Add classes to query and slice the tiledb objects (#3)

Update tests, documentation

.pre-commit-config.yaml

@@ -18,18 +18,18 @@ repos:
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
 - repo: https://github.com/PyCQA/docformatter
-  rev: master
+  rev: eb1df347edd128b30cd3368dddc3aa65edcfac38
   hooks:
     - id: docformatter
       additional_dependencies: [tomli]
       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
       # --config, ./pyproject.toml
 
-- repo: https://github.com/psf/black
-  rev: 24.8.0
-  hooks:
-  - id: black
-    language_version: python3
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.

README.md

@@ -67,17 +67,17 @@ garr.build_genomicarray(
      files=bw_files,
      output_path=tempdir,
      features=features,
-     # agg function to summarize mutiple values 
+     # agg function to summarize mutiple values
      # from bigwig within an input feature interval.
-     feature_annotation_options=garr.FeatureAnnotationOptions( 
+     feature_annotation_options=garr.FeatureAnnotationOptions(
         aggregate_function = np.nanmean
      ),
      # for parallel processing multiple bigwig files
-     num_threads=4 
+     num_threads=4
 )
 ```
 
-The build process stores missing intervals from a bigwig file as `np.nan`. The 
+The build process stores missing intervals from a bigwig file as `np.nan`. The
 default is to choose an aggregate functions that works with `np.nan`.
 
 

pyproject.toml

@@ -7,3 +7,18 @@ build-backend = "setuptools.build_meta"
 # For smarter version schemes and other configuration options,
 # check out https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
+
+[tool.ruff]
+line-length = 120
+src = ["src"]
+exclude = ["tests"]
+extend-ignore = ["F821"]
+
+[tool.ruff.pydocstyle]
+convention = "google"
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+
+[tool.black]
+force-exclude = "__init__.py"

setup.cfg

@@ -5,7 +5,7 @@
 
 [metadata]
 name = GenomicArrays
-description = Genomic region based arrays backed by TileDB 
+description = Genomic region based arrays backed by TileDB
 author = Jayaram Kancherla
 author_email = [email protected]
 license = MIT

setup.py

@@ -1,10 +1,8 @@
-"""
-    Setup file for GenomicArrays.
-    Use setup.cfg to configure your project.
+"""Setup file for GenomicArrays. Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.6.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.6.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 
 from setuptools import setup