Major refactor of code to use HazenTask classes

[laurencejackson]

Following work to separate the webapp and hazenlib functionality of the hazen project the decision was made to take this opportunity to standardise hazen tasks.

This led to the introduction of the HazenTask class, all tasks that hazen performs will inherit from this superclass leading to a number of benefits:

• allows us to easily add new tasks without rewriting boilerplate on new tasks
• the webapp is able to automatically find relevant tasks by searching for HazenTask objects
• reduces code duplication
• standardised data input/output across all tasks using HazenTask
• separating the webapp and hazenlib features massively simplifies the repository install process for most users

Currently, all MagNet object tasks currently performed as part of routine QA at GSTT have been refactored to use the HazenTask syntax. The following tasks have not been converted to the HazenTask syntax but are still available on the CLI interface:

snr_map @pcw24601
relaxometry @pcw24601
acr_uniformity @YassineRMH

These tasks should be converted to the new syntax when possible to allow them to be accessible on the web frontend.

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
hazenlib
HazenTask.py	24	3	88%	29–31
__init__.py	151	41	73%	135, 139, 149, 154, 191, 198–203, 214, 217–224, 244–246, 264–266, 285–287, 296, 301, 307, 358, 378–380, 383–385, 393–394, 398
acr_uniformity.py	92	39	58%	91–107, 114–143, 147
relaxometry.py	317	90	72%	238–256, 630, 689–691, 745, 793–815, 833–848, 1173–1176, 1185–1188, 1200–1213, 1216–1221, 1233–1263
shapes.py	20	9	55%	13, 16, 24–29, 32
snr_map.py	108	5	95%	403, 408–410, 439
tools.py	82	6	93%	43–50, 89
hazenlib/tasks
acr_uniformity.py	7	7	0%	1–11
ghosting.py	150	51	66%	18–32, 47, 109–110, 114, 124–125, 151–153, 170–172, 218–256
relaxometry.py	7	2	71%	10–11
slice_position.py	117	21	82%	31, 40–41, 103–104, 130, 210, 217–233
slice_width.py	356	52	85%	34–37, 107, 166–186, 451, 456–457, 463, 468, 530–531, 780–821
snr.py	163	46	72%	62–67, 221–231, 273–277, 314–327, 332–340, 369–382
snr_map.py	7	7	0%	1–11
spatial_resolution.py	294	90	69%	36–39, 63–121, 134, 219, 255–262, 287, 413–449
uniformity.py	78	19	76%	42–45, 91–92, 99, 133–147
TOTAL	2010	488	76%

Tests	Skipped	Failures	Errors	Time
176	0 💤	0 ❌	0 🔥	2m 20s ⏱️

[tomaroberts]

This is commented out in tests_development.yml but not tests_release.yml – is that intentional or an oversight?

[laurencejackson]

oversight, will correct now

[tomaroberts]

So good we included her twice

[tomaroberts]

Tested:

• CLI version installed via PyPI – worked
• CLI version installed via pip install -r requirements.txt - worked and unit tests successful (albeit with some usual warnings)
• new --output option – worked

Broadly reviewed other files.

Good to go.