Merge pull request #105 from ckmah/v2.1

V2.1

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os : [ubuntu-22.04, macos-11, macos-12, windows-2019]
-        python-version: ['3.8', '3.9']
+        python-version: ['3.9', '3.10']
     steps:
     - uses: actions/[email protected]
     - name: Set up Python ${{ matrix.python-version }}

.gitignore

@@ -134,8 +134,13 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+tests/img
 docs/build.zip
 tests/data/processed/data.pt
 tests/data/processed/pre_filter.pt
 tests/data/processed/pre_transform.pt
 .DS_Store
+
+requirements.lock
+requirements-dev.lock

.readthedocs.yml

@@ -1,10 +1,11 @@
 version: 2
 build:
-  image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
 sphinx:
   configuration: docs/source/conf.py
 python:
-  version: 3.8
   install:
   - method: pip
     path: .

bento/__init__.py

@@ -1,8 +1,7 @@
-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 plotting as pl
+from . import tools as tl
+from . import datasets as ds
+from . import io
 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",
-]