[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

.gitignore

@@ -30,4 +30,4 @@ __pycache__/
 
 Sandbox.ipynb
 test.ipynb
-*.zarr
+*.zarr

.readthedocs.yaml

@@ -1,18 +1,18 @@
 version: 2
 build:
-    os: ubuntu-24.04
-    tools:
-        python: "3.12"
-    commands:
-        - asdf plugin add uv
-        - asdf install uv latest
-        - asdf global uv latest
-        - uv venv
-        - uv pip install .[doc]
-        - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv venv
+    - uv pip install .[doc]
+    - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 sphinx:
-    configuration: docs/conf.py
-    fail_on_warning: false
+  configuration: docs/conf.py
+  fail_on_warning: false
 
 submodules:
-    include: all
+  include: all

CHANGELOG.md

@@ -12,4 +12,4 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
--   Basic tool, preprocessing and plotting functions
+- Basic tool, preprocessing and plotting functions

README.md

@@ -9,6 +9,7 @@ Currently focusing on the following datasets for diversity in testing:
 - `jqmx8`: VisiumHD, Mouse, Intestine
 
 ## Setup vitessce
+
 Currently, the `SpatialDataWrapper` is not yet merged and released. Therefore, we have to install it via
 
 ```bash
@@ -19,10 +20,11 @@ pip install git+https://github.com/vitessce/vitessce-python.git@ig/spatial_data
 from Ilan's PR: https://github.com/vitessce/vitessce-python/pull/333
 
 ## UID logic
+
 - Absolute ID will be a 5 char string of lowercase letters and digits -> 60466176 IDs
 - Leaving out the letters [l, b, o, g, q] due to their similarity to [1, 6, 0, 9, 9] -> 28629151 IDs
 - Reserve ID spaces for technology providers
-  - 10 _ _ _ -> 29791 IDs for 10X Genomics
-  - vg _ _ _ -> 29791 IDs for Vizgen
-  - ns _ _ _ -> 29791 IDs for Nanostring
-  - xx _ _ _ -> 29791 IDs for miscellaneous, such as publication
+  - 10 \_ \_ \_ -> 29791 IDs for 10X Genomics
+  - vg \_ \_ \_ -> 29791 IDs for Vizgen
+  - ns \_ \_ \_ -> 29791 IDs for Nanostring
+  - xx \_ \_ \_ -> 29791 IDs for miscellaneous, such as publication

data/1000j__10X__Visium__Human__large_intestine__20220328__v1.3.0/1000j_to_zarr.py

@@ -1,10 +1,11 @@
 uid = "1000j_"
 
 # CONSTANT
-from spatialdata_io import visium
-import spatialdata as sd
-from pathlib import Path
 import shutil
+from pathlib import Path
+
+import spatialdata as sd
+from spatialdata_io import visium
 
 DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data")
 datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)]
@@ -23,7 +24,7 @@
     path=str(path_read),
     dataset_id="Visium_FFPE_Human_Intestinal_Cancer",
     counts_file=str(path_read / "Visium_FFPE_Human_Intestinal_Cancer_filtered_feature_bc_matrix.h5"),
-    fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"),
+    fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"),
     tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"),
     scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"),
 )
@@ -39,7 +40,7 @@
 ##
 sdata = sd.SpatialData.read(path_write)
 
-with open(dataset_path / f"{dataset_name}.contents", 'w') as file:
+with open(dataset_path / f"{dataset_name}.contents", "w") as file:
     print(sdata, file=file)
 
 print(sdata)

data/1001e__10X__Visium__Mouse__embryo__20230608__v2.1.0/1001e_to_zarr.py

@@ -1,10 +1,11 @@
 uid = "1001e_"
 
 # CONSTANT
-from spatialdata_io import visium
-import spatialdata as sd
-from pathlib import Path
 import shutil
+from pathlib import Path
+
+import spatialdata as sd
+from spatialdata_io import visium
 
 DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data")
 datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)]
@@ -23,7 +24,7 @@
     path=str(path_read),
     dataset_id="CytAssist_11mm_FFPE_Mouse_Embryo",
     counts_file=str(path_read / "CytAssist_11mm_FFPE_Mouse_Embryo_filtered_feature_bc_matrix.h5"),
-    fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"),
+    fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"),
     tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"),
     scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"),
 )
@@ -39,7 +40,7 @@
 ##
 sdata = sd.SpatialData.read(path_write)
 
-with open(dataset_path / f"{dataset_name}.contents", 'w') as file:
+with open(dataset_path / f"{dataset_name}.contents", "w") as file:
     print(sdata, file=file)
 
 print(sdata)

data/10040__10X__Xenium__Human__bone_bone_marrow__20240403__v1.9.0__Non-diseasedBoneMarrow/10040_to_zarr.py

@@ -1,10 +1,11 @@
 uid = "10040_"
 
 # CONSTANT
-from spatialdata_io import xenium
-import spatialdata as sd
-from pathlib import Path
 import shutil
+from pathlib import Path
+
+import spatialdata as sd
+from spatialdata_io import xenium
 
 DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data")
 datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)]
@@ -38,7 +39,7 @@
 ##
 sdata = sd.SpatialData.read(path_write)
 
-with open(dataset_path / f"{dataset_name}.contents", 'w') as file:
+with open(dataset_path / f"{dataset_name}.contents", "w") as file:
     print(sdata, file=file)
 
 print(sdata)

data/10053__10X__Visium__Mouse__brain__20220329__v1.3.0/10053_to_zarr.py

@@ -1,10 +1,11 @@
 uid = "10053_"
 
 # CONSTANT
-from spatialdata_io import visium
-import spatialdata as sd
-from pathlib import Path
 import shutil
+from pathlib import Path
+
+import spatialdata as sd
+from spatialdata_io import visium
 
 DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data")
 datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)]
@@ -23,7 +24,7 @@
     path=str(path_read),
     dataset_id="V1_Adult_Mouse_Brain",
     counts_file=str(path_read / "V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5"),
-    fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"),
+    fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"),
     tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"),
     scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"),
 )
@@ -39,7 +40,7 @@
 ##
 sdata = sd.SpatialData.read(path_write)
 
-with open(dataset_path / f"{dataset_name}.contents", 'w') as file:
+with open(dataset_path / f"{dataset_name}.contents", "w") as file:
     print(sdata, file=file)
 
 print(sdata)

data/10056__10X__Visium__Mouse__brain__20230417__v2.0.1/10056_to_zarr.py

@@ -1,10 +1,11 @@
 uid = "10056_"
 
 # CONSTANT
-from spatialdata_io import visium
-import spatialdata as sd
-from pathlib import Path
 import shutil
+from pathlib import Path
+
+import spatialdata as sd
+from spatialdata_io import visium
 
 DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data")
 datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)]
@@ -23,7 +24,7 @@
     path=str(path_read),
     dataset_id="CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain",
     counts_file=str(path_read / "CytAssist_Fresh_Frozen_Sagittal_Mouse_Brain_filtered_feature_bc_matrix.h5"),
-    fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"),
+    fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"),
     tissue_positions_file=str(path_read / "spatial" / "tissue_positions.csv"),
     scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"),
 )
@@ -39,7 +40,7 @@
 ##
 sdata = sd.SpatialData.read(path_write)
 
-with open(dataset_path / f"{dataset_name}.contents", 'w') as file:
+with open(dataset_path / f"{dataset_name}.contents", "w") as file:
     print(sdata, file=file)
 
 print(sdata)

data/1005m__10X__Visium__Human__prostate__20210609__v1.3.0/1005m_to_zarr.py

@@ -1,10 +1,11 @@
 uid = "1005m_"
 
 # CONSTANT
-from spatialdata_io import visium
-import spatialdata as sd
-from pathlib import Path
 import shutil
+from pathlib import Path
+
+import spatialdata as sd
+from spatialdata_io import visium
 
 DATA_DIR = Path("/lustre/groups/ml01/projects/2024_spatialdata_db/data")
 datasets_with_uid = [DATA_DIR / d.name for d in DATA_DIR.iterdir() if d.is_dir() and uid in str(d.name)]
@@ -23,7 +24,7 @@
     path=str(path_read),
     dataset_id="Visium_FFPE_Human_Normal_Prostate",
     counts_file=str(path_read / "Visium_FFPE_Human_Normal_Prostate_filtered_feature_bc_matrix.h5"),
-    fullres_image_file=str(path_read / "spatial" /"tissue_hires_image.png"),
+    fullres_image_file=str(path_read / "spatial" / "tissue_hires_image.png"),
     tissue_positions_file=str(path_read / "spatial" / "tissue_positions_list.csv"),
     scalefactors_file=str(path_read / "spatial" / "scalefactors_json.json"),
 )
@@ -39,7 +40,7 @@
 ##
 sdata = sd.SpatialData.read(path_write)
 
-with open(dataset_path / f"{dataset_name}.contents", 'w') as file:
+with open(dataset_path / f"{dataset_name}.contents", "w") as file:
     print(sdata, file=file)
 
 print(sdata)