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Use pytorch lightning's seed everything to set seed #1151

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merged 4 commits into from
Sep 28, 2021
Merged

Use pytorch lightning's seed everything to set seed #1151

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c629145
Use seed_everything
mjayasur Sep 9, 2021
260d00f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 9, 2021
4e80584
Lint fix
mjayasur Sep 9, 2021
786684e
Add test for setting seed
mjayasur Sep 28, 2021
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5 changes: 2 additions & 3 deletions scvi/_settings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
from pathlib import Path
from typing import Union

import numpy as np
import pytorch_lightning as pl
import torch
from rich.console import Console
from rich.logging import RichHandler
Expand Down Expand Up @@ -140,10 +140,9 @@ def seed(self) -> int:
@seed.setter
def seed(self, seed: int):
"""Random seed for torch and numpy."""
torch.manual_seed(seed)
torch.backends.cudnn.deterministic = True
torch.backends.cudnn.benchmark = False
np.random.seed(seed)
pl.utilities.seed.seed_everything(seed)
self._seed = seed

@property
Expand Down
18 changes: 18 additions & 0 deletions tests/models/test_lightning.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
import torch

import scvi
from scvi.data import synthetic_iid
from scvi.model import SCVI
from scvi.train._callbacks import SaveBestState
Expand All @@ -9,3 +12,18 @@ def test_save_best_state_callback(save_path):
model = SCVI(adata, n_latent=n_latent)
callbacks = [SaveBestState(verbose=True)]
model.train(3, check_val_every_n_epoch=1, train_size=0.5, callbacks=callbacks)


def test_set_seed(save_path):
scvi.settings.seed = 1
n_latent = 5
adata = synthetic_iid()
model1 = SCVI(adata, n_latent=n_latent)
model1.train(1)
scvi.settings.seed = 1
model2 = SCVI(adata, n_latent=n_latent)
model2.train(1)
assert torch.equal(
model1.module.z_encoder.encoder.fc_layers[0][0].weight,
model2.module.z_encoder.encoder.fc_layers[0][0].weight,
)