7c6e69c87e
ruff unsafe fixes
2024-07-01 23:05:47 -07:00
3768e3ce0d
enable black preview and automatic linebreaks in long strings
2024-07-01 22:12:16 -07:00
d4a0c82d00
some ruff fixes
2024-07-01 22:09:49 -07:00
07aa879bb9
ruff automatic fixes
2024-07-01 21:44:35 -07:00
79fc7f23ad
black formatting
2024-07-01 21:23:31 -07:00
1eddf04400
get tests running again
2024-07-01 18:59:21 -07:00
d522dd84a5
merge from origin
2024-07-01 15:46:23 -07:00
4296b27538
catchup with prior work
2024-07-01 15:44:26 -07:00
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
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
dd956b35c3
Still working on docs!
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Added ability to index datasets wtih arrays with getitem
2023-10-18 21:18:02 -07:00
464d95d64d
omfg another one. i'm done
2023-10-12 00:19:40 -07:00
d2185ee1c3
for pydantic provider test by escaping additional bad chars in numpy field name
2023-10-12 00:02:52 -07:00
3101797b0d
don't render jinja template as having a literal "keys" attr instead of item
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also remove unnecessary warnings
2023-10-11 23:28:22 -07:00
fee86135a3
omfg i hate this bug so much if this works i'll be so mad
2023-10-11 22:38:46 -07:00
92b1a6aac0
holy hell it was a TYPE COERCION in the way linkml handles annotations and a version mismatch between CI and local
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https://github.com/linkml/linkml-model/pull/162
2023-10-11 22:30:26 -07:00
0d29ed279f
hold up can this really be the bug
2023-10-11 22:21:44 -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
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
2d1fe3ad96
read is functional again, calling it a night.
2023-10-10 00:12:33 -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
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
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
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
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
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
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
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
...
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.
...
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
