Merge pull request #16 from YosefLab/scvi_tools_1.0

Updates for `scvi-tools>=1.0`

Author: adamgayoso

.github/workflows/test.yml

@@ -14,7 +14,7 @@ jobs:
         runs-on: ubuntu-latest
         strategy:
             matrix:
-                python-version: ["3.8", "3.9", "3.10"]
+                python-version: ["3.9", "3.10", "3.11"]
 
         steps:
             - uses: actions/checkout@v2

pyproject.toml

@@ -8,9 +8,9 @@ classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Science/Research",
   "Natural Language :: English",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
   "Operating System :: MacOS :: MacOS X",
   "Operating System :: Microsoft :: Windows",
   "Operating System :: POSIX :: Linux",
@@ -25,7 +25,7 @@ packages = [
   {include = "velovi"},
 ]
 readme = "README.md"
-version = "0.2.1"
+version = "0.3.0"
 
 [tool.poetry.dependencies]
 anndata = ">=0.7.5"
@@ -43,12 +43,12 @@ sphinxcontrib-bibtex = {version = "*", optional = true}
 ipykernel = {version = "*", optional = true}
 pytest = {version = ">=4.4", optional = true}
 pytest-cov = {version = "*", optional = true}
-python = ">=3.8,<4.0"
+python = ">=3.9,<4.0"
 python-igraph = {version = "*", optional = true}
 scanpy = {version = ">=1.6", optional = true}
 scanpydoc = {version = ">=0.5", optional = true}
 scvelo = ">=0.2.5"
-scvi-tools = ">=0.20.1"
+scvi-tools = ">=1.0.0"
 scikit-learn = ">=0.21.2"
 sphinx = {version = ">=4.1", optional = true}
 sphinx-autodoc-typehints = {version = "*", optional = true}

velovi/_model.py

@@ -177,7 +177,6 @@ def train(
             train_size=train_size,
             validation_size=validation_size,
             batch_size=batch_size,
-            use_gpu=use_gpu,
         )
         training_plan = TrainingPlan(self.module, **plan_kwargs)