Commit graph

36 commits

Author SHA1 Message Date
0eeea4c517
lint 2024-09-11 21:17:46 -07:00
91b2abf07e
working thru tests for nwb file 2024-09-11 21:04:41 -07:00
d31ac29294
clean up old hdf5 reader methods, fix truncate_hdf5 method, make proper'd test data files with working references 2024-09-11 19:02:15 -07:00
000ddde000
Updating model generation methods to make both loader tests and hdmf include unit tests pass (pending following model update commit) 2024-09-11 15:44:57 -07:00
27b5dddfdd
updating model generation methods, still some models being converted to str instead of being inlined, but almost there 2024-09-04 00:04:21 -07:00
8078492f90
CHECKPOINT WITH IT WORKING before cleanup and model regeneration 2024-09-03 17:48:36 -07:00
d1498a3733
checkpointing working on model loading. it's a sloggggggggg 2024-09-03 00:54:56 -07:00
3641d33cc8
split up fixtures and nwb fixture in particular, add --clean pytest option 2024-09-02 13:40:46 -07:00
49585e467a
working on grpah loading of nwb files 2024-08-31 01:47:42 -07:00
b555ccb199
testing nwb file, and experimenting with yaml format 2024-08-30 00:39:10 -07:00
3d8403e9e3
lint 2024-07-24 22:49:35 -07:00
2e7670a2bd
yaml peek to quickly find the value of a key 2024-07-19 20:50:18 -07:00
2e40506443
requests caching, python 10 2024-07-02 00:34:01 -07:00
07aa879bb9
ruff automatic fixes 2024-07-01 21:44:35 -07:00
79fc7f23ad
black formatting 2024-07-01 21:23:31 -07:00
1eddf04400
get tests running again 2024-07-01 18:59:21 -07:00
4296b27538
catchup with prior work 2024-07-01 15:44:26 -07:00
92b1a6aac0 holy hell it was a TYPE COERCION in the way linkml handles annotations and a version mismatch between CI and local
https://github.com/linkml/linkml-model/pull/162
2023-10-11 22:30:26 -07:00
c6ca97e010 Correctly clone fixed versions in tests, adjusted fixed values to match, set default git clone temp dir from config variables 2023-10-11 19:24:08 -07:00
c4d42cdacf remove split from schema adapter because it turned out to be a bad idea, we just use tree_root instead 2023-10-11 18:32:31 -07:00
2d1fe3ad96 read is functional again, calling it a night. 2023-10-10 00:12:33 -07:00
0508e3b620 re-enable truncate file test 2023-10-09 23:30:39 -07:00
6da6ef281f nevermind need to still fix model generation 2023-10-05 22:15:33 -07:00
06311b21bd [tests] cheap read test 2023-10-05 22:12:27 -07:00
3b11afded6 fix truncate hdf5 file to not try and write while iterating 2023-10-04 20:19:54 -07:00
f672b931e5 Correctly handle container classes, use dicts instead of lists to be able to index by name. overriding __getitem__ and __getattr__ later 2023-09-26 20:50:11 -07:00
50e816bad4 Working on finalizing the mapping operation... doing it single threaded for now and it's very slow but it completes up until the stage where we need to zip up the orphaned objects and other things that can be inferred from the model.
Need to make a proxytable model like proxyarray because reading all these tables takes way too fuckin long and it's not what we want to do anyway.
2023-09-25 22:03:53 -07:00
aac0c7abdd need 2 stop for the night but its sort of happening 2023-09-22 02:48:40 -07:00
40984a6582 figuring out the strategy here...
- added linkml_meta classvar to store additional linkml properties if needed
- injecting path field to metaclass
- sketch of doing a queue-based read
- prune datasets & example allen institute data
2023-09-22 00:31:34 -07:00
e6a41415f5 successfully building many versions of nwb schema.
working on hdf5 importing, come back to it when fresh, just sorta poking at it because it's so close.
2023-09-14 02:45:01 -07:00
095d0bc6a9 fixing tests by using temp directory and changing random prior commit hash from nwb core schema 2023-09-11 19:55:45 -07:00
2e87fa0556 working generation from provider 2023-09-08 19:46:42 -07:00
0b0fb6c67a cute progress bar and also linkml provider works 2023-09-08 16:12:19 -07:00
2b828082e0 perf enhancements to pydantic generation 2023-09-06 22:48:47 -07:00
6a9d612b41 i'm just sorta making a mess here. coming back tomorrow 2023-09-06 00:50:49 -07:00
da2eaea51e some baseline tests, fixing imports, coverage reports 2023-09-05 21:47:41 -07:00