Fix logging pattern

[AndyRae]

Pull Request Contents

♻️ Refactor

Description

This PR fixes the logging pattern to a more pythonic approach - due to how the codebase had evolved, it had a mixed methods approach: some dependency injection (explicitly passing the logger to each function), and some module level singleton (importing it).

This wasn't good - and essentially introduced uncertainty into new logging (which pattern to use where), and how settings were then being instantiated in the two entrypoints. This shown in #92 where we had to rerun the settings (by importing SyncDBManager) to avoid them being cleared where logging was instantiated later in the app.
(with this change, we are now able to remove the import of SyncDBManager that fixed that issue, and make settings instantiation cleaner)

This PR therefore configures the logging once at each entrypoint, and enables each module to import logger instead of it being repeatedly injected and further boilerplate code. This is generally accepted as the Python approach to handling logging configuration: https://docs.python.org/3/howto/logging-cookbook.html#using-logging-in-multiple-modules

• Related Issue Daemon Refactor #92

Screenshots, example outputs/behaviour etc.

✅ Added/updated tests?

• This PR contains relevant tests
  • Or doesn't need to per the below explanation

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[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
src/hutch_bunny
cli.py	34	34	0%	1–60
daemon.py	18	18	0%	1–32
src/hutch_bunny/core
db_manager.py	72	38	47%	35, 49, 60, 71, 87, 89, 91, 93, 95, 109, 121–126, 129–132, 163–182, 194–199, 208–211, 219
enums.py	8	1	88%	23
execute_query.py	27	21	22%	28–62
obfuscation.py	17	1	94%	65
parser.py	5	5	0%	1–22
results_modifiers.py	13	4	69%	40–45
setting_database.py	27	17	37%	17, 20, 28–63
settings.py	45	2	96%	64, 89
src/hutch_bunny/core/rquest_dto
activity_job.py	12	12	0%	1–36
base_dto.py	6	2	67%	3, 7
cohort.py	14	4	71%	17, 32–34
file.py	12	1	92%	24
group.py	14	4	71%	19, 34–36
query.py	38	14	63%	32, 51–52, 79, 102–116
result.py	15	1	93%	38
rule.py	50	32	36%	28–31, 41–52, 64–72, 85–101
src/hutch_bunny/core/solvers
availability_solver.py	180	77	57%	149–150, 155, 182, 198–224, 232, 256–276, 292–301, 325–331, 338–410, 420–429, 436–476, 495–511, 525–531
query_solvers.py	150	6	96%	36, 142, 253, 408–410
src/hutch_bunny/core/upstream
task_api_client.py	48	27	44%	25–27, 44–54, 70–71, 89–90, 100–119
task_handler.py	9	9	0%	1–37
TOTAL	1009	330	67%

Tests	Skipped	Failures	Errors	Time
33	0 💤	0 ❌	0 🔥	1.416s ⏱️