Refactor with more extras_require

.coveragerc_omit

@@ -6,7 +6,8 @@ omit =
     vitessce/widget.py
     vitessce/wrappers.py
     vitessce/repr.py
-    vitessce/data_utils/anndata.py
-    vitessce/data_utils/ome.py
-    vitessce/data_utils/entities.py
-    vitessce/data_utils/multivec.py
+    vitessce/data_utils/anndata/anndata.py
+    vitessce/data_utils/multivec/multivec.py
+    vitessce/data_utils/ome_tiff/ome_tiff.py
+    vitessce/data_utils/ome_zarr/ome_zarr.py
+    vitessce/data_utils/ucsc_cellbrowser/ucsc_cellbrowser.py

docs/api_data.rst

@@ -27,7 +27,13 @@ vitessce.export
 vitessce.data_utils
 *****************
 
-.. automodule:: vitessce.data_utils.ome
+.. automodule:: vitessce.data_utils.anndata.anndata
  :members:
-.. automodule:: vitessce.data_utils.anndata
+.. automodule:: vitessce.data_utils.multivec.multivec
+ :members:
+.. automodule:: vitessce.data_utils.ome_tiff.ome_tiff
+ :members:
+.. automodule:: vitessce.data_utils.ome_zarr.ome_zarr
+ :members:
+.. automodule:: vitessce.data_utils.ucsc_cellbrowser.ucsc_cellbrowser
  :members:

pyproject.toml

@@ -79,8 +79,40 @@ testing = []
 linting = []
 notebook = []
 
+# data_utils extras_require
+# These dependencies are required
+# to use the corresponding data_utils sub-packages.
+anndata = [
+  'zarr>=2.5.0',
+  'numcodecs>=0.5.7',
+  'anndata>=0.7.8,<0.9',
+  'scanpy>=1.9.3'
+]
+ome_zarr = [
+  'zarr>=2.5.0',
+  'numcodecs>=0.5.7',
+  'ome-zarr==0.2.1'
+]
+ome_tiff = [
+  'generate-tiff-offsets>=0.1.7',
+  'tifffile>=2020.10.1'
+]
+multivec = [
+  'zarr>=2.5.0',
+  'numcodecs>=0.5.7',
+  'negspy>=0.2.24'
+]
+
 [project.urls]
 repository = "https://github.com/vitessce/vitessce-python"
 
 [tool.setuptools]
-packages = ["vitessce", "vitessce.data_utils"]
+packages = [
+  "vitessce",
+  "vitessce.data_utils",
+  "vitessce.data_utils.anndata",
+  "vitessce.data_utils.multivec",
+  "vitessce.data_utils.ome_tiff",
+  "vitessce.data_utils.ome_zarr",
+  "vitessce.data_utils.ucsc_cellbrowser"
+]

tests/test_anndata_utils.py

@@ -7,11 +7,13 @@
 from scipy.io import mmread
 import zarr
 
-from vitessce.data_utils import (
+from vitessce.data_utils.anndata import (
     optimize_arr,
     optimize_adata,
     sort_var_axis,
     to_uint8,
+)
+from vitessce.data_utils.multivec import (
     adata_to_multivec_zarr,
 )
 

tests/test_config_converter.py

@@ -2,7 +2,7 @@
 from unittest.mock import patch, Mock
 from copy import deepcopy
 
-from vitessce import (
+from vitessce.data_utils.ucsc_cellbrowser import (
     CellBrowserToAnndataZarrConverter,
     convert_cell_browser_project_to_anndata,
 )

tests/test_ome_utils.py

@@ -3,7 +3,7 @@
 import zarr
 import numpy as np
 
-from vitessce.data_utils import (
+from vitessce.data_utils.ome_zarr import (
     rgb_img_to_ome_zarr,
 )
 

vitessce/__init__.py

@@ -21,11 +21,6 @@
     BASE_URL_PLACEHOLDER,
 )
 
-from .config_converter import (
-    CellBrowserToAnndataZarrConverter,  # only exported for testing.
-    convert_cell_browser_project_to_anndata,
-)
-
 from .wrappers import AbstractWrapper
 
 # We allow installation without all of the dependencies that the widget requires.

vitessce/data_utils/__init__.py

@@ -1,18 +0,0 @@
-from .anndata import (
-    optimize_adata,
-    optimize_arr,
-    to_dense,
-    to_uint8,
-    sort_var_axis,
-    to_diamond,
-    VAR_CHUNK_SIZE,
-)
-from .ome import (
-    rgb_img_to_ome_zarr,
-    multiplex_img_to_ome_zarr,
-    rgb_img_to_ome_tiff,
-    multiplex_img_to_ome_tiff,
-)
-from .multivec import (
-    adata_to_multivec_zarr,
-)

vitessce/data_utils/anndata/__init__.py

@@ -0,0 +1,10 @@
+from .anndata import (
+    optimize_adata,
+    optimize_arr,
+    to_dense,
+    to_uint8,
+    sort_var_axis,
+    to_diamond,
+    VAR_CHUNK_SIZE,
+    cast_arr,
+)