def InitializeNewGitRepo(sim_name):
Print.new_step("Initialize new git repository")
sp.check_output(["git", "init"], cwd=sim_name)
# check if user name and email are set
try:
out = sp.check_output(["git", "config", "user.name"],
cwd=sim_name).decode("utf-8")
except sp.CalledProcessError as err:
# User name not set
print("Your git user name is not set.")
response = input("Please enter your name (e.g. Mona Lisa): ")
out = sp.check_output(["git", "config", "user.name", response],
cwd=sim_name)
try:
out = sp.check_output(["git", "config", "user.email"],
cwd=sim_name).decode("utf-8")
except sp.CalledProcessError as err:
# User name not set
print("Your git user e-mail is not set.")
response = input(
"Please enter your e-mail address that you have used to sign-up for github: "
)
out = sp.check_output(["git", "config", "user.email", response],
cwd=sim_name)
sp.check_output(["git", "add", "."], cwd=sim_name)
sp.check_output(["git", "commit", "-m", "\"Initial commit\""],
cwd=sim_name)
def CustomizeFiles(sim_name):
Print.new_step("Customize files")
try:
# README.md
ModifyFileContent(sim_name + "/README.md",
lambda content: "# " + sim_name + "\n")
# CMakelists.txt
ModifyFileContent(
sim_name + "/CMakeLists.txt",
lambda content: content.replace("my-simulation", sim_name))
# source files
include_guard = sim_name.upper().replace("-", "_") + "_H_"
ModifyFileContent(
sim_name + "/src/my-simulation.h",
lambda c: c.replace("MY_SIMULATION_H_", include_guard))
ModifyFileContent(sim_name + "/src/my-simulation.cc",
lambda c: c.replace("my-simulation", sim_name))
# rename
os.rename(sim_name + "/src/my-simulation.h",
sim_name + "/src/" + sim_name + ".h")
os.rename(sim_name + "/src/my-simulation.cc",
sim_name + "/src/" + sim_name + ".cc")
except:
Print.error("Error: File customizations failed")
CleanupOnError(sim_name)
def DemoCommand(demo_name, destination=None):
if not demo_name:
print("Usage: biodynamo demo <demo name> [target directory]")
print("Known demos:\n {}".format("\n ".join(KNOWN_DEMOS)))
return
if demo_name not in KNOWN_DEMOS:
Print.error("Demo name \"{}\" is not known.".format(demo_name))
print("Known demos:\n {}".format("\n ".join(KNOWN_DEMOS)))
sys.exit(1)
if destination is None:
destination = "."
if os.path.exists(destination):
destination = os.path.join(destination, demo_name)
if os.path.exists(destination):
Print.error("Destination directory \"{}\" exists.".format(destination))
Print.error(
"Please remove it or create the demo in a different place.")
Print.error("Abort \"biodynamo demo {}\".".format(demo_name))
sys.exit(2)
src_dir = os.path.join(DEMO_DIR, demo_name)
print("Copying files from \"{}\" to \"{}\"...".format(
src_dir, destination))
shutil.copytree(src_dir, destination)
CopySupportFiles(destination)
InitializeNewGitRepo(destination)
Print.success("The demo \"{}\" has been created in \"{}\".".format(
demo_name, destination))
def CopySupportFiles(sim_name):
SUPPORT_DIR = os.path.join(os.environ['BDM_INSTALL_DIR'], 'share', 'util',
'support_files')
Print.new_step("Copy additional support files")
for filename in os.listdir(SUPPORT_DIR):
full_file_name = os.path.join(SUPPORT_DIR, filename)
if os.path.isfile(full_file_name):
shutil.copy(full_file_name, sim_name)
def CopySupportFiles(sim_name):
SUPPORT_DIR = os.path.join(os.environ["BDMSYS"], "share", "util",
"support_files")
Print.new_step("Copy additional support files")
for filename in os.listdir(SUPPORT_DIR):
full_file_name = os.path.join(SUPPORT_DIR, filename)
if os.path.isfile(full_file_name):
shutil.copy(full_file_name, sim_name)
def GenerateDebugOutput(sim_name):
Print.new_step("Generate debug output")
# generates cmake_output.log and / or make_output.log (depends if cmake
# ran sucessfully or not)
if BuildCommand(debug=True):
# generates runtime_output.log
RunCommand(debug=True)
# generates root dictionary log(s)
CopyRootDictionaries()
# generates system_info.log
GenerateSystemInfoLog()
def CopyTemplate(sim_name):
Print.new_step("Copy simulation template")
try:
src_path = "{0}/simulation-template".format(os.environ['BDMSYS'])
sp.check_output(["cp", "-R", src_path, "./{0}".format(sim_name)])
except sp.CalledProcessError as err:
Print.error("Error while copying the template project.")
# Do not use CleanupOnError here
# One failure could be an already existing directory
# we must not remove it
sys.exit(1)
def DownloadTemplateRepository(sim_name):
Print.new_step("Download template repository")
try:
sp.check_output([
"git", "clone",
"https://github.com/BioDynaMo/simulation-templates.git", sim_name
])
sp.check_output(["rm", "-rf", sim_name + "/.git"])
except sp.CalledProcessError as err:
Print.error(
"Error while downloading the template project from BioDynaMo")
# Do not use CleanupOnError here
# One failure could be an already existing directory
# we must not remove it
sys.exit(1)
def NewCommand(sim_name, no_github):
print("Info: This command requires a Github.com account.")
print(" Please have your account details ready, or ")
print(" go over to https://github.com/join to sign up.")
ValidateSimName(sim_name)
DownloadTemplateRepository(sim_name)
CustomizeFiles(sim_name)
InitializeNewGitRepo(sim_name)
if (not no_github):
CreateNewGithubRepository(sim_name)
Print.success(sim_name + " has been created successfully!")
print(
'To compile and run this simulation, change the directory by calling '
'"cd %s"' % (sim_name))
def DemoCommand(demo_name, destination=None):
if not demo_name:
print('Usage: biodynamo demo <demo name> [target directory]')
print('Known demos:\n {}'.format('\n '.join(KNOWN_DEMOS)))
return
if demo_name not in KNOWN_DEMOS:
Print.error('Demo name "{}" is not known.'.format(demo_name))
print('Known demos:\n {}'.format('\n '.join(KNOWN_DEMOS)))
sys.exit(1)
if destination is None:
destination = '.'
if os.path.exists(destination):
destination = os.path.join(destination, demo_name)
if os.path.exists(destination):
Print.error('Destination directory "{}" exists.'.format(destination))
sys.exit(2)
src_dir = os.path.join(DEMO_DIR, demo_name)
print('Copying files from "{}" to "{}"...'.format(src_dir, destination))
shutil.copytree(src_dir, destination)
CopySupportFiles(destination)
InitializeNewGitRepo(destination)
Print.success('The demo "{}" has been created in "{}".'.format(
demo_name, destination))
def ValidateSimName(sim_name):
pattern = re.compile("^[a-zA-Z]+[a-zA-Z0-9\-_]+$")
if not pattern.match(sim_name):
Print.error("Error: simulation name '{0}' is not valid.".format(sim_name))
Print.error(" Allowed characters are a-z A-Z 0-9 - and _")
Print.error(" Must start with a-z or A-Z")
sys.exit(1)
def CreateDebugBranch(sim_name):
Print.new_step("Create debug branch")
original_branch = sp.check_output(
["git", "rev-parse", "--abbrev-ref", "HEAD"]).decode('ascii').split("\n")[0]
branch_name = "bdm-assist-" + time.strftime("%Y%m%d_%H%M")
sp.check_output(["git", "checkout", "-b", branch_name])
sp.check_output(["git", "add", "debug"])
sp.check_output(["git", "commit", "-m", '"Add debug information"'])
sp.check_output(["git", "push", "origin", branch_name])
remote_url = sp.check_output(
["git", "remote", "get-url", "origin"]).decode('ascii').split("\n")[0]
branch_url = remote_url[:-4] + "/tree/" + branch_name
print("An assistance branch has been created, called '%s'" % (branch_name))
print(
"Send the following URL to the developers when requesting assistance:")
print("")
print(branch_url)
print("Switching back to the previous branch...")
sp.check_output(["git", "checkout", original_branch])
def GenerateSystemInfoLog():
Print.new_step("Generate system info log")
try:
sfile = open('debug/system_info.log', 'w+')
except sp.CalledProcessError as err:
print("Error: could not create system_info.log in directory 'debug'")
sys.exit(1)
my_os = platform.system()
distro, version = "", ""
architecture = platform.architecture()
if my_os == "Linux":
distro = platform.linux_distribution()[0]
my_os = my_os + " " + distro + " " + platform.linux_distribution()[1]
elif my_os == "Darwin":
version = platform.mac_ver()[0]
cmake_version = sp.check_output(["cmake", "--version"]).decode('ascii')
cmake_version = cmake_version.split("\n")[0].split(" ")[-1].strip()
# root_info = sp.check_output(
# ["cat", "$ROOTSYS/include/RVersion.h", "|", "grep", "'ROOT_RELEASE '"])
# root_version = root_info.split('"')[1::2][0]
sfile.write("%-20s %10s\n" % ("Platform:", my_os))
sfile.write("%-20s %10s\n" % ("Architecture:", architecture))
sfile.write("")
# sfile.write("%-20s %10s" % ("BioDynaMo version:", bdm_version))
sfile.write("%-20s %10s\n" % ("CMake version:", cmake_version))
# sfile.write("%-20s %10s" % ("ROOT version:", root_version))
# sfile.write("%-20s %10s" % ("ParaView version:", paraview_version))
sfile.close()
def CreateNewGithubRepository(sim_name):
Print.new_step("Create Github repository")
gh_user = input("Please enter your Github username: "******"Please enter your Github password: "******"name": sim_name,
"description": "Simulation powered by BioDynaMo"
}
headers = {'Content-Type': 'application/json'}
bytes = json.dumps(data).encode('utf-8')
url = "https://api.github.com/user/repos"
request = urllib.request.Request(url, data=bytes, headers=headers)
credentials = ('%s:%s' % (gh_user, gh_pass))
encoded_credentials = base64.b64encode(credentials.encode('ascii'))
request.add_header('Authorization',
'Basic %s' % encoded_credentials.decode("ascii"))
result = urllib.request.urlopen(request)
except urllib.error.HTTPError as err:
Print.error("Github repository creation failed.")
Print.error(err)
CleanupOnError(sim_name)
# Connect github repository with local
try:
repo_url = "https://github.com/" + gh_user + "/" + sim_name + ".git"
sp.check_output(["git", "remote", "add", "origin", repo_url],
cwd=sim_name)
except sp.CalledProcessError as err:
Print.error(
"Error: Setting remote github url ({0}) failed.".format(repo_url))
CleanupOnError(sim_name)
def UncommittedFiles():
staged_files, unstaged_files = 0, 0
untracked_files = ""
Print.new_step("Check for uncommited files")
try:
sp.check_output(["git", "diff", "--cached", "--quiet"])
except sp.CalledProcessError as err:
staged_files = err.returncode
try:
sp.check_output(["git", "diff", "--quiet"])
except sp.CalledProcessError as err:
unstaged_files = err.returncode
if not staged_files or not unstaged_files:
try:
untracked_files = sp.check_output(
["git", "ls-files", "--exclude-standard",
"--others"]).decode('ascii')
except sp.CalledProcessError as err:
Print.warning(
"Could not perform check on untracked files. Continuing anyway..."
)
pass
if staged_files or unstaged_files:
if staged_files:
print("You have staged files that need to be committed")
if unstaged_files:
print("You have unstaged files that need to be commited")
print("")
Print.warning(
"Rerun biodynamo assistance once you have resolved these issues")
return 1
if untracked_files != "":
sp.call(["git", "status"])
return not query_yes_no(
"You have untracked files. Are you sure they can be ignored?")
return 0
def RunCommand(args, debug=False):
sim_name = GetBinaryName()
args_str = ' '.join(args)
cmd = "./build/" + sim_name
try:
BuildCommand()
Print.new_step("Run " + sim_name + ' ' + args_str)
if debug:
sp.check_output([cmd, "&>", "debug/runtime_output.log"])
else:
print(
sp.check_output([cmd, args_str],
stderr=sp.STDOUT).decode('utf-8'))
Print.success("Finished successfully")
except sp.CalledProcessError as err:
print(err.output.decode("utf-8"))
Print.error("Error during execution of {0}".format(cmd))
def RunCommand(args, debug=False):
sim_name = GetBinaryName()
args_str = " ".join(args)
cmd = "./build/" + sim_name
if platform.system() == "Darwin":
launcher = os.environ["BDMSYS"] + "/bin/launcher.sh"
else:
launcher = ""
try:
BuildCommand()
Print.new_step("Run " + sim_name + " " + args_str)
if debug:
sp.check_output(
[launcher + " " + cmd, "&>", "debug/runtime_output.log"])
else:
print(
sp.check_output([launcher + " " + cmd, args_str],
stderr=sp.STDOUT,
shell=True).decode("utf-8"))
Print.success("Finished successfully")
except sp.CalledProcessError as err:
print(err.output.decode("utf-8"))
Print.error("Error during execution of {0}".format(cmd))
def CleanupOnError(sim_name):
try:
sp.check_output(["rm", "-rf", sim_name])
except:
Print.error("Error: Failed to remove folder {0}".format(sim_name))
sys.exit(1)
def ValidateSimName(sim_name):
pattern = re.compile("^[a-zA-Z]+[a-zA-Z0-9\-_]+$")
if not pattern.match(sim_name):
Print.error(
"Error: simulation name \"{}\" is not valid.".format(sim_name))
Print.error(" Allowed characters are a-z A-Z 0-9 - and _")
Print.error(" Must start with a-z or A-Z")
sys.exit(1)
if os.path.isdir(sim_name):
Print.error("The directory \"{}\" already exists.".format(sim_name))
Print.error("Please remove it or choose a different name.")
Print.error("Abort \"biodynamo new {}\".".format(sim_name))
sys.exit(1)
def BuildCommand(clean=False, debug=False, build=True):
build_dir = "build"
debug_dir = "debug"
Print.new_step("Build")
if clean or debug:
Print.new_step("Clean build directory")
sp.check_output(["rm", "-rf", build_dir])
sp.check_output(["mkdir", build_dir])
else:
if not os.path.exists(build_dir):
sp.check_output(["mkdir", build_dir])
if debug:
if not os.path.exists(debug_dir):
sp.check_output(["mkdir", debug_dir])
with open(debug_dir + '/cmake_output.log', "w") as file:
try:
sp.check_call(
["cmake", "-B./" + build_dir, "-H."],
stdout=file,
stderr=file)
except sp.CalledProcessError as err:
Print.error(
"Failed to run CMake. Generating debug/cmake_output.log..."
)
return
with open(debug_dir + '/make_output.log', "w") as file:
try:
sp.check_call(
["make", "-C", build_dir],
stdout=file,
stderr=file)
except sp.CalledProcessError as err:
Print.error(
"Compilation failed. Generating debug/make_output.log..."
)
return
elif build:
# if CMakeCache.txt does not exist, run cmake
if not Path(build_dir + "/CMakeCache.txt").is_file():
try:
sp.check_output(["cmake", "-B./" + build_dir, "-H."])
except sp.CalledProcessError as err:
Print.error("Failed to run CMake. Check the debug output above.")
sys.exit(1)
try:
sp.check_output(["make", "-j4", "-C", build_dir])
except:
Print.error("Compilation failed. Check the debug output above.")
sys.exit(1)
