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.
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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
