307 improve docopt description

[sophie22]

Simplify and clear up the usage instructions for docopt and consequently had to change how the arguments are parsed to set off the correct tasks to run.

resolves #307

[sophie22]

one unit test in the test_hazenlib is failing due to lack of raising exception in main. I think this test is safe to remove and also to not include an Exception when user provides an optional argument that is not available for the selected task. I think it is okay to 'silently' ignore not applicable CLI args, it is more important to correctly parse and use the ones provided that are actually relevant to the task.

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
hazenlib
HazenTask.py	25	3	88%	32–34
__init__.py	53	16	70%	125–135, 148, 182–184, 187–189, 196–198, 208
exceptions.py	21	4	81%	17–21
relaxometry.py	311	90	71%	248–266, 640, 699–701, 755, 803–825, 843–858, 1186–1189, 1198–1201, 1213–1226, 1229–1234, 1245–1274
utils.py	189	43	77%	61, 65, 75, 80, 117, 124–129, 140, 143–150, 170–172, 190–192, 211–213, 222, 227, 233, 284, 287, 295–300, 303, 346, 355, 371
hazenlib/tasks
acr_geometric_accuracy.py	146	56	62%	38–75, 179–195, 209–233
acr_ghosting.py	117	43	63%	33–55, 93–95, 125–127, 163–196
acr_slice_position.py	155	54	65%	53–76, 154, 215–260
acr_slice_thickness.py	154	64	58%	40–62, 188–243
acr_snr.py	141	62	56%	34–78, 103, 172–182, 215–228, 261–274
acr_spatial_resolution.py	244	74	70%	66–90, 169, 212, 225–234, 323–378
acr_uniformity.py	90	33	63%	34–56, 123–140
ghosting.py	152	53	65%	18–35, 50, 112–113, 117, 127–128, 154–156, 173–175, 221–259
relaxometry.py	7	7	0%	1–11
slice_position.py	117	23	80%	28, 37–38, 49, 103–104, 130, 210, 217–234
slice_width.py	357	53	85%	34–37, 41, 109, 168–188, 453, 458–459, 465, 470, 532–533, 782–823
snr.py	166	67	60%	51, 68–73, 167–185, 200–209, 227–237, 264–274, 279–289, 320–333, 338–346, 375–388
snr_map.py	104	1	99%	291
spatial_resolution.py	247	7	97%	36–39, 64, 149, 208
uniformity.py	79	20	75%	42–45, 51, 93–94, 101, 135–149
TOTAL	2891	773	73%

Tests	Skipped	Failures	Errors	Time
218	0 :zzz:	0 :x:	0 :fire:	2m 56s :stopwatch:

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
hazenlib
HazenTask.py	25	3	88%	32–34
__init__.py	53	16	70%	123–133, 146, 180–182, 185–187, 194–196, 206
exceptions.py	21	4	81%	17–21
relaxometry.py	311	90	71%	248–266, 640, 699–701, 755, 803–825, 843–858, 1186–1189, 1198–1201, 1213–1226, 1229–1234, 1245–1274
utils.py	189	43	77%	61, 65, 75, 80, 117, 124–129, 140, 143–150, 170–172, 190–192, 211–213, 222, 227, 233, 284, 287, 295–300, 303, 346, 355, 371
hazenlib/tasks
acr_geometric_accuracy.py	146	56	62%	38–75, 179–195, 209–233
acr_ghosting.py	117	43	63%	33–55, 93–95, 125–127, 163–196
acr_slice_position.py	155	54	65%	53–76, 154, 215–260
acr_slice_thickness.py	154	64	58%	40–62, 188–243
acr_snr.py	141	62	56%	34–78, 103, 172–182, 215–228, 261–274
acr_spatial_resolution.py	244	74	70%	66–90, 169, 212, 225–234, 323–378
acr_uniformity.py	90	33	63%	34–56, 123–140
ghosting.py	152	53	65%	18–35, 50, 112–113, 117, 127–128, 154–156, 173–175, 221–259
relaxometry.py	7	7	0%	1–11
slice_position.py	117	23	80%	28, 37–38, 49, 103–104, 130, 210, 217–234
slice_width.py	357	53	85%	34–37, 41, 109, 168–188, 453, 458–459, 465, 470, 532–533, 782–823
snr.py	166	67	60%	51, 68–73, 167–185, 200–209, 227–237, 264–274, 279–289, 320–333, 338–346, 375–388
snr_map.py	104	1	99%	291
spatial_resolution.py	247	7	97%	36–39, 64, 149, 208
uniformity.py	79	20	75%	42–45, 51, 93–94, 101, 135–149
TOTAL	2891	773	73%

Tests	Skipped	Failures	Errors	Time
218	0 :zzz:	0 :x:	0 :fire:	2m 47s :stopwatch:

[sophie22]

--report is not available for the relaxometry task and --show_rois, --show_template_fit and --show_relax_fits are not currently generating images due to the way matplotlib is configured in utils.py. I opened a new issue #360 for these, and since it's not directly related to the purpose of this PR focusing on the CLI usage interface, I think this PR is ready for review and potentially merging.