSION.txt")
to_file = os.path.join(proj_src_dir, "VERSION.txt")
print(from_file, " --> ", to_file)
shutil.copy(from_file, to_file)

# We want to copy (and slightly edit) the original config (.xml) file (in /config) into the app's /data directory.
from_file = os.path.join(physicell_fullpath, "config", "PhysiCell_settings.xml")
to_file = os.path.join(proj_fullpath, "data", "PhysiCell_settings.xml")
print(from_file, " --> ", to_file)
shutil.copy(from_file, to_file)

# Edit the output folder: "output" --> "."  (output will be diverted into the app's /tmpdir)
# old_way = False
# print("   Editing ", to_file, ": <folder>output</folder> --> <folder>.</folder>")
# if old_way:
#     with open(to_file, 'r') as myfile:
#         new_text = myfile.read().replace('output', ".")  # a rather hacky way of doing this for now
#     with open(to_file, 'w') as myfile:
#         myfile.write(new_text)
# else:
tree = ET.parse(to_file)
xml_root = tree.getroot()
uep = xml_root.find('.//save//folder')  # find unique entry point
uep.text = '.'

uep = xml_root.find('.//parallel//omp_num_threads')
uep.text = '4'

uep2 = xml_root.find('.//initial_conditions//cell_positions//folder')
print('\n >>>>>>>>>>>  uep2 (cell pos) = ',uep2)
if uep2 != None:
    print('>>>>>>>>>>>  changing <initial_conditions><folder> = data')
    uep2.text = '../data'   # recall, the executable is in /bin

tree.write(to_file)

uep2 = xml_root.find('.//initial_conditions//cell_positions//filename')
if uep2 == None:
    print("******  FYI: no initial_conditions//cell_positions//filename to process.")
else:
    csv_file = uep2.text
    from_file = os.path.join(physicell_fullpath, "config", csv_file)
    to_file = os.path.join(proj_fullpath, "data", csv_file)
    print(from_file, " --> ", to_file)
    shutil.copy(from_file, to_file)

# Similar to the config file going into /data, we also want the original output/initial.xml to be in /data
from_file = os.path.join(physicell_fullpath, "output", "initial.xml")
to_file = os.path.join(proj_fullpath, "data", "initial.xml")
print(from_file, " --> ", to_file)
shutil.copy(from_file, to_file)

#------------------------------------
print("\n\n======  STEP 3: renaming files and file content to have new project and tool names:\n")
# maybe attempt to execute 'make_my_tool.py' from the new project dir?
print("\n----- Now we will prepare your new project. ")
os.chdir(proj_fullpath)

gui_name = os.path.basename(proj_fullpath)
print('gui_name=',gui_name)


# NOTE: let's not do this now; rather edit the invoke script *on* github to avoid 
#        the (Windows) problem of making it a non-executable file
with open('middleware/invoke', 'r') as myfile:
#   new_text = myfile.read().replace('tool4nanobio', gui_name)
   new_text = myfile.read().replace("-t tool4nanobio", "-t " + tool_name)
   new_text = new_text.replace("tool4nanobio", gui_name)
with open('middleware/invoke', 'w') as myfile:
   myfile.write(new_text)

#--------------
old_file = os.path.join("bin", 'tool4nanobio.py')
new_file = os.path.join("bin", gui_name + '.py')
try:
    shutil.move(old_file, new_file)
    print('Renaming ',old_file, ' to ',new_file)
except:
    print("  ---> Cannot rename ",old_file," to ",new_file, ", but we will continue")

print('Replacing gui_name in ',new_file)
with open(new_file, 'r') as myfile:
    new_text = myfile.read().replace('tool4nanobio', gui_name)
with open(new_file, 'w') as myfile:
    myfile.write(new_text)

#--------------
old_file = 'tool4nanobio.ipynb'
new_file = gui_name + '.ipynb'
try:
    shutil.move(old_file, new_file)
    print('Renaming ',old_file, ' to ',new_file)
except:
    print("  ---> Cannot rename ",old_file," to ",new_file, ", but we will continue")

print('Replacing gui_name in ',new_file)
with open(new_file, 'r') as myfile:
    new_text = myfile.read().replace('tool4nanobio', gui_name)
with open(new_file, 'w') as myfile:
    myfile.write(new_text)

#--------------
"""
In /data:
python xml2jupyter.py PhysiCell_settings.xml
Copy the generated user_params.py to ../bin
"""
print('--------------------------------------------------------')
print('Trying to run xml2jupyter.py on your .xml file in /data')
os.chdir("data")
cmd = "python xml2jupyter.py PhysiCell_settings.xml"
print(cmd)
try:
    os.system("python xml2jupyter.py PhysiCell_settings.xml")
except:
    print("  ---> Cannot execute: ",cmd)


new_file = os.path.join("..","bin")
try:
    print("-------------------------------------")
    print("cp user_params.py " + new_file)
    shutil.copy("user_params.py", new_file)
except:
    print("  ---> Cannot copy data/user_params.py to bin/user_params.py")
    print("         You will need to do that manually.\n")


try:
    print("-------------------------------------")
    print("cp microenv_params.py " + new_file)
    shutil.copy("microenv_params.py", new_file)
except:
    print("  ---> Cannot copy data/microenv_params.py to bin/microenv_params.py")
    print("         You will need to do that manually.\n")


print("-------------------------------------")
config_file = "PhysiCell_settings.xml"
tree = ET.parse(config_file)
root = tree.getroot()
if root.find('.//cell_definitions'):
    #os.chdir("..")
    # print('Trying to run create_cell_def.py on your .xml file in /data')
    print('------ <cell_definitions> are present.')
    #os.chdir("data")
    backup_xml_file = "PhysiCell_settings_original.xml"
    print('-- creating a backup of original: ',backup_xml_file)
    shutil.copy(config_file, backup_xml_file)

    # -------- NEW: March 2021
    # Before we create the tab of widgets for cell_definitions, we want to
    # convert a "hierarchical" cell_definitions (using 'parent_type' attribute)
    # to "flattened" cell_definitions (there are no parents; each cell_def is expanded).
    print('------ Convert hierarchical <cell_definitions> to flattened.')
    cmd = 'python xml_hier2flat.py ' + config_file
    print('------> ',cmd)
    try:
        os.system(cmd)
    except:
        print("  ---> Cannot execute: ",cmd)
    # shutil.copy("recurse_xml_out.xml", config_file)
    shutil.copy("flat_xml_out.xml", config_file)

    #-------
    # OK, now continue with the creation of the tab ("Cell Types") of widgets for cell_definitions
    print('-----------------------------------------------------------')
    print('Trying to run create_cell_def.py on your .xml file in /data')
    cmd = "python create_cell_types.py PhysiCell_settings.xml"
    print(cmd)
    try:
        os.system("python create_cell_types.py PhysiCell_settings.xml")
    except:
        print("  ---> Cannot execute: ",cmd)

    new_file = os.path.join("..","bin")
    try:
        print("Trying: cp cell_types.py " + new_file)
        shutil.copy("cell_types.py", new_file)
    except:
        print("  ---> Cannot copy data/cell_types.py to bin/cell_types.py")
        print("         You will need to do that manually.\n")
else:
    print(".xml does not contain <cell_definitions>, so will not create that tab")
    print('---------------------------\n')


#----------------------------------
if platform.system() != 'Windows':
    try:
        print("Trying to import hublib.ui")
        import hublib.ui
    except:
        print("hublib.ui is not found, will try to install it.")
        os.system("pip install -U hublib")

print("\n====================   doing sys.exit(1) =======================")
sys.exit(1)


# NOTE: let's not do this now; rather edit the invoke script *on* github to avoid 
#       the (Windows) problem of making it a non-executable file
#with open('middleware/invoke', 'r') as myfile:
#    new_text = myfile.read().replace('tool4nanobio', gui_name)
#with open('middleware/invoke', 'w') as myfile:
#    myfile.write(new_text)

#--------------
old_file = os.path.join("bin", 'tool4nanobio.py')
new_file = os.path.join("bin", gui_name + '.py')
try:
    shutil.move(old_file, new_file)
    print('Renaming ',old_file, ' to ',new_file)
except:
    print("  ---> Cannot rename ",old_file," to ",new_file, ", but we will continue")

print('Replacing gui_name in ',new_file)
with open(new_file, 'r') as myfile:
    new_text = myfile.read().replace('tool4nanobio', gui_name)
with open(new_file, 'w') as myfile:
    myfile.write(new_text)

#--------------
old_file = 'tool4nanobio.ipynb'
new_file = gui_name + '.ipynb'
try:
    shutil.move(old_file, new_file)
    print('Renaming ',old_file, ' to ',new_file)
except:
    print("  ---> Cannot rename ",old_file," to ",new_file, ", but we will continue")

print('Replacing gui_name in ',new_file)
with open(new_file, 'r') as myfile:
    new_text = myfile.read().replace('tool4nanobio', gui_name)
with open(new_file, 'w') as myfile:
    myfile.write(new_text)


#--------------
"""
In /data:
python xml2jupyter.py PhysiCell_settings.xml
Copy the generated user_params.py to ../bin
"""
print('Trying to run xml2jupyter.py on your .xml file in /data')
os.chdir("data")
cmd = "python xml2jupyter.py PhysiCell_settings.xml"
try:
    os.system("python xml2jupyter.py PhysiCell_settings.xml")
except:
    print("  ---> Cannot execute: ",cmd)


new_file = os.path.join("..","bin")
try:
    shutil.copy("user_params.py", new_file)
except:
    print("  ---> Cannot copy data/user_params.py to bin/user_params.py")
    print("         You will need to do that manually.\n")

if platform.system() != 'Windows':
    try:
        print("Trying to import hublib.ui")
        import hublib.ui
    except:
        print("hublib.ui is not found, will try to install it.")
        os.system("pip install -U hublib")