Merge pull request #799 from theislab/dependency_fix

fix dependencies

.readthedocs.yml

@@ -14,7 +14,7 @@ python:
   install:
     - method: pip
       path: .
-      extra_requirements: [docs]
+      extra_requirements: [docs, neural]
 
 submodules:
   include: [docs/notebooks]

pyproject.toml

@@ -54,7 +54,7 @@ dependencies = [
     "scanpy>=1.9.3",
     "wrapt>=1.13.2",
     "docrep>=0.3.2",
-    "ott-jax[neural]>=0.5.0",
+    "ott-jax>=0.5.0",
     "cloudpickle>=2.2.0",
     "rich>=13.5",
     "docstring_inheritance>=2.0.0",
@@ -70,6 +70,7 @@ neural = [
     "optax",
     "flax",
     "diffrax",
+    "ott-jax[neural]>=0.5.0",
 
 ]
 dev = [
@@ -82,6 +83,7 @@ test = [
     "pytest-mock>=3.5.0",
     "pytest-cov>=4",
     "coverage[toml]>=7",
+    "moscot[neural]"
 ]
 docs = [
     "sphinx>=5.1.1",
@@ -274,7 +276,7 @@ env_list = lint-code,py{3.10,3.11,3.12}
 skip_missing_interpreters = true
 
 [testenv]
-extras = test
+extras = test,neural
 commands =
     python -m pytest {tty:--color=yes} {posargs: \
         --cov={env_site_packages_dir}{/}moscot --cov-config={tox_root}{/}pyproject.toml \
@@ -290,7 +292,7 @@ commands =
 
 [testenv:lint-docs]
 description = Lint the documentation.
-extras = docs
+extras = docs,neural
 ignore_errors = true
 allowlist_externals = make
 pass_env = PYENCHANT_LIBRARY_PATH
@@ -310,7 +312,7 @@ deps =
     jupytext
     nbconvert
     leidenalg
-extras = docs
+extras = docs,neural
 changedir = {tox_root}{/}docs
 commands =
     python -m ipykernel install --user --name=moscot
@@ -328,7 +330,7 @@ commands =
 [testenv:build-docs]
 description = Build the documentation.
 deps =
-extras = docs
+extras = docs,neural
 allowlist_externals = make
 changedir = {tox_root}{/}docs
 commands =