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Performance enhancements, util refactor and and clean up tests #153

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merged 28 commits into from
Jun 7, 2024
Merged

Performance enhancements, util refactor and and clean up tests #153

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00b152f
Cleanup imports
sygao May 22, 2024
58e0044
index_otu() fill out
sygao May 21, 2024
19423e8
Repo._get_source_event_ids() replaces full cache load on init
sygao May 22, 2024
839ed6c
Add true iter_otu() cache option
sygao May 21, 2024
5ded0e1
OTU.__repr__ accessions field printed as list
sygao May 22, 2024
aa39596
Add a bulk add test
sygao May 22, 2024
8e6b2e0
Add more cached NCBI data
sygao May 22, 2024
aa178b2
New src_test files
sygao May 23, 2024
28ed3ba
Modifying tests to accomodate new src_test files
sygao May 23, 2024
fa65575
Move unused prototype utils to utils.deprecated
sygao May 23, 2024
c8f51c9
Move utils.console to legacy.utils
sygao May 23, 2024
31ba6a8
utils.id_generator methods moved to legacy.utils
sygao May 23, 2024
0f0cced
Reintroduce test_utils_hashing() to legacy tests
sygao May 23, 2024
f81f624
Move Molecule and enums to utils.models
sygao Apr 26, 2024
9edaf85
Molecule is now BaseModel
sygao Apr 26, 2024
bfdb10c
Updated tests for BaseModel; Moved bad test mark
sygao May 23, 2024
73cafc5
only omit root .cache
sygao May 23, 2024
70ced9b
Add sort validation to OTUEventCache
sygao May 24, 2024
42bb77f
Add snapshots to bulk test
sygao May 24, 2024
9235093
fix ValueError bug in _get_source_event_ids
sygao May 29, 2024
bccbff1
Repo._iter_events() iterdir fix
sygao May 29, 2024
099edaf
scratch_path and scratch_repo fixtures updated to EventSourcedRepo
sygao May 29, 2024
6801149
Add a try-catch to handle bad accessions
sygao Jun 4, 2024
19d990c
Merge branch 'ncbi-fetch-fix' into cleanup-streamline
sygao Jun 4, 2024
3d9f88e
Remove Abaca Bunchy Top virus test cases from some server-dependent t…
sygao Jun 4, 2024
7f45363
Update ambr
sygao Jun 4, 2024
f5e407b
Move utils.deprecated.is_v1() and .generate_otu_dirname() to legacy.u…
sygao Jun 7, 2024
a15be17
Remove utils.deprecated
sygao Jun 7, 2024
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2 changes: 1 addition & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
.idea
.cache
/.cache
/venv
__pycache__
.pytest_cache
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12 changes: 6 additions & 6 deletions tests/__snapshots__/test_add.ambr
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@@ -1,27 +1,27 @@
# serializer version: 1
# name: TestAddOTU.test_autofill_success[438782]
# name: TestAddOTU.test_autofill_success[345184]
dict({
'acronym': '',
'excluded_accessions': list([
]),
'legacy_id': None,
'molecule': None,
'name': 'Abaca bunchy top virus',
'name': 'Cabbage leaf curl Jamaica virus',
'schema': list([
]),
'taxid': 438782,
'taxid': 345184,
})
# ---
# name: TestAddOTU.test_empty_success[438782]
# name: TestAddOTU.test_empty_success[345184]
dict({
'acronym': '',
'excluded_accessions': list([
]),
'legacy_id': None,
'molecule': None,
'name': 'Abaca bunchy top virus',
'name': 'Cabbage leaf curl Jamaica virus',
'schema': list([
]),
'taxid': 438782,
'taxid': 345184,
})
# ---
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