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))
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 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 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 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 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)
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 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 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 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 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)
