IsoNet2/isonet2_environment.yml at main · IsoNet-cryoET/IsoNet2 · 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
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
name: isonet2_environment
channels:
  - pytorch
  - nvidia
  - conda-forge
  - defaults
dependencies:
  # --- Conda Packages ---
  - python=3.10
  - pip
  - wheel<0.46

  # PyTorch Core
  - pytorch==2.1.1
  - torchvision==0.16.1
  - torchaudio==2.1.1
  - pytorch-cuda=12.1

  # Core PyTorch Dependencies
  - sympy
  - jinja2
  - filelock
  - mpmath
  - typing-extensions

  # Scientific/Binary Packages
  - numpy<2.0
  - scipy
  - pandas
  - scikit-image=0.22.*
  - pillow
  - mrcfile
  - pyarrow
  - simpleitk
  - tifffile
  - matplotlib
  - imageio
  - networkx

  # Binaries
  - graphviz
  - python-blosc
  - pyyaml

  # --- Pip Packages ---
  - pip:
    - aiohttp==3.9.3
    - aiosignal==1.3.1
    - anyio==4.8.0
    - async-timeout==4.0.3
    - attrs==23.2.0
    - backoff==2.2.1
    - boto3==1.35.92
    - botocore==1.35.92
    - certifi==2022.12.7
    - charset-normalizer==2.1.1
    - click==8.1.7
    - contourpy==1.2.0
    - cryoet-data-portal==4.2.1
    - cycler==0.12.1
    - deepmerge==2.0
    - einops==0.8.0
    - exceptiongroup==1.2.2
    - fidder==0.0.8
    - fire==0.5.0
    - focustools==0.2.3
    - fonttools==4.46.0
    - frozenlist==1.4.1
    - fsspec==2024.10.0
    - git-filter-repo==2.47.0
    - gql==3.5.0
    - graphql-core==3.2.5
    - huggingface-hub==0.26.2
    - humanize==4.11.0
    - idna==3.4
    - jmespath==1.0.1
    - joblib==1.4.2
    - kiwisolver==1.4.5
    - lazy-loader==0.3
    - lightning-utilities==0.10.1
    - markdown-it-py==3.0.0
    - markupsafe==2.1.3
    - mdurl==0.1.2
    - mrcz==0.5.7
    - multidict==6.0.5
    - ndjson==0.3.1
    - numexpr==2.10.2
    - packaging==23.2
    - platformdirs==4.3.6
    - pooch==1.8.2
    - pygments==2.18.0
    - pyparsing==3.1.1
    - python-dateutil==2.8.2
    - pytorch-lightning==2.1.4
    - pytz==2024.1
    - requests==2.28.1
    - requests-toolbelt==1.0.0
    - rich==13.7.1
    - s3transfer==0.10.4
    - safetensors==0.4.5
    - shellingham==1.5.4
    - six==1.16.0
    - sniffio==1.3.1
    - starfile==0.5.6
    - strcase==1.0.0
    - termcolor==2.4.0
    - tiler==0.5.7
    - timm==1.0.11
    - torchmetrics==1.3.0.post0
    - torchviz==0.0.2
    - tqdm==4.66.1
    - typer==0.12.3
    - typer-config==1.4.2
    - tzdata