add pre-commit

Author: giovp

.pre-commit-config.yaml

@@ -27,12 +27,3 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
-  - repo: local
-    hooks:
-      - id: forbid-to-commit
-        name: Don't commit rej files
-        entry: |
-          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
-          Fix the merge conflicts manually and remove the .rej files.
-        language: fail
-        files: '.*\.rej$'

pyproject.toml

@@ -51,7 +51,7 @@ dev = [
 docs = [
   'sphinx==4.2.0',
   'sphinx-rtd-theme==1.0.0',
-  
+
   # Pin sub-dependencies of sphinx
   # Reference: https://github.com/sphinx-doc/sphinx/issues/11130
   'sphinxcontrib-applehelp==1.0.4',
@@ -60,7 +60,7 @@ docs = [
   'sphinxcontrib-jsmath==1.0.1',
   'sphinxcontrib-qthelp==1.0.3',
   'sphinxcontrib-serializinghtml==1.1.5',
-  
+
   'nbsphinx==0.8.8',
   'nbclean==0.3.2',
   # Pin sqlalchemy to before 1.4 to fix issue importing nbclean.NotebookCleaner
@@ -99,6 +99,8 @@ packages = ["vitessce", "vitessce.data_utils"]
 [tool.ruff]
 line-length = 120
 src = ["src"]
+exclude = ["docs", "tests", "demos", "binder", "README.md"]
+force-exclude = true
 extend-include = ["*.ipynb"]
 
 [tool.ruff.format]
@@ -153,4 +155,4 @@ convention = "numpy"
 "docs/*" = ["I"]
 "vitessce/constants.py" = ["D"]
 "tests/*" = ["D"]
-"*/__init__.py" = ["F401"]
+"*/__init__.py" = ["F401"]

vitessce/__init__.py

@@ -2,65 +2,62 @@
 from warnings import warn
 
 from .config import (
-    VitessceConfig,
+    CoordinationLevel,
     VitessceChainableConfig,
+    VitessceConfig,
     VitessceConfigDatasetFile,
     hconcat,
     vconcat,
-    CoordinationLevel,
 )
-
-from .utils import (
-    get_initial_coordination_scope_prefix,
-    get_initial_coordination_scope_name,
+from .config_converter import (
+    CellBrowserToAnndataZarrConverter,  # only exported for testing.
+    convert_cell_browser_project_to_anndata,
 )
-
-from .repr import make_repr
-
 from .constants import (
+    BASE_URL_PLACEHOLDER,
     CoordinationType,
-    ViewType,
     DataType,
     FileType,
+    ViewType,
+)
+from .constants import (
     # For backwards compatibility, also export ViewType as Component
     ViewType as Component,
-    BASE_URL_PLACEHOLDER,
 )
-
-from .config_converter import (
-    CellBrowserToAnndataZarrConverter,  # only exported for testing.
-    convert_cell_browser_project_to_anndata,
+from .repr import make_repr
+from .utils import (
+    get_initial_coordination_scope_name,
+    get_initial_coordination_scope_prefix,
 )
-
 from .wrappers import AbstractWrapper
 
 # We allow installation without all of the dependencies that the widget requires.
 # The imports below will fail in that case, and corresponding globals will be undefined.
 try:
     from .widget import VitessceWidget, data_server
 except ModuleNotFoundError as e:  # pragma: no cover
-    warn(f'Extra installs are necessary to use widgets: {e}')
+    warn(f"Extra installs are necessary to use widgets: {e}")
 
 try:
     from .wrappers import (
-        OmeTiffWrapper,
-        OmeZarrWrapper,
-        MultiImageWrapper,
-        CsvWrapper,
         AnnDataWrapper,
-        MultivecZarrWrapper,
+        CsvWrapper,
         ImageOmeTiffWrapper,
-        ObsSegmentationsOmeTiffWrapper,
         ImageOmeZarrWrapper,
+        MultiImageWrapper,
+        MultivecZarrWrapper,
+        ObsSegmentationsOmeTiffWrapper,
         ObsSegmentationsOmeZarrWrapper,
+        OmeTiffWrapper,
+        OmeZarrWrapper,
     )
 except ModuleNotFoundError as e:  # pragma: no cover
-    warn(f'Extra installs are necessary to use wrappers: {e}')
+    warn(f"Extra installs are necessary to use wrappers: {e}")
 
 try:
     from .export import (
-        export_to_s3,
         export_to_files,
+        export_to_s3,
     )
 except ModuleNotFoundError as e:  # pragma: no cover
-    warn(f'Extra installs are necessary to use exports: {e}')
+    warn(f"Extra installs are necessary to use exports: {e}")