Transformations (#30)

* start axis transposition

* fix implementation of axis transposition

* fix a few type errors

* use literal set constructor

* use hatch

* version tweaks

* adjust project description

* tweaks to pyproject.toml

* update test workflow to use hatch

* remove linting action

* add pip listing explicitly

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/workflows/ci.yaml

@@ -4,32 +4,28 @@ on:
   pull_request:
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-      - uses: abatilo/actions-poetry@v2
-      - run: poetry install
-      - run: poetry run pre-commit run --all-files
-
   test:
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version:
-          - "3.9"
-          - "3.10"
-          - "3.10"
-          - "3.12"
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      name: py=${{ matrix.python-version }}
+      runs-on: ubuntu-latest
+      strategy:
+        matrix:
+          python-version: ['3.9', '3.10', '3.11']
+      steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: abatilo/actions-poetry@v2
-      - run: poetry install
-      - run: poetry run pytest --verbose --cov src/pydantic_ome_ngff
+          cache: 'pip'
+      - name: Install Hatch
+        run: |
+          python -m pip install --upgrade pip 
+          pip install hatch
+      - name: Set Up Hatch Env
+        run: |
+          hatch env create test.py${{ matrix.python-version }}
+          hatch env run -e test.py${{ matrix.python-version }} pip list
+      - name: Run Tests
+        run: |
+          hatch env run --env test.py${{ matrix.python-version }} run
+

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 # Pyre type checker
 .pyre/
 .vscode/settings.json
+
+# version file
+src/pydantic_ome_ngff/_version.py

docs/index.md

@@ -467,7 +467,7 @@ except ValidationError as e:
     """
     1 validation error for Group
       Value error, Dataset s0 was specified in multiscale metadata, but no array with that name was found in the hierarchy. All arrays referenced in multiscale metadata must be contained in the group. [type=value_error, input_value={'zarr_version': 2, 'attr...: 'zstd', 'level': 3}}}}, input_type=dict]
-        For further information visit https://errors.pydantic.dev/2.6/v/value_error
+        For further information visit https://errors.pydantic.dev/2.7/v/value_error
     """
 
 group_model_wrong_array = group_model.model_dump()
@@ -482,6 +482,6 @@ except ValidationError as e:
     """
     1 validation error for Group
       Value error, Transform type='scale' scale=(1, 1) has dimensionality 2, which does not match the dimensionality of the array found in this group at s0 (1). Transform dimensionality must match array dimensionality. [type=value_error, input_value={'zarr_version': 2, 'attr...: 'zstd', 'level': 3}}}}, input_type=dict]
-        For further information visit https://errors.pydantic.dev/2.6/v/value_error
+        For further information visit https://errors.pydantic.dev/2.7/v/value_error
     """
 ```

pyproject.toml

@@ -1,35 +1,93 @@
-[tool.poetry]
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
 name = "pydantic-ome-ngff"
-version = "0.5.0"
-description = "Pydantic models for the OME-NGFF"
-authors = ["Davis Vann Bennett <[email protected]>"]
-license = "MIT"
+dynamic = ["version"]
+description = "Pydantic models for the OME-NGFF file format."
 readme = "README.md"
-packages = [{include = "pydantic_ome_ngff", from="src"}]
+requires-python = ">=3.9"
+license = "MIT"
+keywords = ["ngff", "pydantic", "ome-ngff", "zarr"]
+authors = [
+  { name = "Davis Vann Benntt", email = "[email protected]" },
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: Implementation :: CPython",
+]
+dependencies = [
+  "pydantic-zarr == 0.7.0"
+]
 
-[tool.poetry.dependencies]
-python = "^3.9"
-pydantic-zarr = "0.7.0"
+[project.urls]
+Documentation = "https://janeliascicomp.github.io/pydantic-ome-ngff"
+Issues = "https://github.com/janeliascicomp/pydantic-ome-ngff/issues"
+Source = "https://github.com/janeliascicomp/pydantic-ome-ngff"
 
-[tool.poetry.group.dev.dependencies]
-pre-commit = "^3.0.4"
-isort = "^5.12.0"
-jsonschema = "^4.17.3"
-pytest = "^7.2.1"
-mypy = "^1.0.1"
-requests = "^2.28.2"
-pytest-cov = "^4.0.0"
-fsspec = {version = "^2024.2.0", extras=["http"]}
+[tool.hatch]
+version.source = "vcs"
+build.hooks.vcs.version-file = "src/pydantic_ome_ngff/_version.py"
 
+[tool.hatch.envs.test]
+dependencies = [
+  "pytest==8.0.0",
+  "pytest-examples==0.0.9",
+  "fsspec[http]==2024.2.0",
+  "requests==2.32.3",
+  "pytest-cov==5.0.0",
+  "jsonschema==4.17.3"
+  ]
 
-[tool.poetry.group.docs.dependencies]
-mkdocs-material = "^9.5.5"
-mkdocstrings = {extras = ["python"], version = "^0.24.0"}
-pytest-examples = "^0.0.9"
+[tool.hatch.envs.test.scripts]
+run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov=tests"
+run = "run-coverage --no-cov"
+run-verbose = "run-coverage --verbose"
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[[tool.hatch.envs.test.matrix]]
+python = ["3.9", "3.10", "3.11"]
+
+[tool.hatch.envs.types]
+extra-dependencies = [
+  "mypy>=1.0.0",
+]
+
+[tool.hatch.envs.types.scripts]
+check = "mypy --install-types --non-interactive {args:src/pydantic_ome_ngff tests}"
+
+[tool.hatch.env.docs]
+dependencies = [
+  "mkdocs-material==9.5.5",
+  "mkdocstrings==0.24.0"
+  ]
+
+[tool.hatch.envs.docs.scripts]
+serve = "mkdocs serve --watch=src"
+
+[tool.coverage.run]
+source_pkgs = ["pydantic_ome_ngff", "tests"]
+branch = true
+parallel = true
+omit = [
+  "src/pydantic_ome_ngff/__about__.py",
+]
+
+[tool.coverage.paths]
+pydantic_ome_ngff = ["src/pydantic_ome_ngff", "*/pydantic-ome-ngff/src/pydantic_ome_ngff"]
+tests = ["tests", "*/pydantic-ome-ngff/tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+  "no cov",
+  "if __name__ == .__main__.:",
+  "if TYPE_CHECKING:",
+]
 
 [tool.mypy]
 plugins = [
@@ -50,32 +108,4 @@ disallow_untyped_defs = true
 init_forbid_extra = true
 init_typed = true
 warn_required_dynamic_aliases = true
-warn_untyped_fields = true
-
-
-[tool.coverage.run]
-source = ['src']
-branch = true
-context = '${CONTEXT}'
-
-[tool.coverage.report]
-precision = 2
-exclude_lines = [
-    'pragma: no cover',
-    'raise NotImplementedError',
-    'if TYPE_CHECKING:',
-    'if typing.TYPE_CHECKING:',
-    '@overload',
-    '@typing.overload',
-    '\(Protocol\):$',
-    'typing.assert_never',
-    'assert_never',
-]
-
-[tool.coverage.paths]
-source = [
-    'src/'
-]
-
-[tool.coverage.html]
-directory = "htmlcov"
+warn_untyped_fields = true

src/pydantic_ome_ngff/__init__.py

@@ -1,3 +0,0 @@
-from importlib.metadata import version as _version
-
-__version__ = _version(__name__)

src/pydantic_ome_ngff/latest/base.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:

src/pydantic_ome_ngff/latest/multiscale.py

@@ -1,7 +1,9 @@
 from __future__ import annotations
+
 from typing import Literal
-from pydantic_ome_ngff.latest.base import version
+
 import pydantic_ome_ngff.v04.multiscale as msv04
+from pydantic_ome_ngff.latest.base import version
 
 
 class Dataset(msv04.Dataset):
@@ -20,8 +22,6 @@ class Dataset(msv04.Dataset):
         The coordinate transformations for this image.
     """
 
-    ...
-
 
 class MultiscaleMetadata(msv04.MultiscaleMetadata):
     """

src/pydantic_ome_ngff/latest/transform.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
+
 from typing import Union
+
 import pydantic_ome_ngff.v04.transform as tx
 
 
@@ -9,44 +11,34 @@ class Identity(tx.Identity):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
-    ...
-
 
 class PathScale(tx.PathScale):
     """ "
     A coordinateTransform with at "path" field.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
-    ...
-
 
 class PathTranslation(tx.PathTranslation):
     """ "
     A coordinateTransform with at "path" field.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
-    ...
-
 
 class VectorTranslation(tx.VectorTranslation):
     """
     A translation transform with a `translate` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
-    ...
-
 
 class VectorScale(tx.VectorScale):
     """
     A scale transform with a `scale` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
-    ...
-
 
 Scale = Union[VectorScale, PathScale]
 Translation = Union[VectorTranslation, PathTranslation]

src/pydantic_ome_ngff/latest/well.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.v04.well import WellMetadata as WellMetaV04
 

src/pydantic_ome_ngff/utils.py

@@ -1,14 +1,15 @@
 from __future__ import annotations
-from typing import TYPE_CHECKING, runtime_checkable
+
 from collections import Counter
-from typing import Protocol
+from typing import TYPE_CHECKING, Protocol, runtime_checkable
+
 import numpy as np
 
 if TYPE_CHECKING:
-    from typing import Dict, Iterable, Hashable, Tuple, Any
+    from typing import Any, Hashable, Iterable
 
 
-def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
+def duplicates(values: Iterable[Hashable]) -> dict[Hashable, int]:
     """
     Takes a sequence of hashable elements and returns a dict where the keys are the
     elements of the input that occurred at least once, and the values are the
@@ -20,13 +21,13 @@ def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
 
 @runtime_checkable
 class ArrayLike(Protocol):
-    shape: Tuple[int, ...]
+    shape: tuple[int, ...]
     dtype: np.dtype[Any]
 
 
 @runtime_checkable
 class ChunkedArrayLike(ArrayLike, Protocol):
-    chunks: Tuple[int, ...]
+    chunks: tuple[int, ...]
 
 
 def listify_numpy(data: Any) -> Any:

src/pydantic_ome_ngff/v04/__init__.py

@@ -1,10 +1,10 @@
 from pydantic_ome_ngff.v04.axis import Axis
-from pydantic_ome_ngff.v04.transform import Transform
-from pydantic_ome_ngff.v04.multiscale import MultiscaleMetadata
+from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.label import ImageLabel
-from pydantic_ome_ngff.v04.well import WellMetadata
+from pydantic_ome_ngff.v04.multiscale import MultiscaleMetadata
 from pydantic_ome_ngff.v04.plate import PlateMetadata
-from pydantic_ome_ngff.v04.base import version
+from pydantic_ome_ngff.v04.transform import Transform
+from pydantic_ome_ngff.v04.well import WellMetadata
 
 __all__ = [
     "Axis",