neuropoly / spinalcordtoolbox / 10808
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Clarify handling of logger, error and exceptions (#2221)

* sct_utils/printv: Now using print() instead of logging.

Also, removed raised exception if type=error, because this is not the role of this function to deal with exceptions.

* sct_utils/printv: Clarified docstrings

* sct_check_dependencies: Removed log file feature

* sct_testing: Replaced former sct.log with printv

* spinalcordtoolbox.utils: Removed logger

* sct_utils: Removed former sct logger, only keep printv

* sct_dmri_create_noisemask: Removed old sct logger

* msct_register: Removed old sct logger function

* sct_testing: Removed write_to_log_file() and cleanup

* sct_compute_mtsat: Removed start_stream_logger()

* sct_pipeline_makefig: Removed start_stream_logger()

* process_seg: Replaced sct.log by logging

* aggregate_slicewise: Replaced sct.log by logging and cleanup

* straightening: Removed useless import

* sct_utils: Now initializing logging level in sct_init()

* sct_straighten_spinalcord: Now setting logging level for APIs

* image: Replaced old sct.log with logger and cleanup imports

* straightening: Defined logger handler at the beginning of API

* sct_utils/init_sct: Added flag to bypass logger/sentry init

Useful when we want to pass verbose in command-line argument

* sct_straighten_spinalcord: Passing verbose argument from command-line

* sct_straighten_spinalcord: Minor syntax simplification

* msct_parser: Replaced sct.log by logger

* sct_utils/server_log_handler: logger --> logging

* msct_register: Updated comment

* sct_qc: Removed verbose in usage (not used) and added Sentry init

* Updating log_level from verbose param for all command-line functions

* Replaced sct.log --> logger

* Replaced logger --> sct.printv in command-line functions

* Initialize logger in APIs

* Fixed remaining issues

* sct_qc: Fixed typo when calling init_sct()

* sct_qc: Added qc-dataset and qc-subject in param
... (continued)

22503 of 65019 relevant lines covered (34.61%)

0.64 hits per line

Jobs
ID Job ID Ran Files Coverage
1 10808.1 0
26.73
 Travis Job 10808.1
2 10808.2 (SCT_MINICONDA=2) 0
66.8
 Travis Job 10808.2
3 10808.3 (SCT_MINICONDA=2) 0
68.09
 Travis Job 10808.3
Source Files on build 10808
Detailed source file information is not available for this build.