Commit graph

259 commits

Author SHA1 Message Date
3ee7c68e15
fix array casting for dtypes that have a shape attr but nothing in it 2024-08-06 20:41:00 -07:00
edea802ff1
remove dask, nptyping 2024-08-06 20:35:23 -07:00
a309c25c3d
regenerate model, lint 2024-08-06 19:57:45 -07:00
a11d3d042e
working ragged array indexing before rebuilding models 2024-08-06 19:44:04 -07:00
c2e663eca0
fuckin LINT 2024-08-05 21:12:34 -07:00
6431afa7e5
update tests 2024-08-05 21:11:12 -07:00
83dd59d30d
lint! 2024-08-05 20:59:01 -07:00
51ceb14309
regenerate models 2024-08-05 20:56:08 -07:00
c06859a537
first impl of dynamictable working! 2024-08-05 20:51:52 -07:00
e5d1cc52de
regenerate models 2024-08-05 18:41:53 -07:00
da6d0d8608
correctly handle attributes 2024-08-05 18:41:38 -07:00
652ddb3b48
update hdmf common table 2024-08-05 17:09:58 -07:00
374bd8971d
fix name array -> value in hdmf mixins 2024-08-05 17:06:59 -07:00
0a150d6bc2
update models 2024-08-05 16:06:05 -07:00
b3b5b9d793
unify naming of derived child groups, arrays, and values as just all being named "value". Add link building. Fix erroneously collapsing anonymous and named container groups. 2024-08-05 16:05:44 -07:00
e72c860edd
update models with shorter names 2024-08-05 14:19:03 -07:00
9bfee3548e
make names less lengthy by only contatenating one layer of nesting with __ 2024-08-05 14:09:50 -07:00
b2d7b12a78
update numpydantic version and relock 2024-07-31 02:07:44 -07:00
2fef717a62
fix attr access in linkml provider result 2024-07-31 01:58:31 -07:00
0d10ba9d75
regenerate models, lint 2024-07-31 01:56:48 -07:00
1d527d8f71
fix hdmf forwardrefs, remove numpy types temporarily 2024-07-31 01:54:14 -07:00
776078ae67
add pandas 2024-07-31 01:30:06 -07:00
38e8a6f7a0
lint 2024-07-31 01:27:45 -07:00
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
f08216a43f
update models 2024-07-29 18:19:34 -07:00
19e49cf68d
regenerate models after fixing classvar mutation in numpydantic linkml branch 2024-07-29 17:34:28 -07:00
2f0af1ef3c
linting continues 2024-07-29 16:30:53 -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
011902d2cb
update models round 2 for how pycharm always misses half the files for some reason... 2024-07-29 16:18:23 -07:00
76fb58e783
update models 2024-07-29 16:16:02 -07:00
baa5471af7
getting started doing hdmf mixins but am tired 2024-07-26 21:58:07 -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
af11bb61ec
fix imports being inside the any_of range, more manual inspection before finishing for the night 2024-07-24 22:47:06 -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
43187bfa3e
add numpy type to language element types 2024-07-19 20:50:48 -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
ec843a508b
update branch for linkml 2024-07-18 00:39:56 -07:00
1920c9f292
continue removing NDArray type, since it's in numpydantic now. 2024-07-10 00:20:01 -07:00
d6750f8df1
we don't need blosc tho 2024-07-10 00:09:17 -07:00
878c51e069
we do need black as a runtime dep 2024-07-10 00:05:41 -07:00
b83865352c
the hell was that 2024-07-10 00:02:39 -07:00
bf7f62fd8f
lint 2024-07-09 23:54:28 -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
5ccc9e6fbd
black format models 2024-07-09 00:24:08 -07:00
34c8be3a2c
functional docs build 2024-07-08 21:37:02 -07:00
fdf80666fb
regenerate models with numpydantic 2024-07-08 19:29:48 -07:00
8036b3316d
regenerate models 2024-07-08 19:12:11 -07:00
78de59a0f1
regenerate models 2024-07-08 19:10:19 -07:00
b9ed7c0026
testing custom directive for doctests 2024-07-08 19:07:21 -07:00
0cbf1ac1b2
how come ide always misses the schema lol 2024-07-03 23:36:58 -07:00
4211b6058b
improve compound dtype handling, regenerate and add 2.7.0 2024-07-03 23:36:20 -07:00
ec81032ae8
handle compound dtype 2024-07-03 20:39:49 -07:00
c9a2423a9d
missed generated schema somehow... 2024-07-03 16:00:56 -07:00
19d97ad3af
regenerate models, lint 2024-07-03 01:51:48 -07:00
01cfb54a5a
working pydantic generator 2024-07-03 01:34:24 -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
38c7e9ebf8
python 10 compat 2024-07-02 00:20:52 -07:00
444ecbaf04
python 10 compat 2024-07-02 00:19:21 -07:00
566d5211bb
python 10 compat 2024-07-02 00:15:18 -07:00
883c28e6d5
don't fail fast 2024-07-02 00:12:23 -07:00
1de70a1aae
python 3.10 compat & update lockfiles 2024-07-02 00:10:28 -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
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