Karim Ahmed authored 9 months ago and Thomas Kluyver committed 2 months ago

- Replace send_to_db and storing local h5 constant file with write_ccv and inject_ccv
- Replace get_to_db with CalibrationData API
- Get pdu using calibration_client and have a da_to_pdu dict.
- Refactor code based on the new da_to_pdu dict and remove unused variables.
- Bonus: use calcat_creation_time

- Original function Single Cell:
Average time: 1.879472 seconds
Min time: 1.874208 seconds
Max time: 1.882767 seconds

- Cython function Single Cell:
Average time: 0.603006 seconds
Min time: 0.602453 seconds
Max time: 0.603634 seconds

Speedup: 3.12x

- Original function Burst Mode:
Average time: 17.192991 seconds
Min time: 17.174598 seconds
Max time: 17.211236 seconds

- Cython function Burst Mode:
Average time: 1.242232 seconds
Min time: 1.230240 seconds
Max time: 1.258492 seconds

Speedup: 13.84x

refactor:
- chunk_multi: name changed and returns now a list of np.ndarray chunks
- fill_histogram: input argument now is np.ndarray.

test:
Added tests for fill_histogram, chunk_multi, and _peak_position

- Remove object from parent class
- Reduce code duplication
- Remove log level and job id from log info

- New setup_logging.py module to set the global logger handler
- Use new princess feature to run setup_logging.py before executing notebook
- copy setup_logging.py to the CAL_WORKING_DIRECTORY for more simplicity in accessing the file from anywhere (should be enough for reproducability?).
- LOGGING:
  - WARNINGs to warnings.logs
  - ERRORs to errors.logs
  - ALL console logs are not using any special format on purpose