0a9ca82476
[tests] nocover stuff that's just from the source module
2023-10-05 21:42:29 -07:00
033f6c434d
[tests] nocover stuff that's just from the source module
2023-10-05 21:39:15 -07:00
c215e69fd8
[tests] nocover stuff that's just from the source module
2023-10-05 21:35:25 -07:00
a0d96014e1
[tests] pydantic generator
2023-10-05 21:22:00 -07:00
75f39b4914
huh coverage got disabled somehow
2023-10-05 18:10:04 -07:00
799d32ed24
remove hdf5_linkml - it doesn't make sense to be separate since it requires all the rest of the main package
2023-10-05 18:04:14 -07:00
808c63e7c2
skip provider test just to get coverage numbers
2023-10-05 18:03:01 -07:00
d77dec5cc0
decrease deprecation warnings
2023-10-04 22:54:20 -07:00
24e0b704ff
decrease deprecation warnings
2023-10-04 22:49:23 -07:00
15d1f0d7b1
clear repo imports before returning from sys.module
2023-10-04 22:32:53 -07:00
0f4f2dd683
also list linkml versions in the available versions for a pydantic provider
2023-10-04 22:27:36 -07:00
d46e86c676
return None when the module actually doesn't exist
2023-10-04 22:08:01 -07:00
5438b2489b
Fix relative imports in ectopic models --
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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
3b11afded6
fix truncate hdf5 file to not try and write while iterating
2023-10-04 20:19:54 -07:00
ab63ea071c
removing pandas
2023-10-04 18:02:40 -07:00
9947edfed2
Removing DataFrame type from imports, leaving as stub
2023-10-04 17:59:10 -07:00
f682105c1a
it working
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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
34f8969fa9
Like 15 validation errors away from fully reading a file.
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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
eca7a5ec2e
Correct schema for hdf5 path type
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dont double MRO for basemodels in generated dynamictable
2023-09-28 17:58:45 -07:00
6bbf56d1a0
Make all maps exclusive
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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
9fcc1458fb
nearing the end - need to do final top-level packing but we're almost there!
2023-09-27 01:19:10 -07:00
a2da236b2b
Regenerate models
2023-09-26 21:33:14 -07:00
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
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
d16b4757e1
Use dask instead of trying to make a dataframe
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compress arrays when serializing to json
2023-09-26 19:50:49 -07:00
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.
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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
ce75dacf93
autogenerating models for dynamictable
2023-09-23 01:33:28 -07:00
57fa3d34a2
pandas dataframe mimic
2023-09-23 00:08:59 -07:00
aac0c7abdd
need 2 stop for the night but its sort of happening
2023-09-22 02:48:40 -07:00
40984a6582
figuring out the strategy here...
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- 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
321740f674
weird python relative import error from not having version naming
2023-09-15 01:06:50 -07:00
1f61dca46f
weird python relative import error from not having version naming
2023-09-15 01:03:40 -07:00
94c204e8ea
ok but really actually correct paths
2023-09-15 00:53:07 -07:00
b283e8b0bf
get correct path for provider
2023-09-15 00:50:16 -07:00
ccf267babd
regenerating models, some minor code cleanup and coverage omissions
2023-09-15 00:37:20 -07:00
3e2e6915cf
Add ability to make JSON schema with numpy arrays!
2023-09-14 23:43:00 -07:00
e6a41415f5
successfully building many versions of nwb schema.
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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
32f81fd409
more toctree limiting?
2023-09-11 22:26:15 -07:00
054ca8fd5e
add monkeypatch to schemaview
2023-09-11 22:23:42 -07:00
6ff7e6baab
correct docs toctree depth so homepage isn't so hectic
2023-09-11 19:57:29 -07:00
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
c69cbdfb38
Docstrings and basic tests for providers.
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bugfix - remove redundant language elements that cause a recursion error (eg. subtyping "float" with "float")
2023-09-11 19:38:29 -07:00
2e87fa0556
working generation from provider
2023-09-08 19:46:42 -07:00
0b0fb6c67a
cute progress bar and also linkml provider works
2023-09-08 16:12:19 -07:00
d15ba8e2e1
fixing docs build
2023-09-07 19:58:38 -07:00
0cc1dbd862
fixing docs build
2023-09-07 19:53:12 -07:00
42ac8e6d7b
fixing docs build
2023-09-07 19:48:58 -07:00
43f35c50d8
fixing docs build
2023-09-07 19:39:19 -07:00
75b710c3eb
docs!
2023-09-07 19:32:17 -07:00
a01bb49b1e
working on providers to cache generated models
2023-09-07 18:50:50 -07:00
