legacy code to port

.gitignore

@@ -25,3 +25,4 @@ __pycache__/
 
 # data
 spatialdata-sandbox
+*.zarr

.pre-commit-config.yaml

@@ -7,11 +7,11 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 22.6.0
+      rev: 22.8.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v2.7.1
+      rev: v3.0.0-alpha.0
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
@@ -23,7 +23,7 @@ repos:
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.971
+      rev: v0.981
       hooks:
           - id: mypy
             additional_dependencies: [numpy==1.22.0, types-requests]
@@ -50,7 +50,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/myint/autoflake
-      rev: v1.4
+      rev: v1.6.1
       hooks:
           - id: autoflake
             args:
@@ -70,7 +70,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v2.37.3
+      rev: v2.38.2
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]

spatialdata/__init__.py

@@ -2,5 +2,42 @@
 
 __version__ = version("spatialdata")
 
-from spatialdata._core.spatialdata import SpatialData
-from spatialdata._core.transform import Transform
+__all__ = [
+    "SpatialData",
+    "Identity",
+    "MapIndex",
+    "MapAxis",
+    "Translation",
+    "Scale",
+    "Affine",
+    "Rotation",
+    "Sequence",
+    "Displacements",
+    "Coordinates",
+    "VectorField",
+    "InverseOf",
+    "Bijection",
+    "ByDimension",
+    "compose_transformations",
+    "CoordinateSystem",
+]
+
+from spatialdata._core._spatialdata import SpatialData
+from spatialdata._core.coordinate_system import CoordinateSystem
+from spatialdata._core.transform import (
+    Affine,
+    Bijection,
+    ByDimension,
+    Coordinates,
+    Displacements,
+    Identity,
+    InverseOf,
+    MapAxis,
+    MapIndex,
+    Rotation,
+    Scale,
+    Sequence,
+    Translation,
+    VectorField,
+    compose_transformations,
+)

spatialdata/__main__.py

@@ -0,0 +1,36 @@
+import os
+
+import click
+
+
+@click.command(help="Peek inside the SpatialData .zarr file")
+@click.argument("path", default=False, type=str)
+def peek(path):
+    if not os.path.isdir(path):
+        print(
+            f"Error: .zarr storage not found at {path}. Please specify a valid OME-NGFF spatial data (.zarr) file. "
+            "Example "
+            '"python -m '
+            'spatialdata peek data.zarr"'
+        )
+    else:
+        import spatialdata as sd
+
+        sdata = sd.SpatialData.read(path, filter_table=True)
+        print(sdata)
+
+
+@click.group()
+def cli():
+    pass
+
+
+cli.add_command(peek)
+
+
+def main():
+    cli()
+
+
+if __name__ == "__main__":
+    main()

spatialdata/_core/__init__.py

@@ -1 +1,2 @@
-from spatialdata._core.spatialdata import SpatialData
+from spatialdata._core._spatialdata import SpatialData
+from spatialdata._core.elements import Image, Labels, Points, Polygons