Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
merged 28 commits into from
Jun 7, 2024
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
28 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
2 changes: 1 addition & 1 deletion .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
.idea
.cache
/.cache
/venv
__pycache__
.pytest_cache
Expand Down
12 changes: 6 additions & 6 deletions tests/__snapshots__/test_add.ambr
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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,
})
# ---
Loading
Loading