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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

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90507a9
feat: use pydantic-zarr for representing multiscale groups
d-v-b Jun 6, 2023
7295c26
chore: update type signature of version in latest multiscale, althoug…
d-v-b Jun 6, 2023
20c4a8c
feat: update to pydantic 2 / pydantic-zarr 0.5.2
d-v-b Nov 8, 2023
9c72f28
feat: pointless renaming
d-v-b Nov 8, 2023
00ee033
feat: big refactor: split validators into separate functions, rename …
d-v-b Dec 20, 2023
dd469b6
feat: use python 3.10 as baseline, refactor the test suite a bit, use…
d-v-b Jan 1, 2024
87dad87
lint
d-v-b Jan 1, 2024
ec6649f
feat: use a tighter module-local name convention for specialized Grou…
d-v-b Jan 9, 2024
4044348
begin adding docs and convenience function for multiscale creation
d-v-b Feb 4, 2024
845bf4e
docs: add mkdocs.yml
d-v-b Feb 12, 2024
62ab448
merge branch "use_pydantic_zarr" from origin
d-v-b Feb 15, 2024
192d6e0
tighten some names and type annotations
d-v-b Feb 15, 2024
7d28336
start handling deeper arrays
d-v-b Feb 15, 2024
601972b
flattening and unflattening routines for GroupSpec
d-v-b Feb 20, 2024
ba81fa0
fix: use tuple instead of list for transforms; defer to pydantic-zarr…
d-v-b Mar 3, 2024
f50108b
chore: add gha
d-v-b Mar 3, 2024
ae5fb4a
feat: use pydantic-zarr for representing multiscale groups
d-v-b Jun 6, 2023
64fbfa8
chore: update type signature of version in latest multiscale, althoug…
d-v-b Jun 6, 2023
45ce1c4
feat: update to pydantic 2 / pydantic-zarr 0.5.2
d-v-b Nov 8, 2023
41bdf3f
feat: pointless renaming
d-v-b Nov 8, 2023
6dab0a8
feat: big refactor: split validators into separate functions, rename …
d-v-b Dec 20, 2023
fb777cb
feat: use python 3.10 as baseline, refactor the test suite a bit, use…
d-v-b Jan 1, 2024
02e09ee
lint
d-v-b Jan 1, 2024
675992f
feat: use a tighter module-local name convention for specialized Grou…
d-v-b Jan 9, 2024
2825b07
begin adding docs and convenience function for multiscale creation
d-v-b Feb 4, 2024
c502b36
docs: add mkdocs.yml
d-v-b Feb 12, 2024
94e08dd
merge branch "use_pydantic_zarr" from origin
d-v-b Feb 15, 2024
5f7b90d
tighten some names and type annotations
d-v-b Feb 15, 2024
5e2cbbe
start handling deeper arrays
d-v-b Feb 15, 2024
5296cce
flattening and unflattening routines for GroupSpec
d-v-b Feb 20, 2024
9a226ab
fix: use tuple instead of list for transforms; defer to pydantic-zarr…
d-v-b Mar 3, 2024
0887e4a
chore: add gha
d-v-b Mar 3, 2024
81afac6
chore: fix broken tests
d-v-b Mar 3, 2024
07b2e1e
Merge branch 'use_pydantic_zarr' of https://github.com/JaneliaSciComp…
d-v-b Mar 3, 2024
a365bfa
remove redundant ci
d-v-b Mar 3, 2024
0087042
lint
d-v-b Mar 4, 2024
007438b
ci: increment the python version used for linting
d-v-b Mar 4, 2024
8b871f7
chore: use typing_extensions for self import
d-v-b Mar 4, 2024
475ecca
remove extra script
d-v-b Mar 4, 2024
bb349cc
fix: remove support for group_scale and group_translation in Group.fr…
d-v-b Mar 4, 2024
c2a6831
Update pyproject.toml
d-v-b Mar 6, 2024
474e541
Update poetry.lock
d-v-b Mar 6, 2024
ce03791
add doctests, set minimum python version to 3.9
d-v-b Mar 11, 2024
c7d0f3a
handle numpy arrays as arguments to and transforms
d-v-b Mar 11, 2024
2af58d7
dont cast to list
d-v-b Mar 11, 2024
516d35d
add multiscale creation example
d-v-b Mar 11, 2024
c4c1cd7
add chunking to group creation example
d-v-b Mar 11, 2024
a63fef5
simplify array creation in example, and remove incorrect translation
d-v-b Mar 11, 2024
a40f2bc
chore: depluralize module names
d-v-b Mar 12, 2024
7a28df7
docs: update docs
d-v-b Mar 12, 2024
0214f65
docs: more docs
d-v-b Mar 12, 2024
8d0e640
test: remove unnecessary transform validation logic
d-v-b Mar 12, 2024
cb86c5d
docs: add links, remove unused var from examples
d-v-b Mar 20, 2024
a3e4b4f
bump deps, using latest version of pydantic-zarr
d-v-b Mar 20, 2024
2923fdd
add chunks keyword argument to from_arrays, and corresponding normali…
d-v-b Mar 20, 2024
f5156b8
add from __future__ imports, and use Union instead of |
d-v-b Mar 20, 2024
b8e55ab
add chunks to from_array tests
d-v-b Mar 20, 2024
e6407f7
chore: update lockfile
d-v-b Mar 20, 2024
d80a120
chore: add python 3.9 to ci
d-v-b Mar 20, 2024
26f1fe8
docs: fix example
d-v-b Mar 20, 2024
d1808e2
feat: expand function signature of from_arrays to include compressor,…
d-v-b Mar 20, 2024
fd0c19a
feat: use tuples instead of lists
d-v-b Mar 20, 2024
b5e6ba9
update tests for tuples
d-v-b Mar 20, 2024
88290a4
add validation example
d-v-b Mar 20, 2024
472d75e
docs
d-v-b Mar 20, 2024
297338d
docstring
d-v-b Mar 20, 2024
e7228f7
more text about
d-v-b Mar 21, 2024
53fcc82
chore: bump deps
d-v-b Mar 27, 2024
fa3f922
test: parametrize test_coordinate_transforms_invalid_ndims
d-v-b Mar 27, 2024
9e915f7
test: shorten the names of some test functions
d-v-b Mar 27, 2024
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5 changes: 3 additions & 2 deletions .github/workflows/ci.yaml
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Expand Up @@ -10,7 +10,7 @@ jobs:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
with:
python-version: "3.9"
python-version: "3.10"
- uses: abatilo/actions-poetry@v2
- run: poetry install
- run: poetry run pre-commit run --all-files
Expand All @@ -22,7 +22,8 @@ jobs:
python-version:
- "3.9"
- "3.10"
- "3.11"
- "3.10"
- "3.12"
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
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14 changes: 6 additions & 8 deletions .pre-commit-config.yaml
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Expand Up @@ -5,18 +5,16 @@ default_stages: [commit, push]
default_language_version:
python: python3
repos:
- repo: https://github.com/psf/black
rev: 22.12.0
hooks:
- id: black
language_version: python3.9
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.4.0
hooks:
- id: check-yaml
- repo: https://github.com/charliermarsh/ruff-pre-commit
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
rev: 'v0.0.245'
rev: v0.1.8
hooks:
# Run the linter.
- id: ruff
args: [--fix, --exit-non-zero-on-fix]
args: [ --fix ]
# Run the formatter.
- id: ruff-format
3 changes: 0 additions & 3 deletions README.md
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Expand Up @@ -14,9 +14,6 @@ supported metadata models:
`omero` and `bioformats2raw` are not currently supported, but contributions adding
support for those models would be welcome.

Support for container-level validation (i.e., checking that multiscale or coordinate
transformation metadata is compatible with a hierarchical array / group layout) is being added incrementally.

## installation

```bash
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1 change: 1 addition & 0 deletions docs/api/v04/axis.md
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::: pydantic_ome_ngff.v04.axis
1 change: 1 addition & 0 deletions docs/api/v04/label.md
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::: pydantic_ome_ngff.v04.label
1 change: 1 addition & 0 deletions docs/api/v04/multiscale.md
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::: pydantic_ome_ngff.v04.multiscale
1 change: 1 addition & 0 deletions docs/api/v04/plate.md
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::: pydantic_ome_ngff.v04.plate
1 change: 1 addition & 0 deletions docs/api/v04/transform.md
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::: pydantic_ome_ngff.v04.transform
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