Merge pull request #189 from scverse/refactoring/modules_hierarcy

Module hierarchy refactoring

Author: LucaMarconato

.flake8

@@ -47,7 +47,7 @@ per-file-ignores =
     tests/*: D
     */__init__.py: F401
     # Ignore for compat checks at top of file
-    spatialdata/__init__.py: E402
+    src/spatialdata/__init__.py: E402
     # TODO: this file is weird, but it's not actually causing a bug and fixing it is
     # signifigantly harder than ignoring it
-    spatialdata/_constants/_enum.py: B024
+    src/spatialdata/_constants/_enum.py: B024

.gitignore

@@ -25,7 +25,6 @@ __pycache__/
 .vscode
 
 # data
-spatialdata-sandbox
 *.zarr/
 
 # temp files
@@ -38,6 +37,8 @@ docs/generated
 napari-spatialdata
 spatialdata-io
 spatialdata-notebooks
+spatialdata-plot
+spatialdata-sandbox
 
 # notebooks
 *.ipynb

.pre-commit-config.yaml

@@ -28,8 +28,8 @@ repos:
       rev: v1.1.1
       hooks:
           - id: mypy
-            additional_dependencies: [numpy==1.24, types-requests]
-            exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
+            additional_dependencies: [numpy, types-requests]
+            exclude: tests/|docs/|temp/
     - repo: https://github.com/asottile/yesqa
       rev: v1.4.0
       hooks: