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setup_libroadrunner.py
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# This script attempts to download the libRoadrunner (binary) libraries and
# headers for your particular operating system. It installs them in
# the appropriate /addons directory which the Makefile can find.
#
# Author: Randy Heiland
import platform
import urllib.request
import os
import sys
import tarfile
import zipfile
def reminder_dynamic_link_path_macos():
print("\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n")
print("* NOTE: if you have not yet done this, you need to specify where the shared libs can be found, e.g., via bash shell:")
print('export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:./addons/libRoadrunner/roadrunner/lib')
print("\n* To make this permanent, add this line to the bottom of the respective shell startup file, e.g., .bashrc, .bash_profile, or .zshenv in your home directory.")
print("\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n")
def reminder_dynamic_link_path_linux():
print("\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n")
print("* NOTE: if you have not yet done this, you need to specify where the shared libs can be found, e.g., via bash shell:")
print('export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:./addons/libRoadrunner/roadrunner/lib')
print("\n* To make this permanent, add this line to the bottom of the respective shell startup file, e.g., .bashrc, .bash_profile, or .zshenv in your home directory.")
print("\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n")
os_type = platform.system()
# Old:
# if os.path.exists(os.path.join(os.path.dirname(os.path.dirname(__file__)), "addons", "libRoadrunner", "roadrunner")):
# New: July 2023 - trying to be smarter about deciding whether to (re)download libRR
# NOTE: needs to be tested cross-platform!
if os.path.exists(os.path.join(os.path.dirname(os.path.dirname(__file__)), "addons", "libRoadrunner", "roadrunner","include","rr","C","rrc_api.h")):
print('\nlibroadrunner already installed.\n')
# regardless, let's remind the user about the env var requirement!
if os_type.lower() == 'darwin':
reminder_dynamic_link_path_macos()
elif os_type.lower().startswith("linux"):
reminder_dynamic_link_path_linux()
else:
print('\nThis model requires the libRoadrunner libraries which will now be downloaded.')
print('(for your ',os_type, ' operating system)')
# Assume Windows
rr_file = ""
url = ""
mac_silicon = False
if os_type.lower() == 'darwin':
reminder_dynamic_link_path_macos()
if "ARM64" in platform.uname().version:
# pass
# print('... for the arm64 processor.')
# url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/ode/libs/macos12_arm64/libroadrunner_c_api.dylib"
rr_file = "roadrunner_macos_arm64.tar.gz"
url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/ode/roadrunner_macos_arm64.tar.gz"
mac_silicon = True
else:
rr_file = "roadrunner-osx-10.9-cp36m.tar.gz"
url = "https://sourceforge.net/projects/libroadrunner/files/libroadrunner-1.4.18/" + rr_file + "/download"
elif os_type.lower().startswith("win"):
rr_file = "roadrunner-win64-vs14-cp35m.zip"
url = "https://sourceforge.net/projects/libroadrunner/files/libroadrunner-1.4.18/" + rr_file + "/download"
elif os_type.lower().startswith("linux"):
reminder_dynamic_link_path_linux()
rr_file = "cpplibroadrunner-1.3.0-linux_x86_64.tar.gz"
url = "https://sourceforge.net/projects/libroadrunner/files/libroadrunner-1.3/" + rr_file + "/download"
else:
print("Your operating system seems to be unsupported. Please submit a ticket at https://sourceforge.net/p/physicell/tickets/ ")
sys.exit(1)
print("url=",url)
if mac_silicon:
fname = url.split('/')[-1]
else:
fname = url.split('/')[-2]
print("fname=",fname)
# home = os.path.expanduser("~")
print('libRoadRunner will now be installed into this location:')
# dir_name = os.path.join(home, 'libroadrunner')
dir_name = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'addons', 'libRoadrunner')
print(dir_name + '\n')
# print(' - Press ENTER to confirm the location')
# print(' - Press CTL-C to abort the installation')
# print(' - Or specify a different location below\n')
prompt_str = '[' + dir_name + '] >>> '
try:
# response = input(prompt_str)
# if (response == ""):
if (True):
# print('got Enter')
if not os.path.exists(dir_name):
try:
os.makedirs(dir_name)
except:
print('Error trying to create directory: ',dir_name)
exit(1)
# else:
# print(type(response))
# dir_name = os.path.expanduser(response)
# if not os.path.exists(dir_name):
# try:
# os.makedirs(dir_name)
# except:
# print('Error trying to create directory: ',dir_name)
# exit(1)
except:
print(' installation canceled\n')
exit(1)
print('Beginning download of libroadrunner into ' + dir_name + ' ...')
print(url)
my_file = os.path.join(dir_name, fname)
print('my_file = ',my_file)
if os_type.lower().startswith("win"):
rrlib_dir = my_file[:-4]
else: # darwin or linux
if mac_silicon:
# idx_end = my_file.rindex('/')
# rrlib_dir = my_file[:idx_end]
rrlib_dir = my_file[:-7]
# rrlib_dir = my_file
else:
rrlib_dir = my_file[:-7]
print('rrlib_dir = ',rrlib_dir)
def download_cb(blocknum, blocksize, totalsize):
readsofar = blocknum * blocksize
if totalsize > 0:
percent = readsofar * 1e2 / totalsize
s = "\r%5.1f%% %*d / %d" % (
percent, len(str(totalsize)), readsofar, totalsize)
sys.stderr.write(s)
if readsofar >= totalsize: # near the end
sys.stderr.write("\n")
else: # total size is unknown
sys.stderr.write("read %d\n" % (readsofar,))
urllib.request.urlretrieve(url, my_file, download_cb)
new_dir_name = "roadrunner"
os.chdir(dir_name)
print('installing (uncompressing) the file...')
if os_type.lower().startswith("win"):
try:
with zipfile.ZipFile(rr_file) as zf:
zf.extractall('.')
os.rename("roadrunner-win64-vs14-cp35m", new_dir_name)
except:
print('error unzipping the file')
exit(1)
else: # Darwin or Linux
try:
print("untarring ",rr_file)
tar = tarfile.open(rr_file)
tar.extractall()
tar.close()
if 'darwin' in os_type.lower():
if mac_silicon:
os.rename("roadrunner_macos_arm64", new_dir_name)
else:
os.rename("roadrunner-osx-10.9-cp36m", new_dir_name)
else:
os.rename("libroadrunner", new_dir_name)
except:
if mac_silicon:
print()
# pass
else:
print('error untarring the file')
exit(1)
print('Done.\n')
# # LIBRR_DIR := /Users/heiland/libroadrunner/roadrunner-osx-10.9-cp36m
# print("Replace the following variables in your PhysiCell Makefile with these:\n")
# #print("LIBRR_DIR := /Users/heiland/libroadrunner/roadrunner-osx-10.9-cp36m")
# print("LIBRR_DIR := " + rrlib_dir)
# if os_type == 'Windows':
# print("LIBRR_LIBS := " + rrlib_dir + "/bin\n")
# else:
# print("LIBRR_LIBS := " + rrlib_dir + "/lib\n")