Umair Khan commited on
Commit
8cb988a
·
1 Parent(s): 6b43a2d

put installation and imports at beginning of app

Browse files
Files changed (1) hide show
  1. app.py +10 -15
app.py CHANGED
@@ -1,14 +1,22 @@
1
- # non-GPU imports
 
 
 
 
2
  import gc
3
- import spaces
4
  import tempfile
 
5
  import gradio as gr
6
  import anndata as ad
7
  import pandas as pd
8
  import numpy as np
9
  import scanpy as sc
10
  from pathlib import Path
 
11
  from omegaconf import OmegaConf as om
 
 
 
12
 
13
  # hardcoded configuration
14
  EMB_KEY = "X_tx1-70m"
@@ -56,21 +64,8 @@ def _save_outputs(adata, emb):
56
  return str(parquet_path), str(out_h5ad)
57
 
58
  # compute embeddings
59
- @spaces.GPU
60
  def _embed(adata_bytes, layer_name, feature_col, batch_size):
61
 
62
- # install package
63
- import os
64
- # os.system("pip install --no-build-isolation flash-attn")
65
- os.system("pip install --no-deps ./mosaicfm-0.1.2-py3-none-any.whl")
66
-
67
- # imports inside GPU scope
68
- import torch
69
- from composer import Trainer
70
- from mosaicfm.model.model import ComposerSCGPTModel
71
- from mosaicfm.data import CountDataset, DataCollator
72
- from mosaicfm.tokenizer import GeneVocab
73
-
74
  # retrieve AnnData from bytes
75
  with tempfile.TemporaryDirectory() as td:
76
  fpath = Path(td) / "input.h5ad"
 
1
+ # install custom package
2
+ import os
3
+ os.system("pip install --no-deps ./mosaicfm-0.1.2-py3-none-any.whl")
4
+
5
+ # imports
6
  import gc
 
7
  import tempfile
8
+ import torch
9
  import gradio as gr
10
  import anndata as ad
11
  import pandas as pd
12
  import numpy as np
13
  import scanpy as sc
14
  from pathlib import Path
15
+ from composer import Trainer
16
  from omegaconf import OmegaConf as om
17
+ from mosaicfm.model.model import ComposerSCGPTModel
18
+ from mosaicfm.data import CountDataset, DataCollator
19
+ from mosaicfm.tokenizer import GeneVocab
20
 
21
  # hardcoded configuration
22
  EMB_KEY = "X_tx1-70m"
 
64
  return str(parquet_path), str(out_h5ad)
65
 
66
  # compute embeddings
 
67
  def _embed(adata_bytes, layer_name, feature_col, batch_size):
68
 
 
 
 
 
 
 
 
 
 
 
 
 
69
  # retrieve AnnData from bytes
70
  with tempfile.TemporaryDirectory() as td:
71
  fpath = Path(td) / "input.h5ad"