268 commits

Author	SHA1	Message	Date
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
sneakers-the-rat	825b5914db	allow lists and singletons in generator	2023-10-10 00:50:51 -07:00
sneakers-the-rat	2d1fe3ad96	read is functional again, calling it a night.	2023-10-10 00:12:33 -07:00
sneakers-the-rat	729da40dfd	install hdf5	2023-10-09 23:40:31 -07:00
sneakers-the-rat	0508e3b620	re-enable truncate file test	2023-10-09 23:30:39 -07:00
sneakers-the-rat	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
sneakers-the-rat	f071705ac8	remove translate	2023-10-09 23:15:46 -07:00
sneakers-the-rat	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
sneakers-the-rat	adaf939497	classes adapter	2023-10-09 20:13:42 -07:00
sneakers-the-rat	79397ec398	dict not list	2023-10-09 19:05:08 -07:00
sneakers-the-rat	2b530c4b33	don't require warning when at wrong git version	2023-10-09 19:04:00 -07:00
sneakers-the-rat	a7b0f8880e	fix tests, cant assign to tuple	2023-10-09 18:59:53 -07:00
sneakers-the-rat	6f32a5bfd3	super annoying you have to import all fixtures and dependencies manually	2023-10-09 16:37:07 -07:00
sneakers-the-rat	edf7a4c445	[tests] - test adapter + results	2023-10-09 16:33:02 -07:00
sneakers-the-rat	39c600fda1	Regenerate nwb_schema_language models	2023-10-09 15:06:53 -07:00
sneakers-the-rat	6da6ef281f	nevermind need to still fix model generation	2023-10-05 22:15:33 -07:00
sneakers-the-rat	06311b21bd	[tests] cheap read test	2023-10-05 22:12:27 -07:00
sneakers-the-rat	8405ea948a	[tests] ndarray proxy and serialization	2023-10-05 22:05:10 -07:00
sneakers-the-rat	0a9ca82476	[tests] nocover stuff that's just from the source module	2023-10-05 21:42:29 -07:00
sneakers-the-rat	033f6c434d	[tests] nocover stuff that's just from the source module	2023-10-05 21:39:15 -07:00
sneakers-the-rat	c215e69fd8	[tests] nocover stuff that's just from the source module	2023-10-05 21:35:25 -07:00
sneakers-the-rat	a0d96014e1	[tests] pydantic generator	2023-10-05 21:22:00 -07:00
sneakers-the-rat	75f39b4914	huh coverage got disabled somehow	2023-10-05 18:10:04 -07:00
sneakers-the-rat	808c63e7c2	skip provider test just to get coverage numbers	2023-10-05 18:03:01 -07:00
sneakers-the-rat	d77dec5cc0	decrease deprecation warnings	2023-10-04 22:54:20 -07:00
sneakers-the-rat	24e0b704ff	decrease deprecation warnings	2023-10-04 22:49:23 -07:00
sneakers-the-rat	15d1f0d7b1	clear repo imports before returning from sys.module	2023-10-04 22:32:53 -07:00
sneakers-the-rat	0f4f2dd683	also list linkml versions in the available versions for a pydantic provider	2023-10-04 22:27:36 -07:00
sneakers-the-rat	d46e86c676	return None when the module actually doesn't exist	2023-10-04 22:08:01 -07:00
sneakers-the-rat	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
sneakers-the-rat	3b11afded6	fix truncate hdf5 file to not try and write while iterating	2023-10-04 20:19:54 -07:00
sneakers-the-rat	ab63ea071c	removing pandas	2023-10-04 18:02:40 -07:00
sneakers-the-rat	9947edfed2	Removing DataFrame type from imports, leaving as stub	2023-10-04 17:59:10 -07:00
sneakers-the-rat	f682105c1a	it working ... had to very hackily handle special cases on NWBFile class but it working. Now badly in need of a tidying, docs, and tests.	2023-10-02 23:26:43 -07:00
sneakers-the-rat	34f8969fa9	Like 15 validation errors away from fully reading a file. ... Just going to make a special completion phase for the top-level NWBFile because it's so special cased it's not worth trying to generalize. - Resolving hardlinked datasets in read maps - Resolving 2nd-order empty groups - Completing container groups - Move fixing references to recursive function - Multiple passes for a given phase - NDArrayProxies should resolve dask or h5py reading on their own - Correctly build split schema from PydanticProvider instead of needing external logic	2023-10-02 22:19:11 -07:00
sneakers-the-rat	eca7a5ec2e	Correct schema for hdf5 path type ... dont double MRO for basemodels in generated dynamictable	2023-09-28 17:58:45 -07:00
sneakers-the-rat	6bbf56d1a0	Make all maps exclusive ... Track dependencies in build results and dont try and complete model if dependencies not alreay completed (ie. need multiple passes to complete, which is the correct behavior) Use base models in dynamic tables, we should fix the dynamictable base class rather than just having everything be an anonymous BaseModel in order to satisfy type validation Clear completed queue when advancing stages - we should make sure to move everything to completed with maps rather than implicitly keeping things in completed when they aren't - so we might be getting old versions of results that aren't actually fully completed but have some reference stubs still in them.	2023-09-27 20:07:39 -07:00
sneakers-the-rat	9fcc1458fb	nearing the end - need to do final top-level packing but we're almost there!	2023-09-27 01:19:10 -07:00
sneakers-the-rat	a2da236b2b	Regenerate models	2023-09-26 21:33:14 -07:00
sneakers-the-rat	8a9b6903b6	Fix generation to use actual class in type annotation even when has identifier value, while also making dicts for container classes	2023-09-26 21:30:53 -07:00
sneakers-the-rat	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
sneakers-the-rat	d16b4757e1	Use dask instead of trying to make a dataframe ... compress arrays when serializing to json	2023-09-26 19:50:49 -07:00
sneakers-the-rat	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
sneakers-the-rat	ce75dacf93	autogenerating models for dynamictable	2023-09-23 01:33:28 -07:00
sneakers-the-rat	57fa3d34a2	pandas dataframe mimic	2023-09-23 00:08:59 -07:00
sneakers-the-rat	aac0c7abdd	need 2 stop for the night but its sort of happening	2023-09-22 02:48:40 -07:00
sneakers-the-rat	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
sneakers-the-rat	321740f674	weird python relative import error from not having version naming	2023-09-15 01:06:50 -07:00
sneakers-the-rat	1f61dca46f	weird python relative import error from not having version naming	2023-09-15 01:03:40 -07:00
sneakers-the-rat	94c204e8ea	ok but really actually correct paths	2023-09-15 00:53:07 -07:00
sneakers-the-rat	b283e8b0bf	get correct path for provider	2023-09-15 00:50:16 -07:00
sneakers-the-rat	ccf267babd	regenerating models, some minor code cleanup and coverage omissions	2023-09-15 00:37:20 -07:00
sneakers-the-rat	3e2e6915cf	Add ability to make JSON schema with numpy arrays!	2023-09-14 23:43:00 -07:00
sneakers-the-rat	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
sneakers-the-rat	054ca8fd5e	add monkeypatch to schemaview	2023-09-11 22:23:42 -07:00
sneakers-the-rat	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
sneakers-the-rat	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
sneakers-the-rat	2e87fa0556	working generation from provider	2023-09-08 19:46:42 -07:00
sneakers-the-rat	0b0fb6c67a	cute progress bar and also linkml provider works	2023-09-08 16:12:19 -07:00
sneakers-the-rat	43f35c50d8	fixing docs build	2023-09-07 19:39:19 -07:00
sneakers-the-rat	75b710c3eb	docs!	2023-09-07 19:32:17 -07:00
sneakers-the-rat	a01bb49b1e	working on providers to cache generated models	2023-09-07 18:50:50 -07:00
sneakers-the-rat	2b828082e0	perf enhancements to pydantic generation	2023-09-06 22:48:47 -07:00
sneakers-the-rat	7b97b749ef	monkeypatch to fix perf problems from nptyping	2023-09-06 19:32:33 -07:00
sneakers-the-rat	6a9d612b41	i'm just sorta making a mess here. coming back tomorrow	2023-09-06 00:50:49 -07:00
sneakers-the-rat	85beef4276	trying to get absolute paths out of coverage report	2023-09-05 22:54:20 -07:00
sneakers-the-rat	ecbb106581	proper .coveragerc formatting	2023-09-05 22:45:26 -07:00
sneakers-the-rat	456a5315d2	abandoning github action build	2023-09-05 22:42:46 -07:00
sneakers-the-rat	ce5cd18212	move to .coveragerc	2023-09-05 22:37:41 -07:00
sneakers-the-rat	2e1130c3f6	passing test directory???	2023-09-05 22:29:48 -07:00
sneakers-the-rat	fcd4f70442	explicit configuration passing	2023-09-05 22:21:30 -07:00
sneakers-the-rat	3d69213afe	optional?	2023-09-05 22:13:43 -07:00
sneakers-the-rat	3cb5e74ab8	upload to pypi	2023-09-05 22:10:10 -07:00
sneakers-the-rat	3bcf68d319	correct path	2023-09-05 21:59:19 -07:00
sneakers-the-rat	536de57ce4	correct path	2023-09-05 21:57:19 -07:00
sneakers-the-rat	2d8df6d2dc	cant include package when out of working directory	2023-09-05 21:55:41 -07:00
sneakers-the-rat	201ed569de	no working-directory in actions	2023-09-05 21:53:16 -07:00
sneakers-the-rat	da2eaea51e	some baseline tests, fixing imports, coverage reports	2023-09-05 21:47:41 -07:00