Modularize starfish.core.experiment.builder (#1738)

We need to be able to import modules in starfish.core.experiment.builder without slurping in the whole thing.  As it stands, if I add a dependency from starfish.core.imagestack to any module in  starfish.core.experiment.builder, it creates a circular dependency.  This moves the contents of starfish.core.experiment.builder.__init__.py to a standalone module.

The external api (starfish.experiment.builder) is maintained.

Test plan: `make -j lint mypy fast-test`

starfish/core/experiment/builder/structured_formatter.py

@@ -21,7 +21,7 @@
 from slicedimage import ImageFormat, WriterContract
 
 from starfish.core.types import Axes, Coordinates, CoordinateValue, Number
-from . import TileIdentifier, write_irregular_experiment_json
+from .builder import TileIdentifier, write_irregular_experiment_json
 from .inplace import InplaceFetchedTile, InplaceWriterContract
 from .providers import FetchedTile, TileFetcher
 

starfish/core/experiment/builder/test/factories/all_purpose.py

@@ -4,14 +4,16 @@
 import numpy as np
 import slicedimage
 
-from starfish.core.experiment.builder import (
+from starfish.core.types import Axes, Coordinates, CoordinateValue
+from ...builder import (
     build_irregular_image,
-    FetchedTile,
     tile_fetcher_factory,
-    TileFetcher,
     TileIdentifier,
 )
-from starfish.core.types import Axes, Coordinates, CoordinateValue
+from ...providers import (
+    FetchedTile,
+    TileFetcher,
+)
 
 
 class LocationAwareFetchedTile(FetchedTile, metaclass=ABCMeta):

starfish/core/experiment/builder/test/structured_formatter/test_multiple_fov.py

@@ -10,12 +10,12 @@
 from starfish.core.types import Axes, Coordinates, CoordinateValue
 from .util import (
     render_coordinates_to_rows,
-    UniqueTiles,
     write_coordinates_csv,
     write_tile_data,
 )
 from ..factories import unique_data
-from ... import (
+from ..factories.unique_tiles import UniqueTiles
+from ...builder import (
     tile_fetcher_factory,
     TileFetcher,
     TileIdentifier,

starfish/core/experiment/builder/test/structured_formatter/test_single_fov.py

@@ -12,12 +12,12 @@
 from starfish.core.types import Axes, Coordinates, CoordinateValue
 from .util import (
     render_coordinates_to_rows,
-    UniqueTiles,
     write_coordinates_csv,
     write_tile_data,
 )
 from ..factories import unique_data
-from ... import (
+from ..factories.unique_tiles import UniqueTiles
+from ...builder import (
     tile_fetcher_factory,
     TileFetcher,
     TileIdentifier,

starfish/core/experiment/builder/test/structured_formatter/test_tilepath.py

@@ -18,12 +18,12 @@
 from starfish.core.types import Axes, Coordinates, CoordinateValue, Number
 from .util import (
     render_coordinates_to_rows,
-    UniqueTiles,
     write_coordinates_csv,
     write_tile_data,
 )
 from ..factories import unique_data
-from ... import (
+from ..factories.unique_tiles import UniqueTiles
+from ...builder import (
     tile_fetcher_factory,
     TileFetcher,
     TileIdentifier,

starfish/core/experiment/builder/test/structured_formatter/util.py

@@ -9,7 +9,8 @@
 
 from starfish.core.types import Axes, Coordinates, CoordinateValue
 from ..factories import unique_data
-from ... import FetchedTile, TileFetcher, TileIdentifier
+from ...builder import TileFetcher, TileIdentifier
+from ...providers import FetchedTile
 from ...structured_formatter import TILE_COORDINATE_NAMES
 
 

starfish/core/experiment/builder/test/test_inplace.py

@@ -7,12 +7,13 @@
 from skimage.io import imsave
 from slicedimage import ImageFormat
 
-from starfish.core.experiment.builder import FetchedTile, TileFetcher, write_experiment_json
-from starfish.core.experiment.builder.inplace import (
+from starfish.core.types import Axes, Coordinates, CoordinateValue
+from ..builder import write_experiment_json
+from ..inplace import (
     InplaceFetchedTile, InplaceWriterContract,
 )
-from starfish.core.experiment.experiment import Experiment, FieldOfView
-from starfish.core.types import Axes, Coordinates, CoordinateValue
+from ..providers import FetchedTile, TileFetcher
+from ...experiment import Experiment, FieldOfView
 
 
 SHAPE = {Axes.Y: 500, Axes.X: 1390}

starfish/core/experiment/builder/test/test_orderediterator.py

@@ -1,5 +1,5 @@
-from starfish.core.experiment.builder.orderediterator import ordered_iterator
 from starfish.core.types import Axes
+from ..orderediterator import ordered_iterator
 
 
 def test_round_then_ch():

starfish/core/experiment/builder/test/test_small_axis.py

@@ -7,7 +7,7 @@
 from starfish.core.types import Coordinates, CoordinateValue
 from .factories.all_purpose import collection_factory
 from .factories.unique_tiles import UniqueTiles
-from .. import TileIdentifier
+from ..builder import TileIdentifier
 
 
 @pytest.mark.parametrize(

starfish/core/imagestack/test/factories/all_purpose.py

@@ -1,6 +1,6 @@
 from typing import Callable, Collection, Mapping, Optional, Sequence, Tuple, Type
 
-from starfish.core.experiment.builder import TileIdentifier
+from starfish.core.experiment.builder.builder import TileIdentifier
 from starfish.core.experiment.builder.test.factories.all_purpose import (
     collection_factory,
     LocationAwareFetchedTile,

starfish/core/imagestack/test/factories/synthetic_stack.py

@@ -1,5 +1,6 @@
-from starfish.core.experiment.builder import build_image, TileFetcher
+from starfish.core.experiment.builder.builder import build_image
 from starfish.core.experiment.builder.defaultproviders import OnesTile, tile_fetcher_factory
+from starfish.core.experiment.builder.providers import TileFetcher
 from starfish.core.imagestack.imagestack import ImageStack
 from starfish.core.types import Axes
 

starfish/core/imagestack/test/test_coordinates.py

@@ -3,7 +3,8 @@
 import numpy as np
 from slicedimage import ImageFormat
 
-from starfish.core.experiment.builder import FetchedTile, tile_fetcher_factory
+from starfish.core.experiment.builder.builder import tile_fetcher_factory
+from starfish.core.experiment.builder.providers import FetchedTile
 from starfish.types import Axes, Coordinates, CoordinateValue
 from .factories import synthetic_stack
 from .imagestack_test_utils import verify_physical_coordinates

starfish/core/imagestack/test/test_slicedimage_dtype.py

@@ -7,7 +7,7 @@
 from slicedimage import ImageFormat
 
 from starfish.core.errors import DataFormatWarning
-from starfish.core.experiment.builder import FetchedTile, TileFetcher
+from starfish.core.experiment.builder.providers import FetchedTile, TileFetcher
 from starfish.core.types import Axes, Coordinates, CoordinateValue
 from .factories import synthetic_stack
 

starfish/core/test/test_multiprocessing_workflow.py

@@ -6,11 +6,9 @@
 
 from slicedimage import ImageFormat
 
-from starfish.core.experiment.builder import (
-    tile_fetcher_factory,
-    TileFetcher,
-    TileIdentifier,
-)
+from starfish.core.experiment.builder.builder import TileIdentifier
+from starfish.core.experiment.builder.defaultproviders import tile_fetcher_factory
+from starfish.core.experiment.builder.providers import TileFetcher
 from starfish.core.experiment.builder.structured_formatter import format_structured_dataset
 from starfish.core.experiment.builder.test.structured_formatter.util import (
     render_coordinates_to_rows,

starfish/experiment/builder.py

@@ -1,7 +1,7 @@
-from starfish.core.experiment.builder import (   # noqa: F401
+from starfish.core.experiment.builder import inplace  # noqa: F401
+from starfish.core.experiment.builder.builder import (   # noqa: F401
     build_image,
     build_irregular_image,
-    inplace,
     TileIdentifier,
     write_experiment_json,
     write_irregular_experiment_json,