Commit graph

88 commits

Author SHA1 Message Date
abf1b0e6c0
update hdmf models/schema 2024-07-31 01:17:39 -07:00
d118477d8a
add dynamictable, vectordata, vectorindex mixins 2024-07-31 01:13:31 -07:00
c39d464e89
fix tests - update docstring tests, fix numpydantic import injects 2024-07-29 18:20:30 -07:00
73ae5be91c
lint 2024-07-29 16:28:48 -07:00
04b08f10fc
wtf and a third commit, i gotta figure out what thats about 2024-07-29 16:22:29 -07:00
c98f25f973
Named generic for dynamictableregions, etc. 2024-07-26 19:54:35 -07:00
3d8403e9e3
lint 2024-07-24 22:49:35 -07:00
781b667952
working pydantic provider (at least superficially) 2024-07-24 21:51:55 -07:00
974058ce5f
assorted cleanings but i am tired 2024-07-19 21:28:24 -07:00
2e7670a2bd
yaml peek to quickly find the value of a key 2024-07-19 20:50:18 -07:00
27d18b69d8
continue stripping out old linkml monkeypatching 2024-07-18 01:01:29 -07:00
1920c9f292
continue removing NDArray type, since it's in numpydantic now. 2024-07-10 00:20:01 -07:00
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