Wizards-Staff/environment.yml at main · ArcInstitute/Wizards-Staff · 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
name: wizards_staff
channels:
  - conda-forge
dependencies:
  - python=3.11
  - pip
  - setuptools<78

  - pip:
    # Core scientific stack
    - numpy==1.26.4
    - pandas>=2.2,<2.3
    - scipy>=1.14,<1.15
    - matplotlib>=3.9,<3.10
    - scikit-image==0.24.0
    - scikit-learn>=1.5,<1.6
    - statsmodels>=0.14
    - jinja2>=3.1
    - pims>=0.7
    - h5py>=3.12
    - zarr>=2.18,<3
    - tifffile>=2024.6
    - tqdm>=4.66
    - opencv-python>=4.10

    # Visualization
    - bokeh>=3.6
    - holoviews>=1.20

    # Jupyter stack
    - ipykernel==6.29.5
    - traitlets==5.14.3
    - jupyter-client==8.6.3
    - jupyter-core==5.7.2
    - ipython>=8.0
    - ipywidgets>=8.1
    - ipyparallel>=8.8

    # ML/Analysis
    - tensorflow>=2.18
    - peakutils>=1.3
    - psutil>=6.0

    # CaImAn (from git, matching working environment)
    - caiman @ git+https://github.com/flatironinstitute/CaImAn.git@v1.11.3

    # Data formats
    - pynwb>=2.8

    # Database
    - sqlalchemy>=2.0
    - psycopg2-binary>=2.9

    # Additional
    - pypika>=0.48
    - python-dotenv>=1.0
    - aicspylibczi>=3.1
    - xmltodict
    - glob2

    # Install wizards_staff in editable mode
    - -e .