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
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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
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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!
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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
2b530c4b33
don't require warning when at wrong git version
2023-10-09 19:04:00 -07:00
a7b0f8880e
fix tests, cant assign to tuple
2023-10-09 18:59:53 -07:00
6f32a5bfd3
super annoying you have to import all fixtures and dependencies manually
2023-10-09 16:37:07 -07:00
edf7a4c445
[tests] - test adapter + results
2023-10-09 16:33:02 -07:00
0de6535c5a
Schema language v0.1.2 - trivial rebuild to change date to datetime type and update linkml deps
2023-10-09 15:10:29 -07:00
39c600fda1
Regenerate nwb_schema_language models
2023-10-09 15:06:53 -07:00
6da6ef281f
nevermind need to still fix model generation
2023-10-05 22:15:33 -07:00
06311b21bd
[tests] cheap read test
2023-10-05 22:12:27 -07:00
8405ea948a
[tests] ndarray proxy and serialization
2023-10-05 22:05:10 -07:00
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.
...
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
