Feature: improve coverage, fix warnings, fix bugs

[oanabotezat]

improve coverage from 67% to 80%

running a full test with coverage:
pytest --cov oceanstream

results in a bunch of warnings (-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html) and:

---------- coverage: platform darwin, python 3.9.18-final-0 ----------
Name                                                    Stmts   Miss  Cover
---------------------------------------------------------------------------
oceanstream/__init__.py                                     0      0   100%
oceanstream/cli.py                                        108    108     0%
oceanstream/denoise/__init__.py                             2      0   100%
oceanstream/denoise/apply_masks.py                         35     26    26%
oceanstream/denoise/applying_masks_handler.py              34      3    91%
oceanstream/denoise/background_noise_remover.py            16      0   100%
oceanstream/denoise/create_masks.py                        44     31    30%
oceanstream/denoise/noise_masks.py                         46      6    87%
oceanstream/denoise/types.py                               53      0   100%
oceanstream/echodata/__init__.py                            5      0   100%
oceanstream/echodata/ensure_time_continuity.py             17      1    94%
oceanstream/echodata/processed_data_io.py                  46      9    80%
oceanstream/echodata/raw_handler.py                       179     40    78%
oceanstream/echodata/read_file.py                          48     39    19%
oceanstream/echodata/sv_computation.py                     54     16    70%
oceanstream/echodata/sv_dataset_extension.py               30      4    87%
oceanstream/echodata/sv_interpolation.py                   88      0   100%
oceanstream/echodata/target_strength_computation.py        41      6    85%
oceanstream/exports/__init__.py                             3      0   100%
oceanstream/exports/csv/__init__.py                         3      0   100%
oceanstream/exports/csv/csv_export_from_Sv.py              30      9    70%
oceanstream/exports/csv/csv_export_from_raw.py             30      9    70%
oceanstream/exports/csv/csv_export_nasc.py                 58      4    93%
oceanstream/exports/frequency_differencing_handler.py      30      0   100%
oceanstream/exports/mvbs_computation.py                    19      1    95%
oceanstream/exports/nasc.py                                15     11    27%
oceanstream/exports/nasc_computation.py                    15      1    93%
oceanstream/exports/plot.py                                27      1    96%
oceanstream/exports/shoals/__init__.py                      1      0   100%
oceanstream/exports/shoals/shoal_detection_handler.py      13      0   100%
oceanstream/exports/shoals/shoal_process.py                76      5    93%
oceanstream/exports/shoals/shoals_handler.py               28     19    32%
oceanstream/report/__init__.py                              1      0   100%
oceanstream/report/echogram.py                             30     30     0%
oceanstream/report/profiling.py                            37     32    14%
oceanstream/settings/__init__.py                            1      1     0%
oceanstream/settings/config.py                             12     12     0%
oceanstream/utils.py                                       26      0   100%
---------------------------------------------------------------------------
TOTAL                                                    1301    424    67%

=============== 83 passed, 591 warnings in 1120.57s (0:18:40) =====================================

[oanabotezat]

what is actually useful from the list above (stripped ---init.py and >= 70% covered files):

Name                                                    Stmts   Miss  Cover
---------------------------------------------------------------------------
oceanstream/cli.py                                        108    108     0%
oceanstream/denoise/apply_masks.py                         35     26    26%
oceanstream/denoise/create_masks.py                        44     31    30%
oceanstream/echodata/read_file.py                          48     39    19%
oceanstream/exports/nasc.py                                15     11    27%
oceanstream/exports/shoals/shoals_handler.py               28     19    32%
oceanstream/report/echogram.py                             30     30     0%
oceanstream/report/profiling.py                            37     32    14%
oceanstream/settings/config.py                             12     12     0%

[oanabotezat]

24 warnings:

• 14 DeprecationWarning
• 3 UserWarning
• 2 PytestUnknownMarkWarning

most are in 3rd party libraries...

remaining: 6.