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[WIP] container-level validation, add docs #19

Merged
merged 70 commits into from
Mar 27, 2024
Merged

[WIP] container-level validation, add docs #19

merged 70 commits into from
Mar 27, 2024

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d-v-b
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@d-v-b d-v-b commented Feb 12, 2024

  • add pydantic-zarr models of Zarr array and Zarr group for container validation, e.g. checking that dimensional attributes (like number of axes, dimensionality of transforms) are consistent with the shape of the arrays in a multiscale group.
  • this PR also add docs using mkdocs
  • I'm also working on at least one convenience method for creating a model of a multiscale group from a collection of arrays + spatial metadata. this will greatly simplify some of the logic in xarray-ome-ngff

d-v-b added 10 commits June 6, 2023 12:00
@d-v-b
feat: use pydantic-zarr for representing multiscale groups
90507a9
@d-v-b
chore: update type signature of version in latest multiscale, althoug…
7295c26 
…h the version is still untyped. also use conlist for axes.
@d-v-b
feat: update to pydantic 2 / pydantic-zarr 0.5.2
20c4a8c
@d-v-b
feat: pointless renaming
9c72f28
@d-v-b
feat: big refactor: split validators into separate functions, rename …
00ee033 
…transforms, etc
@d-v-b
feat: use python 3.10 as baseline, refactor the test suite a bit, use…
dd469b6 
… inheritance more for the latest classes, start looking at coverage and adjusting things accordingly
@d-v-b
lint
87dad87
@d-v-b
feat: use a tighter module-local name convention for specialized Grou…
ec6649f 
…pSpec instances, and expand ImageLabel metadata
@d-v-b
begin adding docs and convenience function for multiscale creation
4044348
@d-v-b
docs: add mkdocs.yml
845bf4e
@d-v-b d-v-b mentioned this pull request Feb 12, 2024
Closed
d-v-b added 19 commits February 15, 2024 14:04
@d-v-b
merge branch "use_pydantic_zarr" from origin
62ab448
@d-v-b
tighten some names and type annotations
192d6e0
@d-v-b
start handling deeper arrays
7d28336
@d-v-b
flattening and unflattening routines for GroupSpec
601972b
@d-v-b
fix: use tuple instead of list for transforms; defer to pydantic-zarr…
ba81fa0 
… for flattening / unflattening; handle arrays in subgroups when validating multiscale metadata
@d-v-b
chore: add gha
f50108b
@d-v-b
feat: use pydantic-zarr for representing multiscale groups
ae5fb4a
@d-v-b
chore: update type signature of version in latest multiscale, althoug…
64fbfa8 
…h the version is still untyped. also use conlist for axes.
@d-v-b
feat: update to pydantic 2 / pydantic-zarr 0.5.2
45ce1c4
@d-v-b
feat: pointless renaming
41bdf3f
@d-v-b
feat: big refactor: split validators into separate functions, rename …
6dab0a8 
…transforms, etc
@d-v-b
feat: use python 3.10 as baseline, refactor the test suite a bit, use…
fb777cb 
… inheritance more for the latest classes, start looking at coverage and adjusting things accordingly
@d-v-b
lint
02e09ee
@d-v-b
feat: use a tighter module-local name convention for specialized Grou…
675992f 
…pSpec instances, and expand ImageLabel metadata
@d-v-b
begin adding docs and convenience function for multiscale creation
2825b07
@d-v-b
docs: add mkdocs.yml
c502b36
@d-v-b
merge branch "use_pydantic_zarr" from origin
94e08dd
@d-v-b
tighten some names and type annotations
5f7b90d
@d-v-b
start handling deeper arrays
5e2cbbe
d-v-b added 26 commits March 11, 2024 14:23
@d-v-b
dont cast to list
2af58d7
@d-v-b
add multiscale creation example
516d35d
@d-v-b
add chunking to group creation example
c4c1cd7
@d-v-b
simplify array creation in example, and remove incorrect translation
a63fef5
@d-v-b
chore: depluralize module names
a40f2bc
@d-v-b
docs: update docs
7a28df7
@d-v-b
docs: more docs
0214f65
@d-v-b
test: remove unnecessary transform validation logic
8d0e640
@d-v-b
docs: add links, remove unused var from examples
cb86c5d
@d-v-b
bump deps, using latest version of pydantic-zarr
a3e4b4f
@d-v-b
add chunks keyword argument to from_arrays, and corresponding normali…
2923fdd 
…zation function
@d-v-b
add from __future__ imports, and use Union instead of |
f5156b8
@d-v-b
add chunks to from_array tests
b8e55ab
@d-v-b
chore: update lockfile
e6407f7
@d-v-b
chore: add python 3.9 to ci
d80a120
@d-v-b
docs: fix example
26f1fe8
@d-v-b
feat: expand function signature of from_arrays to include compressor,…
d1808e2 
… order, fill value
@d-v-b
feat: use tuples instead of lists
fd0c19a
@d-v-b
update tests for tuples
b5e6ba9
@d-v-b
add validation example
88290a4
@d-v-b
docs
472d75e
@d-v-b
docstring
297338d
@d-v-b
more text about
e7228f7
@d-v-b
chore: bump deps
53fcc82
@d-v-b
test: parametrize test_coordinate_transforms_invalid_ndims
fa3f922
@d-v-b
test: shorten the names of some test functions
9e915f7
@d-v-b
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d-v-b commented Mar 27, 2024

too long has this lingered. it's going in.

@d-v-b d-v-b merged commit 919caad into main Mar 27, 2024
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@d-v-b d-v-b deleted the use_pydantic_zarr branch March 27, 2024 14:48
@d-v-b d-v-b mentioned this pull request Mar 29, 2024
Closed
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