245 commits

Author	SHA1	Message	Date
sneakers-the-rat	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
sneakers-the-rat	e72c860edd	update models with shorter names	2024-08-05 14:19:03 -07:00
sneakers-the-rat	9bfee3548e	make names less lengthy by only contatenating one layer of nesting with __	2024-08-05 14:09:50 -07:00
sneakers-the-rat	b2d7b12a78	update numpydantic version and relock	2024-07-31 02:07:44 -07:00
sneakers-the-rat	2fef717a62	fix attr access in linkml provider result	2024-07-31 01:58:31 -07:00
sneakers-the-rat	0d10ba9d75	regenerate models, lint	2024-07-31 01:56:48 -07:00
sneakers-the-rat	1d527d8f71	fix hdmf forwardrefs, remove numpy types temporarily	2024-07-31 01:54:14 -07:00
sneakers-the-rat	776078ae67	add pandas	2024-07-31 01:30:06 -07:00
sneakers-the-rat	38e8a6f7a0	lint	2024-07-31 01:27:45 -07:00
sneakers-the-rat	abf1b0e6c0	update hdmf models/schema	2024-07-31 01:17:39 -07:00
sneakers-the-rat	d118477d8a	add dynamictable, vectordata, vectorindex mixins	2024-07-31 01:13:31 -07:00
sneakers-the-rat	c39d464e89	fix tests - update docstring tests, fix numpydantic import injects	2024-07-29 18:20:30 -07:00
sneakers-the-rat	f08216a43f	update models	2024-07-29 18:19:34 -07:00
sneakers-the-rat	19e49cf68d	regenerate models after fixing classvar mutation in numpydantic linkml branch	2024-07-29 17:34:28 -07:00
sneakers-the-rat	2f0af1ef3c	linting continues	2024-07-29 16:30:53 -07:00
sneakers-the-rat	73ae5be91c	lint	2024-07-29 16:28:48 -07:00
sneakers-the-rat	04b08f10fc	wtf and a third commit, i gotta figure out what thats about	2024-07-29 16:22:29 -07:00
sneakers-the-rat	011902d2cb	update models round 2 for how pycharm always misses half the files for some reason...	2024-07-29 16:18:23 -07:00
sneakers-the-rat	76fb58e783	update models	2024-07-29 16:16:02 -07:00
sneakers-the-rat	baa5471af7	getting started doing hdmf mixins but am tired	2024-07-26 21:58:07 -07:00
sneakers-the-rat	c98f25f973	Named generic for dynamictableregions, etc.	2024-07-26 19:54:35 -07:00
sneakers-the-rat	3d8403e9e3	lint	2024-07-24 22:49:35 -07:00
sneakers-the-rat	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
sneakers-the-rat	781b667952	working pydantic provider (at least superficially)	2024-07-24 21:51:55 -07:00
sneakers-the-rat	974058ce5f	assorted cleanings but i am tired	2024-07-19 21:28:24 -07:00
sneakers-the-rat	43187bfa3e	add numpy type to language element types	2024-07-19 20:50:48 -07:00
sneakers-the-rat	2e7670a2bd	yaml peek to quickly find the value of a key	2024-07-19 20:50:18 -07:00
sneakers-the-rat	27d18b69d8	continue stripping out old linkml monkeypatching	2024-07-18 01:01:29 -07:00
sneakers-the-rat	ec843a508b	update branch for linkml	2024-07-18 00:39:56 -07:00
sneakers-the-rat	1920c9f292	continue removing NDArray type, since it's in numpydantic now.	2024-07-10 00:20:01 -07:00
sneakers-the-rat	d6750f8df1	we don't need blosc tho	2024-07-10 00:09:17 -07:00
sneakers-the-rat	878c51e069	we do need black as a runtime dep	2024-07-10 00:05:41 -07:00
sneakers-the-rat	b83865352c	the hell was that	2024-07-10 00:02:39 -07:00
sneakers-the-rat	bf7f62fd8f	lint	2024-07-09 23:54:28 -07:00
sneakers-the-rat	2f59f0a69b	refactor providers into modules	2024-07-09 23:52:58 -07:00
sneakers-the-rat	b6af8c9718	lint	2024-07-09 03:32:37 -07:00
sneakers-the-rat	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
sneakers-the-rat	ce902476d1	working version of pretty doctests with sybil :)	2024-07-09 00:27:22 -07:00
sneakers-the-rat	5ccc9e6fbd	black format models	2024-07-09 00:24:08 -07:00
sneakers-the-rat	34c8be3a2c	functional docs build	2024-07-08 21:37:02 -07:00
sneakers-the-rat	fdf80666fb	regenerate models with numpydantic	2024-07-08 19:29:48 -07:00
sneakers-the-rat	8036b3316d	regenerate models	2024-07-08 19:12:11 -07:00
sneakers-the-rat	78de59a0f1	regenerate models	2024-07-08 19:10:19 -07:00
sneakers-the-rat	b9ed7c0026	testing custom directive for doctests	2024-07-08 19:07:21 -07:00
sneakers-the-rat	0cbf1ac1b2	how come ide always misses the schema lol	2024-07-03 23:36:58 -07:00
sneakers-the-rat	4211b6058b	improve compound dtype handling, regenerate and add 2.7.0	2024-07-03 23:36:20 -07:00
sneakers-the-rat	ec81032ae8	handle compound dtype	2024-07-03 20:39:49 -07:00
sneakers-the-rat	c9a2423a9d	missed generated schema somehow...	2024-07-03 16:00:56 -07:00
sneakers-the-rat	19d97ad3af	regenerate models, lint	2024-07-03 01:51:48 -07:00
sneakers-the-rat	01cfb54a5a	working pydantic generator	2024-07-03 01:34:24 -07:00
sneakers-the-rat	087064be48	adjusting array adapters to linkml arrays	2024-07-03 00:41:16 -07:00
sneakers-the-rat	2e40506443	requests caching, python 10	2024-07-02 00:34:01 -07:00
sneakers-the-rat	38c7e9ebf8	python 10 compat	2024-07-02 00:20:52 -07:00
sneakers-the-rat	444ecbaf04	python 10 compat	2024-07-02 00:19:21 -07:00
sneakers-the-rat	566d5211bb	python 10 compat	2024-07-02 00:15:18 -07:00
sneakers-the-rat	883c28e6d5	don't fail fast	2024-07-02 00:12:23 -07:00
sneakers-the-rat	1de70a1aae	python 3.10 compat & update lockfiles	2024-07-02 00:10:28 -07:00
sneakers-the-rat	de30f83edd	import fixtures	2024-07-02 00:01:54 -07:00
sneakers-the-rat	1d6584573a	one last straggler	2024-07-01 23:56:56 -07:00
sneakers-the-rat	f50275473c	All ruff and black fixes done	2024-07-01 23:52:32 -07:00
sneakers-the-rat	7c6e69c87e	ruff unsafe fixes	2024-07-01 23:05:47 -07:00
sneakers-the-rat	084bceaa2e	continuing manual ruff fixes	2024-07-01 22:58:55 -07:00
sneakers-the-rat	3768e3ce0d	enable black preview and automatic linebreaks in long strings	2024-07-01 22:12:16 -07:00
sneakers-the-rat	d4a0c82d00	some ruff fixes	2024-07-01 22:09:49 -07:00
sneakers-the-rat	07aa879bb9	ruff automatic fixes	2024-07-01 21:44:35 -07:00
sneakers-the-rat	79fc7f23ad	black formatting	2024-07-01 21:23:31 -07:00
sneakers-the-rat	3e5e73d186	add formatting config	2024-07-01 21:22:35 -07:00
sneakers-the-rat	a0f0b06d66	bump version	2024-07-01 19:01:15 -07:00
sneakers-the-rat	1eddf04400	get tests running again	2024-07-01 18:59:21 -07:00
sneakers-the-rat	25536c053e	docs dependencies	2024-07-01 16:35:10 -07:00
sneakers-the-rat	9eb4f0dec6	conversion from poetry to pdm	2024-07-01 16:19:13 -07:00
sneakers-the-rat	d522dd84a5	merge from origin	2024-07-01 15:46:23 -07:00
sneakers-the-rat	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
Jonny Saunders	4ee97263ed	Cleanup ndarray validator ... Remove outdated comments, rename inner function to match	2024-01-16 02:06:08 -08:00
sneakers-the-rat	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
sneakers-the-rat	23a5412854	remove unused code	2023-10-19 04:01:48 -07:00
sneakers-the-rat	2276a7b501	docs, but need to sleep, come back in morning	2023-10-19 02:52:15 -07:00
sneakers-the-rat	dd956b35c3	Still working on docs! ... Added ability to index datasets wtih arrays with getitem	2023-10-18 21:18:02 -07:00
sneakers-the-rat	af5b947d12	a bunch of docs stuff	2023-10-18 01:01:15 -07:00
sneakers-the-rat	464d95d64d	omfg another one. i'm done	2023-10-12 00:19:40 -07:00
sneakers-the-rat	d2185ee1c3	for pydantic provider test by escaping additional bad chars in numpy field name	2023-10-12 00:02:52 -07:00
sneakers-the-rat	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
sneakers-the-rat	fee86135a3	omfg i hate this bug so much if this works i'll be so mad	2023-10-11 22:38:46 -07:00
sneakers-the-rat	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
sneakers-the-rat	0d29ed279f	hold up can this really be the bug	2023-10-11 22:21:44 -07:00
sneakers-the-rat	338369a540	trying to debug on CI by abusing warnings lol	2023-10-11 22:07:01 -07:00
sneakers-the-rat	f54f5a8153	trying to debug on CI by abusing warnings lol	2023-10-11 21:57:39 -07:00
sneakers-the-rat	3164f92387	trying to debug on CI by abusing warnings lol	2023-10-11 21:49:45 -07:00
sneakers-the-rat	282acc063e	trying to debug on CI by abusing warnings lol	2023-10-11 21:38:29 -07:00
sneakers-the-rat	3a426454c6	trying to debug on CI by abusing warnings lol	2023-10-11 21:31:00 -07:00
sneakers-the-rat	52754112aa	make allow_repo an instance-level setting	2023-10-11 20:55:03 -07:00
sneakers-the-rat	38d83f3279	fix JsonObj bug https://github.com/linkml/linkml/issues/1665	2023-10-11 20:42:27 -07:00
sneakers-the-rat	d4493146b5	give language elements a schema annotation	2023-10-11 20:09:22 -07:00
sneakers-the-rat	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
sneakers-the-rat	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
sneakers-the-rat	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
sneakers-the-rat	615b006e4a	updating nwb_schema_language to have proper single/multi fields for author/contact	2023-10-10 01:08:25 -07:00