def create_subject(project_name,
subject_name: str = "_iblrig_test_mouse",
force=False):
project_name = alyx2local_names.get(project_name, project_name)
project_path = IBLRIG_PARAMS_FOLDER / project_name
p = Project()
print(f"Loading [{project_path}]")
p.load(project_path)
subject = p.find_subject(subject_name)
if force or subject is None:
subject = p.create_subject()
subject.name = subject_name
p.save(project_path)
print(f" Created subject: [{subject_name}]")
# Create default subjects for project {project_name} if they don't exist
if p.find_subject("_iblrig_test_mouse") is None:
create_subject(project_name,
subject_name="_iblrig_test_mouse",
force=True)
if p.find_subject("_iblrig_calibration") is None:
create_subject(project_name,
subject_name="_iblrig_calibration",
force=True)
return subject
def create_experiment_setups(iblproject_path, exp_name: str):
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
if not exp:
print(f'Experiment {exp} not found')
raise KeyError
else:
exp = exp[0]
if exp.name == '_iblrig_calibration':
screen = create_setup(exp, 'screen', p.boards[0].name,
exp.name) # noqa
water = create_setup(exp, 'water', p.boards[0].name, exp.name) # noqa
if exp.name == '_iblrig_misc':
flush_water = create_setup( # noqa
exp, 'flush_water', p.boards[0].name, '_iblrig_test_mouse')
if exp.name == '_iblrig_tasks':
biasedChoiceWorld = create_setup( # noqa
exp, 'biasedChoiceWorld', p.boards[0].name, None)
habituationChoiceWorld = create_setup( # noqa
exp, 'habituationChoiceWorld', p.boards[0].name, None)
trainingChoiceWorld = create_setup( # noqa
exp, 'trainingChoiceWorld', p.boards[0].name, None)
ephysChoiceWorld = create_setup( # noqa
exp, 'ephysChoiceWorld', p.boards[0].name, None)
p.save(iblproject_path)
def config_task(iblproject_path, task_name: str):
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
print(f" Configuring task <{task.name}>")
task._commands = []
if task.name == '_iblrig_calibration_screen':
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == '_iblrig_calibration_water':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_misc_flush_water':
task = create_task_cleanup_command(task)
# For all of tasks stop the stim 7110, stop the recording 7111 and cleanup
if '_iblrig_tasks' in task.name:
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_bonsai_stop_command(task, port=7111)
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, onoff=1, when='POST')
if task.name == '_iblrig_tasks_habituationChoiceWorld':
task = create_task_create_command(task, patch=True)
if task.name == '_iblrig_tasks_trainingChoiceWorld':
task = create_task_create_command(task, patch=True)
if task.name == '_iblrig_tasks_biasedChoiceWorld':
task = create_task_create_command(task, patch=False)
if task.name == '_iblrig_tasks_ephysChoiceWorld':
task = create_task_create_command(task, patch=False)
p.save(iblproject_path)
print(" Task configured")
def create_experiment_setups(iblproject_path, exp_name: str): # XXX:THIS!
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
calib_subj = [s for s in p.subjects if s.name == "_iblrig_calibration"][0]
test_subj = [s for s in p.subjects if s.name == "_iblrig_test_mouse"][0]
if not exp:
raise KeyError(f"Experiment {exp} not found")
else:
exp = exp[0]
if exp.name == "_iblrig_calibration":
screen = create_setup(exp, "screen", p.boards[0].name, calib_subj) # noqa
water = create_setup(exp, "water", p.boards[0].name, calib_subj) # noqa
input_listner = create_setup( # noqa
exp, "input_listner", p.boards[0].name, calib_subj
)
frame2TTL = create_setup(exp, "frame2TTL", p.boards[0].name, calib_subj) # noqa
if exp.name == "_iblrig_misc":
flush_water = create_setup( # noqa
exp, "flush_water", p.boards[0].name, test_subj
)
bpod_ttl_test = create_setup( # noqa
exp, "bpod_ttl_test", p.boards[0].name, test_subj
)
frame2TTL_freq_test = create_setup( # noqa
exp, "frame2TTL_freq_test", p.boards[0].name, test_subj
)
if exp.name == "_iblrig_tasks":
biasedChoiceWorld = create_setup( # noqa
exp, "biasedChoiceWorld", p.boards[0].name, None
)
habituationChoiceWorld = create_setup( # noqa
exp, "habituationChoiceWorld", p.boards[0].name, None
)
trainingChoiceWorld = create_setup( # noqa
exp, "trainingChoiceWorld", p.boards[0].name, None
)
ephys_certification = create_setup( # noqa
exp, "ephys_certification", p.boards[0].name, None
)
ephysChoiceWorld = create_setup( # noqa
exp,
"ephysChoiceWorld_testing",
p.boards[0].name,
test_subj,
task="_iblrig_tasks_ephysChoiceWorld",
)
passiveChoiceWorld = create_setup( # noqa
exp,
"passiveChoiceWorld_testing",
p.boards[0].name,
test_subj,
task="_iblrig_tasks_passiveChoiceWorld",
)
p.save(iblproject_path)
def create_subject(iblproject_path, subject_name: str):
p = Project()
p.load(iblproject_path)
# if p.find_subject(subject_name) is None:
subject = p.create_subject()
subject.name = subject_name
p.save(iblproject_path)
print(f" Created subject: {subject_name}")
def config_task(iblproject_path, task_name: str): # XXX: THIS!
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
print(f" Configuring task <{task.name}>")
task._commands = []
if task.name == "_iblrig_calibration_screen":
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == "_iblrig_calibration_water":
task = create_task_cleanup_command(task)
if task.name == "_iblrig_calibration_input_listner":
task = create_task_cleanup_command(task)
if task.name == "_iblrig_calibration_frame2TTL":
task = create_task_cleanup_command(task)
if task.name == "_iblrig_misc_flush_water":
task = create_task_cleanup_command(task)
if task.name == "_iblrig_misc_bpod_ttl_test":
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == "_iblrig_misc_frame2TTL_freq_test":
task = create_task_cleanup_command(task)
# For all bpod tasks turn off bpod lights, stop the stim 7110, stop the camera 7111 and cleanup
btasks = [
"_iblrig_tasks_habituationChoiceWorld",
"_iblrig_tasks_trainingChoiceWorld",
"_iblrig_tasks_biasedChoiceWorld",
"_iblrig_tasks_ephysChoiceWorld",
]
if task.name in btasks:
task = create_task_bonsai_stop_command(task, port=7110) # visual stimulus
task = create_task_bonsai_stop_command(task, port=7111) # camera recording
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, 1, when="POST")
if task.name == "_iblrig_tasks_habituationChoiceWorld":
task = create_task_create_command(task, poop=True)
if task.name == "_iblrig_tasks_trainingChoiceWorld":
task = create_task_create_command(task, poop=True)
if task.name == "_iblrig_tasks_biasedChoiceWorld":
task = create_task_create_command(task, poop=False)
if task.name == "_iblrig_tasks_ephysChoiceWorld":
task = create_task_create_command(task, poop=False)
if task.name == "_iblrig_tasks_ephys_certification":
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, 0, when="PRE")
task = create_task_bpod_lights_command(task, 1, when="POST")
if task.name == "_iblrig_tasks_passiveChoiceWorld":
task = create_task_cleanup_command(task)
task = create_task_poop_command(task, when="POST")
task = create_task_bonsai_stop_command(task, port=7110) # stim
task = create_task_bonsai_stop_command(task, port=7112) # record_mic
task = create_task_bpod_lights_command(task, 0, when="PRE")
task = create_task_bpod_lights_command(task, 1, when="POST")
task = create_task_move_passive_command(task, when="POST")
p.save(iblproject_path)
print(" Task configured")
def create_experiment(iblproject_path, exp_name: str):
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
# if not exp:
exp = p.create_experiment()
exp.name = exp_name
p.save(iblproject_path)
print(f"Created experiment: {exp.name}")
def create_task(iblproject_path, task_name: str):
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
# if task is None:
task = p.create_task()
task.name = task_name
p.save(iblproject_path)
print(f"Created task: {task_name}")
def create_ibl_project(iblproject_path):
p = Project()
try:
p.load(iblproject_path)
print(f"Skipping creation: IBL project found <{iblproject_path}>")
except: # noqa
p.name = 'IBL'
p.save(iblproject_path)
print("Created: IBL project")
def config_task(iblproject_path, task_name: str): # XXX: THIS!
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
print(f" Configuring task <{task.name}>")
task._commands = []
if task.name == '_iblrig_calibration_screen':
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == '_iblrig_calibration_water':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_calibration_input_listner':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_calibration_frame2TTL':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_misc_flush_water':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_misc_bpod_ttl_test':
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == '_iblrig_misc_frame2TTL_freq_test':
task = create_task_cleanup_command(task)
# For all bpod tasks turn off bpod lights, stop the stim 7110, stop the camera 7111 and cleanup
btasks = [
'_iblrig_tasks_habituationChoiceWorld',
'_iblrig_tasks_trainingChoiceWorld',
'_iblrig_tasks_biasedChoiceWorld',
'_iblrig_tasks_ephysChoiceWorld',
]
if task.name in btasks:
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_bonsai_stop_command(task, port=7111)
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, onoff=1, when='POST')
if task.name == '_iblrig_tasks_habituationChoiceWorld':
task = create_task_create_command(task, poop=True)
if task.name == '_iblrig_tasks_trainingChoiceWorld':
task = create_task_create_command(task, poop=True)
if task.name == '_iblrig_tasks_biasedChoiceWorld':
task = create_task_create_command(task, poop=False)
if task.name == '_iblrig_tasks_ephysChoiceWorld':
task = create_task_create_command(task, poop=False)
if task.name == '_iblrig_tasks_ephys_certification':
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, onoff=0, when='PRE')
task = create_task_bpod_lights_command(task, onoff=1, when='POST')
if task.name == '_iblrig_tasks_passiveChoiceWorld':
task = create_task_cleanup_command(task)
task = create_task_poop_command(task, when='POST')
task = create_task_bpod_lights_command(task, onoff=0, when='PRE')
task = create_task_bpod_lights_command(task, onoff=1, when='POST')
task = create_task_move_passive_command(task, when='POST')
p.save(iblproject_path)
print(" Task configured")
def create_ibl_project(iblproject_path):
p = Project()
print("Creating IBL project")
try:
p.load(iblproject_path)
print(f" Skipping creation: IBL project found in: {iblproject_path}")
except: # noqa
p.name = "IBL"
p.save(iblproject_path)
print(" Created: IBL project")
def create_subject(iblproject_path, subject_name: str):
p = Project()
p.load(iblproject_path)
if p.find_subject(subject_name) is None:
subject = p.create_subject()
subject.name = subject_name
p.save(iblproject_path)
print(f"Created subject: {subject_name}")
else:
subject = p.find_subject(subject_name)
print(f"Skipping creation: Subject <{subject.name}> already exists")
def create_ibl_users(iblproject_path):
p = Project()
p.load(iblproject_path)
if p.find_user('_iblrig_test_user') is None:
user = p.create_user()
user.name = '_iblrig_test_user'
p.save(iblproject_path)
print(f"Created: IBL default user <{user.name}>")
else:
user = p.find_user('_iblrig_test_user')
print(f"Skipping creation: User <{user.name}> already exists")
def create_ibl_board(iblproject_path):
p = Project()
p.load(iblproject_path)
if not p.boards:
BOARD_NAME = 'SELECT_BOARD_NAME_(e.g.[_iblrig_mainenlab_behavior_0])'
b = p.create_board()
b.name = BOARD_NAME
p.save(iblproject_path)
print("Created: IBL default board (please remember to rename it)")
else:
print(f"Skipping creation: Board found with name <{p.boards[0].name}>")
def create_task(iblproject_path, task_name: str):
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
if task is None:
task = p.create_task()
task.name = task_name
p.save(iblproject_path)
print(f"Created task: {task_name}")
else:
print(f"Skipping creation: Task {task.name} already exists")
def create_experiment(iblproject_path, exp_name: str):
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
if not exp:
exp = p.create_experiment()
exp.name = exp_name
p.save(iblproject_path)
print(f"Created experiment: {exp.name}")
else:
exp = exp[0]
print(f"Skipping creation: Experiment {exp.name} already exists")
def create_experiment_setups(iblproject_path, exp_name: str): # XXX:THIS!
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
calib_subj = [s for s in p.subjects if s.name == '_iblrig_calibration'][0]
test_subj = [s for s in p.subjects if s.name == '_iblrig_test_mouse'][0]
if not exp:
raise KeyError(f'Experiment {exp} not found')
else:
exp = exp[0]
if exp.name == '_iblrig_calibration':
screen = create_setup(exp, 'screen', p.boards[0].name,
calib_subj) # noqa
water = create_setup(exp, 'water', p.boards[0].name,
calib_subj) # noqa
input_listner = create_setup(exp, 'input_listner', p.boards[0].name,
calib_subj) # noqa
frame2TTL = create_setup(exp, 'frame2TTL', p.boards[0].name,
calib_subj) # noqa
if exp.name == '_iblrig_misc':
flush_water = create_setup( # noqa
exp, 'flush_water', p.boards[0].name, test_subj)
bpod_ttl_test = create_setup( # noqa
exp, 'bpod_ttl_test', p.boards[0].name, test_subj)
frame2TTL_freq_test = create_setup( # noqa
exp, 'frame2TTL_freq_test', p.boards[0].name, test_subj)
if exp.name == '_iblrig_tasks':
biasedChoiceWorld = create_setup( # noqa
exp, 'biasedChoiceWorld', p.boards[0].name, None)
habituationChoiceWorld = create_setup( # noqa
exp, 'habituationChoiceWorld', p.boards[0].name, None)
trainingChoiceWorld = create_setup( # noqa
exp, 'trainingChoiceWorld', p.boards[0].name, None)
ephys_certification = create_setup( # noqa
exp, 'ephys_certification', p.boards[0].name, None)
ephysChoiceWorld = create_setup( # noqa
exp,
'ephysChoiceWorld_testing',
p.boards[0].name,
test_subj,
task='_iblrig_tasks_ephysChoiceWorld')
passiveChoiceWorld = create_setup( # noqa
exp,
'passiveChoiceWorld_testing',
p.boards[0].name,
test_subj,
task='_iblrig_tasks_passiveChoiceWorld')
p.save(iblproject_path)
def create_project(project_name, force=False):
project_name = alyx2local_names.get(project_name, project_name)
project_path = IBLRIG_PARAMS_FOLDER / project_name
p = Project()
if force or not pybpod_project_exists(project_name):
p.name = project_name
p.save(project_path)
print(f" Project created: [{project_name}]")
else:
print(
f" Skipping creation: project [{project_name}] found in: [{project_path}]"
)
p = Project()
p.load(project_path)
return p
def setups_to_remove(iblproject_path):
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == "_iblrig_calibration"]
if not exp:
raise KeyError(f"Experiment {exp} not found")
else:
exp = exp[0]
setup = [s for s in exp.setups if s.name == "screen"]
if not setup:
print(f"Setup {setup} not found")
else:
setup = setup[0]
print()
exp -= setup
p.save(iblproject_path)
def create_board_from_main_project_to(project_name, force=False):
project_name = alyx2local_names.get(project_name, project_name)
if project_name == "IBL":
print("Can't create board of main project")
return
project_path = IBLRIG_PARAMS_FOLDER / project_name
iblproj = Project()
iblproj.load(IBLRIG_PARAMS_FOLDER / "IBL")
print("Looking for boards in default project")
if not iblproj.boards or len(iblproj.boards) > 1:
print(
f"0 or 2+ boards found in main project: {[x.name for x in iblproj.boards]}"
)
return
bname = iblproj.boards[0].name
print("Board found: [{}]".format(bname))
p = Project()
if not pybpod_project_exists(project_name):
return
print(f"Loading [{project_path}]")
p.load(project_path)
if force or not p.boards:
board = p.create_board()
board.name = iblproj.boards[0].name
p.save(project_path)
print(f" Created board: [{board.name}] in project [{project_name}]")
elif len(p.boards) > 1:
print(
f" Skipping creation: project [{project_name}] already has [{len(p.boards)}] boards"
)
elif len(p.boards) == 1:
bname = p.boards[0].name
print(
f" Skipping creation: Board [{bname}] already exists in project [{project_name}]"
)
return
def create_user(project_name, username="******", force=False):
project_name = alyx2local_names.get(project_name, project_name)
project_path = IBLRIG_PARAMS_FOLDER / project_name
p = Project()
print(f"Loading [{project_path}]")
if not pybpod_project_exists(project_name):
return
p.load(project_path)
if force or p.find_user(username) is None:
user = p.create_user()
user.name = username
p.save(project_path)
print(f" Created user: [{user.name}] in project [{project_name}]")
else:
user = p.find_user(username)
print(
f" Skipping creation: User [{user.name}] already exists in project [{project_name}]"
)
if p.find_user("_iblrig_test_user") is None:
create_user(project_name, username="******", force=True)
return user
def save(self, project_path=None):
if project_path:
Project.save(self, project_path)
elif self.path:
Project.save(self, self.path)
else:
folder = QFileDialog.getExistingDirectory(
self, "Select a directory to save the project: {0}".format(
self.name))
if folder:
folder = os.path.join(folder, self.name)
try:
Project.save(self, str(folder))
except FileExistsError as err:
logger.warning(str(err))
QMessageBox.warning(
self, 'Project exists',
'Project with same name already exists. Please select another path.'
)
# add a setup to the project
stp = exp.create_setup()
stp.name = 'First setup'
# add a board to the project
board = proj.create_board()
board.name = 'First board'
board.serial_port = 'COM3'
# add subjects to the project
subj = proj.create_subject()
subj.name = 'First animal'
subj2 = proj.create_subject()
subj2.name = 'Second animal'
# add a new task\protocol to the project
task = proj.create_task()
task.name = 'First task'
exp.task = task # set the task\protocol to the experiment
stp.board = board # set the board to the setup
stp += [subj, subj2] # add a subject to the setup
proj.save('my-project-folder')
task.code = 'print("My first protocol")'
proj.save(proj.path)
class pybpod_helper():
def __init__(self, root_path, project_path):
self.root_path = root_path
self.project_path = project_path
self.project = Project()
self.hostname = os.environ['COMPUTERNAME']
def populate_project_folder(self):
"""copy all the necessary files for the bpod setup to the folder of this setup"""
# create project
self.create_project()
# boards
print("Creating: Bpod board")
board = self.create_board()
# create project.json files
user, subject = self.create_defaults()
# tasks
# gambl task
exp_gamble = self.create_experiment("gamble_task")
# training
task_name = 'gamble_task_training'
self.create_task(task_name)
self.create_setup(exp_gamble, task_name, board, subject)
# recording
task_name = 'gamble_task_recording'
self.create_task(task_name)
self.create_setup(exp_gamble, task_name, board, subject)
# choice task
# self.create_experiment("choice_task")
# habituation
# training
# recording
# calibration, administer reward etc
self.create_experiment("calibration_etc")
print("Creating: default usersettings, user, and subject")
self.create_defaults()
# create project.json files
# helper functions for task folder createion =======================================
def create_task(self, task_name):
"""copy files for given task to poject dir
Args:
task_name (str): name of the task
"""
print(f"Creating {task_name} setup")
task = self.project.find_task(task_name)
if task != None:
print(
f"Found task config file in {str(self.project_path)}/{str(task_name)}",
"\nDo you want to overwrite config? (y/n)",
)
user_input = input()
if user_input == "n":
return
elif user_input == "y":
# copy files to new task
src = self.root_path / "tasks" / task_name
dest = self.project_path / "tasks" / task_name
task = self.project.create_task()
task.name = task_name
self.project.save(self.project_path)
self.copytree(src, dest)
print(f"Created task: {task_name}")
else:
# copy files to new task
src = self.root_path / "tasks" / task_name
dest = self.project_path / "tasks" / task_name
task = self.project.create_task()
task.name = task_name
self.project.save(self.project_path)
self.copytree(src, dest)
print(f"Created task: {task_name}")
def create_board(self):
"""create new bpod board for new setup
Returns:
bpod.board:
"""
if not self.project.boards:
# copy files to new board
board = self.project.create_board()
board.name = ("board_" + self.hostname)
self.project.save(self.project_path)
print("Created borad")
else:
print("Board already exists")
board = self.project.boards[0].name
return board
def create_experiment(self, exp_name):
"""create new experiment for setup
Args:
exp_name (str): name of the experiment to create
Returns:
bpod.experiment:
"""
exp = self.project.create_experiment()
exp.name = exp_name
self.project.save(self.project_path)
print(f"Created experiment: {exp.name}")
return exp
def create_setup(self, experiment, setup_name, board, subject):
"""create new setup for setup
Args:
experiment (bpod.experiment): experminet under which the setup is created
setup_name (str): name of the setup
board (bpod.board): board which will be added as default to the setup
subject (bpod.subject): subject which will be added as default to the setup
"""
# create experiment
setup = experiment.create_setup()
setup.name = setup_name
setup.task = setup_name
setup + subject
setup.detached = True
self.project.save(self.project_path)
def create_defaults(self):
"""routine to create default elements for new bpod setup
user: create new default user - test_user
subject: create new default subject - test_subject
Returns:
bpod.user:
bpod.subject:
"""
# copy usersettings
src = self.root_path / ("scripts/user_settings.py")
dest = self.project_path / "user_settings.py"
shutil.copy(src, dest)
# add default prject to user settings
with open(dest, 'a') as f:
f.write(f"\nDEFAULT_PROJECT_PATH = \"{self.project_path}\"\n")
# create default user
if self.project.find_user("test_user") is None:
user = self.project.create_user()
user.name = "test_user"
self.project.save(self.project_path)
print(f" Created: default user {user.name}")
else:
user = self.project.find_user("test_user")
print(f" Skipping creation: User {user.name} already exists")
# create default subject
subject_name = "test_subject"
subject = self.project.find_subject(subject_name)
if subject is None:
subject = self.project.create_subject()
subject.name = subject_name
self.project.save(self.project_path)
print(f" Created subject: {subject_name}")
else:
print(
f"Skipping creation: Subject <{subject.name}> already exists")
return user, subject
def create_project(self):
"""create maxland project for new setup"""
print("Creating default project")
try:
self.project.load(self.project_path)
print(
f" Skipping creation: maxland project found in: {self.project_path}"
)
except: # noqa
self.project.name = ("maxland_" + self.hostname)
self.project.save(self.project_path)
print(f"Created: project maxland_{self.hostname}")
def copytree(self, src, dst, symlinks=False, ignore=None):
"""helper function to copy all files from one directory to another
Args:
src (os.path): path to source folder
dst (os.path): path to destination folder
symlinks (bool, optional): dont copy but use symbolic links to original files. Defaults to False.
ignore (list, optional): ignore items in source. Defaults to None.
"""
for item in os.listdir(src):
s = os.path.join(src, item)
d = os.path.join(dst, item)
if os.path.isdir(s):
copytree(s, d, symlinks, ignore)
elif item in os.listdir(dst):
os.remove(d)
shutil.copy2(s, d)
else:
shutil.copy2(s, d)