Misc fixes (#41)

docs/conf.py

@@ -93,9 +93,9 @@
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
-    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
-    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
+    "anndata": ("https://anndata.readthedocs.io/en/stable", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
 }
 
 # List of patterns, relative to source directory, that match files and

pyproject.toml

@@ -7,7 +7,7 @@ name = "ehrdata"
 version = "0.0.1"
 description = "A Python package for EHR data"
 readme = "README.md"
-license = { file = "LICENSE" }
+license = "Apache-2.0"
 maintainers = [
   { name = "Eljas Roellin", email = "[email protected]" },
 ]
@@ -36,7 +36,7 @@ optional-dependencies.dev = [
 ]
 optional-dependencies.doc = [
   "docutils>=0.8,!=0.18.*,!=0.19.*",
-  "ehrapy[lamin]",
+  "ehrdata[lamin]",
   "ipykernel",
   "ipython",
   "myst-nb>=1.1",

src/ehrdata/core/ehrdata.py

@@ -188,10 +188,7 @@ def layers(self, key, input):
     @property
     def r(self):
         """3-Dimensional tensor, aligned with obs along first axis, var along second axis, and allowing a 3rd axis."""
-        if R_LAYER_KEY not in self._adata.layers.keys():
-            return None
-        else:
-            return self._adata.layers[R_LAYER_KEY]
+        return self._adata.layers.get(R_LAYER_KEY)
 
     @r.setter
     def r(self, input):

src/ehrdata/pl/__init__.py

@@ -1 +1,3 @@
+__all__ = ["BasicClass", "basic_plot"]
+
 from .basic import BasicClass, basic_plot