tiktorch/environment.yml at main · ilastik/tiktorch · 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
name: tiktorch-server-env
channels:
  - conda-forge
dependencies:
  # - bioimage.spec via submodule
  # - bioimage.core via submodule
  - python 3.11.*
  - numpy >=2,<3
  - grpcio=1.69.0 # protobuf 5 requires protoc version > 3.19.0 that requires grpcio >= 1.44
  - marshmallow-union
  - marshmallow=3.12.*
  - marshmallow-jsonschema
  - protobuf
  - pyyaml>5
  - requests
  - scikit-learn
  - scipy
  - typing-extensions
  - xarray
  - pytorch-3dunet =1.9.2
  - setuptools
  - pip

  # pytorch
  # remove cpuonly, add cudatoolkit and cudnn for gpu support
  - pytorch=2.7.*
  # currently it's necessary to force the cpu version, remove
  # torchvision pin when going for gpu
  # - torchvision
  # - cudatoolkit >=10.2
  # - cudnn
  - torchvision

  # tensorflow (1.14 is the latest 1.x version on cf)
  # so far we don't have any 2.x models in the model zoo
  # tensorflow skipped for now, as it conflicts with grpcio version 1.41
  # - tensorflow >=2.9,<3.0

  # bioimageio.spec / bioimageio.core dependencies:
  - annotated-types >=0.5.0,<1
  - anyio
  - email_validator
  - exceptiongroup
  - genericache==0.5.2
  - h5py
  - imageio >=2.10
  - loguru
  - markdown
  - packaging >=17.0
  - platformdirs
  - pooch >=1.5,<2
  - pydantic >=2.10.3,<2.12
  - pydantic-core
  - pydantic-settings>=2.5,<3
  - python-dateutil
  - respx
  - rich
  - ruyaml
  - tifffile
  - typing-extensions
  - tqdm
  - typer
  - zipp


  # dev stuff
  - pytest
  - pytest-cov
  - pytest-grpc
  - pytest-timeout
  - bump2version
  - mypy
  - pre_commit