pyp.system package¶

Submodules¶

pyp.system.db_comm module¶

pyp.system.local_run module¶

pyp.system.logging module¶

pyp.system.mongo_handler module¶

class MongoFormatter(fmt=None, datefmt=None, style='%', validate=True)[source]¶

Bases: logging.Formatter

format(record)[source]¶: Format exception object as a string

class MongoHandler(collection, db='mongolog', host='localhost', port=None, username=None, password=None, level=0)[source]¶

Bases: logging.Handler

Custom log handler

Logs all messages to a mongo collection. This handler is designed to be used with the standard python logging mechanism.

emit(record)[source]¶: Store the record to the collection. Async insert

classmethod to(collection, db='mongolog', host='localhost', port=None, username=None, password=None, level=0)[source]¶: Create a handler for a given

pyp.system.mpi module¶

pyp.system.project_params module¶

pyp.system.set_up module¶

pyp.system.singularity module¶

pyp.system.slurm module¶

pyp.system.user_comm module¶

pyp.system.utils module¶

clear_scratch()[source]¶

ctime(path)[source]¶: Returns the number of milliseconds since path was last modified.

eman_load_command()[source]¶

get_bfactor_path()[source]¶

get_bm4d_path()[source]¶

get_bsoft_path()[source]¶

get_csp_path()[source]¶

get_ctffind4_path()[source]¶

get_ctffind_tilt_path()[source]¶

get_embfactor_path()[source]¶

get_frealign_paths()[source]¶

get_imod_path()[source]¶

get_multirun_path()[source]¶

get_parameter_files_path()[source]¶

get_relion_path()[source]¶

get_shell_multirun_path()[source]¶

get_slurm_path()[source]¶

get_summovie_path()[source]¶

get_tomo_path()[source]¶

get_tomoctf_path()[source]¶

get_unblur2_path()[source]¶

get_unblur_path()[source]¶

imod_load_command()[source]¶

is_atrf()[source]¶

is_atrf_bad()[source]¶

is_biowulf2()[source]¶

is_dcc()[source]¶

phenix_load_command()[source]¶

qos(partition)[source]¶

timeout_command(command, time, full_path=False)[source]¶

pyp.system package

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