Commit graph

136 commits

Author SHA1 Message Date
f50275473c
All ruff and black fixes done 2024-07-01 23:52:32 -07:00
7c6e69c87e
ruff unsafe fixes 2024-07-01 23:05:47 -07:00
084bceaa2e
continuing manual ruff fixes 2024-07-01 22:58:55 -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
3e5e73d186
add formatting config 2024-07-01 21:22:35 -07:00
a0f0b06d66
bump version 2024-07-01 19:01:15 -07:00
1eddf04400
get tests running again 2024-07-01 18:59:21 -07:00
25536c053e
docs dependencies 2024-07-01 16:35:10 -07:00
9eb4f0dec6
conversion from poetry to pdm 2024-07-01 16:19:13 -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
2e2ecf10c0 [DATALAD RUNCMD] Do interactive fixing of leftover ambigous typos
=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w -i 3 -C 2",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
2024-04-17 16:00:34 -04:00
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
4ee97263ed
Cleanup ndarray validator
Remove outdated comments, rename inner function to match
2024-01-16 02:06:08 -08:00
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
23a5412854 remove unused code 2023-10-19 04:01:48 -07:00
2276a7b501 docs, but need to sleep, come back in morning 2023-10-19 02:52:15 -07:00
dd956b35c3 Still working on docs!
Added ability to index datasets wtih arrays with getitem
2023-10-18 21:18:02 -07:00
af5b947d12 a bunch of docs stuff 2023-10-18 01:01:15 -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
338369a540 trying to debug on CI by abusing warnings lol 2023-10-11 22:07:01 -07:00
f54f5a8153 trying to debug on CI by abusing warnings lol 2023-10-11 21:57:39 -07:00
3164f92387 trying to debug on CI by abusing warnings lol 2023-10-11 21:49:45 -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
38d83f3279 fix JsonObj bug https://github.com/linkml/linkml/issues/1665 2023-10-11 20:42:27 -07:00
d4493146b5 give language elements a schema annotation 2023-10-11 20:09:22 -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
615b006e4a updating nwb_schema_language to have proper single/multi fields for author/contact 2023-10-10 01:08:25 -07:00
825b5914db allow lists and singletons in generator 2023-10-10 00:50:51 -07:00
2d1fe3ad96 read is functional again, calling it a night. 2023-10-10 00:12:33 -07:00
729da40dfd install hdf5 2023-10-09 23:40:31 -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
f071705ac8 remove translate 2023-10-09 23:15:46 -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