Merge pull request #104 from ckmah/spatialdata_refactor

[BPT-155] Spatial Data Refactor

README.md

@@ -2,6 +2,7 @@
 [![PyPI version](https://badge.fury.io/py/bento-tools.svg)](https://badge.fury.io/py/bento-tools)
 [![codecov](https://codecov.io/gh/ckmah/bento-tools/branch/master/graph/badge.svg?token=XVHDKNDCDT)](https://codecov.io/gh/ckmah/bento-tools)
 [![Documentation Status](https://readthedocs.org/projects/bento-tools/badge/?version=latest)](https://bento-tools.readthedocs.io/en/latest/?badge=latest)
+[![Downloads](https://static.pepy.tech/badge/bento-tools)](https://pepy.tech/project/bento-tools)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/bento-tools)
 [![GitHub stars](https://badgen.net/github/stars/ckmah/bento-tools)](https://GitHub.com/Naereen/ckmah/bento-tools) 
 

bento/__init__.py

@@ -1,10 +1,7 @@
-from ._settings import settings
-
-from . import datasets as ds
 from . import io
 from . import plotting as pl
 from . import tools as tl
 from . import _utils as ut
 from . import geometry as geo
+from . import query as qy
 from .plotting import _colors as colors
-from ._utils import sync

bento/_constants.py

@@ -1,18 +1,3 @@
 PATTERN_COLORS = ["#17becf", "#1f77b4", "#7f7f7f", "#ff7f0e", "#d62728"]
 PATTERN_NAMES = ["cell_edge", "cytoplasmic", "none", "nuclear", "nuclear_edge"]
 PATTERN_PROBS = [f"{p}_p" for p in PATTERN_NAMES]
-PATTERN_FEATURES = [
-    "cell_inner_proximity",
-    "nucleus_inner_proximity",
-    "nucleus_outer_proximity",
-    "cell_inner_asymmetry",
-    "nucleus_inner_asymmetry",
-    "nucleus_outer_asymmetry",
-    "l_max",
-    "l_max_gradient",
-    "l_min_gradient",
-    "l_monotony",
-    "l_half_radius",
-    "point_dispersion_norm",
-    "nucleus_dispersion_norm",
-]