Remove hard scvi-tools dependency

.github/workflows/ci.yml

@@ -45,7 +45,7 @@ jobs:
             fail-fast: false
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.9, "3.10"]
+                python-version: ["3.9", "3.10"]
         steps:
             - uses: actions/checkout@v2
             - name: Set up Python ${{ matrix.python-version }}

pyproject.toml

@@ -50,11 +50,13 @@ dependencies = [
     "pandas>=1.1.1, !=1.4.0",
     "scipy>=1.4.1",
     "scikit-learn>=0.21.2, <1.2.0",
-    "scvi-tools>=0.20.1",
     "matplotlib>=3.3.0"
 ]
 
 [project.optional-dependencies]
+vi = [
+    "scvi-tools>=0.20.1",
+]
 louvain = [
     "igraph",
     "louvain"
@@ -78,7 +80,8 @@ dev = [
     "pybind11",
     "pytest-cov",
     "igraph",
-    "setuptools_scm"
+    "scvi-tools>=0.20.1",
+    "setuptools_scm",
 ]
 docs = [
     # Just until rtd.org understands pyproject.toml

scvelo/tools/__init__.py

@@ -1,3 +1,5 @@
+import contextlib
+
 from scanpy.tools import diffmap, dpt, louvain, tsne, umap
 
 from ._em_model import ExpectationMaximizationModel
@@ -11,7 +13,6 @@
     recover_latent_time,
 )
 from ._steady_state_model import SecondOrderSteadyStateModel, SteadyStateModel
-from ._vi_model import VELOVI
 from .paga import paga
 from .rank_velocity_genes import rank_velocity_genes, velocity_clusters
 from .score_genes_cell_cycle import score_genes_cell_cycle
@@ -23,6 +24,10 @@
 from .velocity_graph import velocity_graph
 from .velocity_pseudotime import velocity_map, velocity_pseudotime
 
+with contextlib.suppress(ImportError):
+    from ._vi_model import VELOVI
+
+
 __all__ = [
     "align_dynamics",
     "differential_kinetic_test",
@@ -54,5 +59,8 @@
     "SteadyStateModel",
     "SecondOrderSteadyStateModel",
     "ExpectationMaximizationModel",
-    "VELOVI",
 ]
+if "VELOVI" in locals():
+    __all__ += ["VELOVI"]
+
+del contextlib