Commit graph

126 commits

Author SHA1 Message Date
2f59f0a69b
refactor providers into modules 2024-07-09 23:52:58 -07:00
b6af8c9718
lint 2024-07-09 03:32:37 -07:00
f4d397cde1
more docs for dataset adapters.
also:
- fix search for initial - in dataset doctest
- don't clear git repos on repeated test runs
- fix string handling in load_yaml
2024-07-09 03:26:45 -07:00
ce902476d1
working version of pretty doctests with sybil :) 2024-07-09 00:27:22 -07:00
b9ed7c0026
testing custom directive for doctests 2024-07-08 19:07:21 -07:00
ec81032ae8
handle compound dtype 2024-07-03 20:39:49 -07:00
19d97ad3af
regenerate models, lint 2024-07-03 01:51:48 -07:00
087064be48
adjusting array adapters to linkml arrays 2024-07-03 00:41:16 -07:00
2e40506443
requests caching, python 10 2024-07-02 00:34:01 -07:00
de30f83edd
import fixtures 2024-07-02 00:01:54 -07:00
1d6584573a
one last straggler 2024-07-01 23:56:56 -07:00
7c6e69c87e
ruff unsafe fixes 2024-07-01 23:05:47 -07:00
3768e3ce0d
enable black preview and automatic linebreaks in long strings 2024-07-01 22:12:16 -07:00
d4a0c82d00
some ruff fixes 2024-07-01 22:09:49 -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
d522dd84a5
merge from origin 2024-07-01 15:46:23 -07:00
4296b27538
catchup with prior work 2024-07-01 15:44:26 -07:00
Yaroslav Halchenko
63a405f4aa [DATALAD RUNCMD] run codespell throughout fixing typo automagically but ignoring the failure due to ambigous typos
=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w || :",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
2024-04-17 15:59:53 -04:00
Yaroslav Halchenko
190a5de0e3 Use _ for a variable which is not used 2024-04-17 15:55:52 -04:00
eac5ef4c80 more docs work
move conftest to root so we find doctests? maybe we don't want to keep that tho
2023-10-19 21:20:50 -07:00
dd956b35c3 Still working on docs!
Added ability to index datasets wtih arrays with getitem
2023-10-18 21:18:02 -07:00
464d95d64d omfg another one. i'm done 2023-10-12 00:19:40 -07:00
d2185ee1c3 for pydantic provider test by escaping additional bad chars in numpy field name 2023-10-12 00:02:52 -07:00
3101797b0d don't render jinja template as having a literal "keys" attr instead of item
also remove unnecessary warnings
2023-10-11 23:28:22 -07:00
fee86135a3 omfg i hate this bug so much if this works i'll be so mad 2023-10-11 22:38:46 -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
0d29ed279f hold up can this really be the bug 2023-10-11 22:21:44 -07:00
282acc063e trying to debug on CI by abusing warnings lol 2023-10-11 21:38:29 -07:00
3a426454c6 trying to debug on CI by abusing warnings lol 2023-10-11 21:31:00 -07:00
52754112aa make allow_repo an instance-level setting 2023-10-11 20:55:03 -07:00
d9d62618bc Add source namespace to all generated linkml schemas
change `namespace` annotation to `is_namespace` and use `namespace` for name of namespace
dont change commit when commit is None - otherwise always reset to recent version when we don't intend to
2023-10-11 20:03:08 -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
91875dabb2 re-enable janky hdmf mapping test just to have it on the board for morale
Fix serializing datasets
2023-10-09 23:27:33 -07:00
42e64dce75 Refactor dataset adapter to use check/apply style maps!
General cleaning around maps module, getting ready to remove translate module
2023-10-09 23:06:24 -07:00
adaf939497 classes adapter 2023-10-09 20:13:42 -07:00
79397ec398 dict not list 2023-10-09 19:05:08 -07:00
2b530c4b33 don't require warning when at wrong git version 2023-10-09 19:04:00 -07:00
a7b0f8880e fix tests, cant assign to tuple 2023-10-09 18:59:53 -07:00
6f32a5bfd3 super annoying you have to import all fixtures and dependencies manually 2023-10-09 16:37:07 -07:00
edf7a4c445 [tests] - test adapter + results 2023-10-09 16:33:02 -07:00
39c600fda1 Regenerate nwb_schema_language models 2023-10-09 15:06:53 -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
8405ea948a [tests] ndarray proxy and serialization 2023-10-05 22:05:10 -07:00
033f6c434d [tests] nocover stuff that's just from the source module 2023-10-05 21:39:15 -07:00
c215e69fd8 [tests] nocover stuff that's just from the source module 2023-10-05 21:35:25 -07:00
a0d96014e1 [tests] pydantic generator 2023-10-05 21:22:00 -07:00
808c63e7c2 skip provider test just to get coverage numbers 2023-10-05 18:03:01 -07:00
d77dec5cc0 decrease deprecation warnings 2023-10-04 22:54:20 -07:00
5438b2489b Fix relative imports in ectopic models --
Use a MetaPathFinder to allow python to resolve imports from the temporary model directory
Build dependent versions in split builds
Clear package imports when allow_repo=False
2023-10-04 22:06:26 -07:00
3b11afded6 fix truncate hdf5 file to not try and write while iterating 2023-10-04 20:19:54 -07:00
ab63ea071c removing pandas 2023-10-04 18:02:40 -07:00
9947edfed2 Removing DataFrame type from imports, leaving as stub 2023-10-04 17:59:10 -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
d16b4757e1 Use dask instead of trying to make a dataframe
compress arrays when serializing to json
2023-09-26 19:50:49 -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
ce75dacf93 autogenerating models for dynamictable 2023-09-23 01:33:28 -07:00
57fa3d34a2 pandas dataframe mimic 2023-09-23 00:08:59 -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
3e2e6915cf Add ability to make JSON schema with numpy arrays! 2023-09-14 23:43:00 -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
c69cbdfb38 Docstrings and basic tests for providers.
bugfix - remove redundant language elements that cause a recursion error (eg. subtyping "float" with "float")
2023-09-11 19:38:29 -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
201ed569de no working-directory in actions 2023-09-05 21:53:16 -07:00
da2eaea51e some baseline tests, fixing imports, coverage reports 2023-09-05 21:47:41 -07:00
ccc09de400 refactor nwb_linkml to src layout 2023-09-05 19:25:20 -07:00