Remove hard scvi-tools dependency (#1185)

* Remove hard `scvi-tools` dependency

* Skip VELOVI tests if `scvi-tools` not installed

* Remove `torch` dependency

* Remove unused `skip_file`

.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 +80,7 @@ dev = [
     "pybind11",
     "pytest-cov",
     "igraph",
-    "setuptools_scm"
+    "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

scvelo/tools/_core.py

@@ -1,8 +1,6 @@
 from abc import abstractmethod
 from typing import NamedTuple
 
-import torch
-
 from anndata import AnnData
 
 
@@ -13,8 +11,6 @@ class _REGISTRY_KEYS_NT(NamedTuple):
 
 REGISTRY_KEYS = _REGISTRY_KEYS_NT()
 
-DEFAULT_ACTIVATION_FUNCTION = torch.nn.Softplus()
-
 
 class BaseInference:
     """Base Inference class for all velocity methods."""

scvelo/tools/_vi_module.py

@@ -11,7 +11,9 @@
 from scvi.module.base import auto_move_data, BaseModuleClass, LossOutput
 from scvi.nn import Encoder, FCLayers
 
-from ._core import DEFAULT_ACTIVATION_FUNCTION, REGISTRY_KEYS
+from ._core import REGISTRY_KEYS
+
+DEFAULT_ACTIVATION_FUNCTION = torch.nn.Softplus()
 
 torch.backends.cudnn.benchmark = True
 

tests/tools/test_vi_model.py

@@ -1,7 +1,16 @@
-from scvi.data import synthetic_iid
+import contextlib
+
+import pytest
 
 import scvelo as scv
-from scvelo.tools import VELOVI
+
+with contextlib.suppress(ImportError):
+    from scvi.data import synthetic_iid
+
+    from scvelo.tools import VELOVI
+
+
+_ = pytest.importorskip("scvi")
 
 
 def test_preprocess_data():