From f51ce487205f9ab7e777b77d823fae3191ace69c Mon Sep 17 00:00:00 2001 From: keviny2 Date: Fri, 25 Apr 2025 14:23:07 -0700 Subject: [PATCH] Make module names all lowercase --- src/spatialexperiment/__init__.py | 4 ++-- src/spatialexperiment/_combineutils.py | 3 +-- src/spatialexperiment/_imgutils.py | 2 +- src/spatialexperiment/_initutils.py | 2 +- src/spatialexperiment/io/tenx_visium.py | 2 +- .../{SpatialExperiment.py => spatialexperiment.py} | 2 +- src/spatialexperiment/{SpatialImage.py => spatialimage.py} | 0 tests/test_get_img.py | 2 +- tests/test_img_raster.py | 6 +++--- tests/test_img_source.py | 6 +++--- tests/test_spi.py | 4 ++-- 11 files changed, 16 insertions(+), 17 deletions(-) rename src/spatialexperiment/{SpatialExperiment.py => spatialexperiment.py} (99%) rename src/spatialexperiment/{SpatialImage.py => spatialimage.py} (100%) diff --git a/src/spatialexperiment/__init__.py b/src/spatialexperiment/__init__.py index e31286f..de0c505 100644 --- a/src/spatialexperiment/__init__.py +++ b/src/spatialexperiment/__init__.py @@ -16,8 +16,8 @@ del version, PackageNotFoundError from .io import read_tenx_visium -from .SpatialExperiment import SpatialExperiment -from .SpatialImage import ( +from .spatialexperiment import SpatialExperiment +from .spatialimage import ( LoadedSpatialImage, RemoteSpatialImage, StoredSpatialImage, diff --git a/src/spatialexperiment/_combineutils.py b/src/spatialexperiment/_combineutils.py index 51233eb..0ff2805 100644 --- a/src/spatialexperiment/_combineutils.py +++ b/src/spatialexperiment/_combineutils.py @@ -7,7 +7,6 @@ from biocframe import BiocFrame import biocutils as ut -from spatialexperiment import SpatialExperiment def _append_indices_to_samples(bframes: List[BiocFrame]) -> List[BiocFrame]: @@ -30,7 +29,7 @@ def _append_indices_to_samples(bframes: List[BiocFrame]) -> List[BiocFrame]: return modified_bframes -def merge_spatial_frames(x: List[SpatialExperiment], relaxed: bool = False) -> Tuple[BiocFrame, BiocFrame]: +def merge_spatial_frames(x: List["SpatialExperiment"], relaxed: bool = False) -> Tuple[BiocFrame, BiocFrame]: """Merge column data and image data from multiple ``SpatialExperiment`` objects. If duplicate sample IDs exist across objects, appends indices to make them unique. diff --git a/src/spatialexperiment/_imgutils.py b/src/spatialexperiment/_imgutils.py index 36dcea7..6d47b0c 100644 --- a/src/spatialexperiment/_imgutils.py +++ b/src/spatialexperiment/_imgutils.py @@ -7,7 +7,7 @@ import numpy as np from PIL import Image from biocframe import BiocFrame -from .SpatialImage import construct_spatial_image_class +from .spatialimage import construct_spatial_image_class __author__ = "keviny2" __copyright__ = "keviny2" diff --git a/src/spatialexperiment/_initutils.py b/src/spatialexperiment/_initutils.py index e1fe0b5..2f794af 100644 --- a/src/spatialexperiment/_initutils.py +++ b/src/spatialexperiment/_initutils.py @@ -3,7 +3,7 @@ from biocframe import BiocFrame from PIL import Image -from .SpatialImage import construct_spatial_image_class +from .spatialimage import construct_spatial_image_class from summarizedexperiment._frameutils import _sanitize_frame __author__ = "keviny2" diff --git a/src/spatialexperiment/io/tenx_visium.py b/src/spatialexperiment/io/tenx_visium.py index cf76b58..43c3855 100644 --- a/src/spatialexperiment/io/tenx_visium.py +++ b/src/spatialexperiment/io/tenx_visium.py @@ -9,7 +9,7 @@ from biocframe import BiocFrame import biocutils as ut from singlecellexperiment import read_tenx_mtx -from ..SpatialExperiment import SpatialExperiment +from ..spatialexperiment import SpatialExperiment from .._imgutils import construct_img_data from .._initutils import construct_spatial_coords_from_names diff --git a/src/spatialexperiment/SpatialExperiment.py b/src/spatialexperiment/spatialexperiment.py similarity index 99% rename from src/spatialexperiment/SpatialExperiment.py rename to src/spatialexperiment/spatialexperiment.py index b364cdc..31f2cf0 100644 --- a/src/spatialexperiment/SpatialExperiment.py +++ b/src/spatialexperiment/spatialexperiment.py @@ -29,7 +29,7 @@ _validate_spatial_coords, _validate_spatial_coords_names, ) -from .SpatialImage import VirtualSpatialImage, construct_spatial_image_class +from .spatialimage import VirtualSpatialImage, construct_spatial_image_class __author__ = "keviny2" __copyright__ = "keviny2" diff --git a/src/spatialexperiment/SpatialImage.py b/src/spatialexperiment/spatialimage.py similarity index 100% rename from src/spatialexperiment/SpatialImage.py rename to src/spatialexperiment/spatialimage.py diff --git a/tests/test_get_img.py b/tests/test_get_img.py index 6da0bc1..9b31411 100644 --- a/tests/test_get_img.py +++ b/tests/test_get_img.py @@ -2,7 +2,7 @@ from copy import deepcopy import numpy as np -from spatialexperiment.SpatialImage import VirtualSpatialImage +from spatialexperiment import VirtualSpatialImage __author__ = "keviny2" __copyright__ = "keviny2" diff --git a/tests/test_img_raster.py b/tests/test_img_raster.py index c53d153..0b67505 100644 --- a/tests/test_img_raster.py +++ b/tests/test_img_raster.py @@ -2,11 +2,11 @@ from copy import deepcopy from PIL import Image import numpy as np -from spatialexperiment import construct_spatial_image_class -from spatialexperiment.SpatialImage import ( +from spatialexperiment import ( LoadedSpatialImage, StoredSpatialImage, - RemoteSpatialImage + RemoteSpatialImage, + construct_spatial_image_class ) def test_loaded_spatial_image_img_raster(): diff --git a/tests/test_img_source.py b/tests/test_img_source.py index 4346924..aebe2ab 100644 --- a/tests/test_img_source.py +++ b/tests/test_img_source.py @@ -3,11 +3,11 @@ from pathlib import Path from PIL import Image import numpy as np -from spatialexperiment import construct_spatial_image_class -from spatialexperiment.SpatialImage import ( +from spatialexperiment import ( LoadedSpatialImage, StoredSpatialImage, - RemoteSpatialImage + RemoteSpatialImage, + construct_spatial_image_class ) def test_loaded_spatial_image_img_source(): diff --git a/tests/test_spi.py b/tests/test_spi.py index f5a8ad4..fd8f2bf 100644 --- a/tests/test_spi.py +++ b/tests/test_spi.py @@ -1,11 +1,11 @@ import pytest from PIL import Image -from spatialexperiment import construct_spatial_image_class -from spatialexperiment.SpatialImage import ( +from spatialexperiment import ( VirtualSpatialImage, StoredSpatialImage, LoadedSpatialImage, RemoteSpatialImage, + construct_spatial_image_class ) __author__ = "keviny2"