def initialise_file_manager(self, rootdir):
self.file_manager = FileManager(rootdir=rootdir)
return self.file_manager
class Program(object):
"""Class meant to provide basic functionality for programs and pipelines"""
_NAME = None
_TEXT = None
_VERSION = None
_allowed_statuses = ['running', 'done', 'errored']
log = Log()
file_manager = None
def write_running_parameters_to_log(self, params):
self.log.heading('Processed parameters')
self.log(self.master_phil.format(python_object=params).as_str())
self.log.heading('Parameters different to the defaults')
self.log(
self.master_phil.fetch_diff(source=self.master_phil.format(
python_object=params)).as_str())
def check_for_matplotlib(self, backend=None, interactive=False):
"""Check to see whether we can load matplotlib"""
self.log('Checking for matplotlib:')
try:
import matplotlib
matplotlib.interactive(interactive)
from matplotlib import pyplot
if backend:
pyplot.switch_backend(backend)
current_backend = pyplot.get_backend()
assert current_backend == backend, 'Backend loaded ({}) is not the one requested ({})'.format(
current_backend, backend)
assert pyplot.isinteractive(
) is interactive, 'Interactive setting is incorrect ({} is not {})'.format(
pyplot.isinteractive(), interactive)
pyplot.style.use('ggplot')
self.log('pyplot loaded successfully. Using backend "{!s}"'.format(
current_backend))
return True
except:
self.log('===================================>>>')
self.log(
'>> COULD NOT IMPORT MATPLOTLIB. WILL NOT BE ABLE TO GENERATE GRAPHS.'
)
self.log('===================================>>>')
return False
def initialise_file_manager(self, rootdir):
self.file_manager = FileManager(rootdir=rootdir)
return self.file_manager
def update_status(self, status):
"""Set log files to indicate the status of the program"""
assert status in self._allowed_statuses
# Delete any that may exist
existing_files = [
self.file_manager.get_file('status').format(f)
for f in self._allowed_statuses
]
[os.remove(f) for f in existing_files if os.path.exists(f)]
# Create the new status file
with open(self.file_manager.get_file('status').format(status),
'w') as fh:
fh.write('')
def pickle(self, pickle_file, pickle_object, overwrite=True):
"""Takes an object and pickles it"""
if os.path.exists(pickle_file) and not overwrite:
self.log('NOT PICKLING: {!s}'.format(
os.path.relpath(pickle_file, start=self.out_dir)))
else:
self.log('Pickling Object: {!s}'.format(
os.path.relpath(pickle_file, start=self.out_dir)))
easy_pickle.dump(pickle_file, pickle_object)
def unpickle(self, pickle_file):
"""Takes an object and unpickles it"""
self.log('Unpickling File: {!s}'.format(
os.path.relpath(pickle_file, start=self.out_dir)))
return easy_pickle.load(pickle_file)
def initialise_output_directory(self, dir):
"""Initialise a dataset output directory"""
# Create a file and directory organiser
self.file_manager = FileManager(rootdir=easy_directory(dir))