SOORENA/environment.yml at main · jafarilab/SOORENA · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
name: autoregulatory
channels:
  - conda-forge
channel_priority: strict

dependencies:
  - python=3.11
  - pip
  - ipykernel
  - jupyterlab
  - matplotlib
  - pandas
  - seaborn
  - scikit-learn
  - nltk
  - spacy
  - plotly
  - ipywidgets
  - jupyter-dash
  - pyreadr
  - openpyxl  # For reading Excel files (external resources integration)
  - tqdm
  - nb_conda_kernels
  - numpy
  - regex
  - tokenizers
  - safetensors
  - psutil
  - python-dateutil
  # leave torch and protobuf out; install torch per-platform later
  - pip:
      - transformers>=4.41
      - datasets
      - accelerate
      - torch-summary
      - kaleido
      - pyppeteer
      - iterative-stratification
      - evaluate
      - wandb
      - tensorboard
      - torchmetrics
      # do NOT add sentence-transformers here; install it after torch