Reorganize dependencies (#481)

This makes some of the heavier ones groups that aren't part of normal
installs

Author: cthoyt

pyproject.toml

@@ -152,11 +152,28 @@ release = [
     "uv",
     "keyring",
 ]
+# note that scispacy currently only works on <= 3.12
+# because of its transitive dependencies. It also has
+# a hard cutoff on scipy because it relied on (private/unstable?)
+# functionality that no longer exists in newer versions
+scispacy = [
+    #"scispacy; python_version <= '3.12'",
+    #"spacy; python_version <= '3.12'",
+    #"scipy<1.11; python_version <= '3.12'",
+]
+pykeen = [
+    "pykeen",
+]
+grape = [
+    "grape",
+    "embiggen",
+    "ensmallen",
+]
 
 # see https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#dependencies-optional-dependencies
 [project.optional-dependencies]
 gilda = [
-    "ssslm[gilda]",
+    "ssslm[gilda-slim]",
 ]
 gilda-slim = [
     "ssslm[gilda-slim]",
@@ -172,23 +189,7 @@ drugcentral =[
 pid = [
     "protmapper",
 ]
-# note that scispacy currently only works on <= 3.12
-# because of its transitive dependencies. It also has
-# a hard cutoff on scipy because it relied on (private/unstable?)
-# functionality that no longer exists in newer versions
-scispacy = [
-    "scispacy; python_version <= '3.12'",
-    "spacy; python_version <= '3.12'",
-    "scipy<1.11; python_version <= '3.12'",
-]
-pykeen = [
-    "pykeen",
-]
-grape = [
-    "grape",
-    "embiggen",
-    "ensmallen",
-]
+
 
 # See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#urls
 # and also https://packaging.python.org/en/latest/specifications/well-known-project-urls/