update lightning to >=1.9, bump other minimums, stage 0.20.0b1 (#1863)

* update lightning * bump minimums * remove ray import in init * update installation * bump beta version
scverse · Jan 23, 2023 · 47bf4a5 · 47bf4a5
1 parent 5fe6c4d
commit 47bf4a5
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Showing 5 changed files with 9 additions and 15 deletions.
diff --git a/docs/installation.md b/docs/installation.md
@@ -43,8 +43,8 @@ pip install "jax[cpu]" -f https://whls.blob.core.windows.net/unstable/index.html
 All scvi-tools models will be faster when accelerated with a GPU. Before installing scvi-tools, you can install GPU versions of PyTorch and jax using conda as follows:
 
 ```
-conda install pytorch torchvision torchaudio cudatoolkit=11.6 -c pytorch -c conda-forge
-conda install jax jaxlib cuda-nvcc -c conda-forge -c nvidia
+conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia
+conda install jax jaxlib -c conda-forge
 ```
 
 Please go to the respective package website for more information on how to install with pip.

diff --git a/pyproject.toml b/pyproject.toml
@@ -5,7 +5,7 @@ requires = ["hatchling"]
 
 [project]
 name = "scvi-tools"
-version = "0.20.0b0"
+version = "0.20.0b1"
 description = "Deep probabilistic analysis of single-cell omics data."
 readme = "README.md"
 requires-python = ">=3.8"
@@ -44,11 +44,11 @@ dependencies = [
     "scipy",
     "scikit-learn>=0.21.2",
     "openpyxl>=3.0",
-    "rich>=9.1.0",
+    "rich>=12.0.0",
     "h5py>=2.9.0",
     "torch>=1.8.0",
-    "pytorch-lightning>=1.8.0,<1.9.0",
-    "torchmetrics>=0.6.0",
+    "pytorch-lightning>=1.9.0,<1.10.0",
+    "torchmetrics>=0.11.0",
     "pyro-ppl>=1.6.0",
     "tqdm>=4.56.0",
     "scikit-learn>=0.21.2",

diff --git a/scvi/__init__.py b/scvi/__init__.py
@@ -3,12 +3,6 @@
 # Set default logging handler to avoid logging with logging.lastResort logger.
 import logging
 
-try:
-    # necessary as importing scvi after ray causes kernel crash
-    from ray import tune  # noqa
-except ImportError:
-    pass
-
 from ._constants import REGISTRY_KEYS
 from ._settings import settings
 

diff --git a/scvi/_settings.py b/scvi/_settings.py
@@ -4,7 +4,7 @@
 from typing import Literal, Union
 
 import torch
-from lightning_lite import seed_everything
+from pytorch_lightning import seed_everything
 from rich.console import Console
 from rich.logging import RichHandler
 

diff --git a/scvi/train/_trainer.py b/scvi/train/_trainer.py
@@ -4,7 +4,7 @@
 
 import numpy as np
 import pytorch_lightning as pl
-from pytorch_lightning.loggers import LightningLoggerBase
+from pytorch_lightning.loggers import Logger
 
 from scvi import settings
 from scvi.autotune._types import Tunable, TunableMixin
@@ -103,7 +103,7 @@ def __init__(
         enable_progress_bar: bool = True,
         progress_bar_refresh_rate: int = 1,
         simple_progress_bar: bool = True,
-        logger: Union[Optional[LightningLoggerBase], bool] = None,
+        logger: Union[Optional[Logger], bool] = None,
         log_every_n_steps: int = 10,
         replace_sampler_ddp: bool = False,
         **kwargs,