worms/environment_working.yml at main · baker-laboratory/worms · 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
name: worms
channels:
  - schrodinger
  - conda-forge
  - defaults
  - bioconda
  - https://pose:foldtree@conda.rosettacommons.org/
dependencies:
  # Core Python
  - python=3.6.8
  - pip
  - setuptools
  - wheel

  # Scientific computing core
  - numpy=1.16.3
  - scipy
  - pandas
  - matplotlib
  - h5py
  - netcdf4
  - xarray

  # Parallel/distributed computing
  - dask
  - dask-core
  - distributed
  - numba=0.38.1

  # Development tools
  - ipython
  - pytest
  - pytest-cov
  - coverage
  - sphinx_rtd_theme

  # Data formats and compression
  - blosc
  - hdf5
  - pytables
  - snappy

  # Molecular visualization/computation (try without versions first)
  - apbs
  #- pymol-open-source

  # System libraries
  - openssl
  - curl
  - zlib
  - ca-certificates
  - certifi

  # Qt/GUI (if needed)
  - pyqt
  - qt

  # Other scientific
  - pillow
  - pyyaml
  - requests
  - click
  - jinja2

  # Pyrosetta
  - pyrosetta=2019.13+release.6fad4d4

  # Missing stuff
  - pympler=0.5

  # Pip packages
  - pip:
      - alabaster==0.7.12
      - attrs
      - babel
      - beautifulsoup4==4.9.3
      - black
      - breathe
      - bs4==0.0.1
      - docutils==0.16
      - exhale
      - hypothesis
      - imagesize
      - jupyter-console==6.0
      - lxml==4.6.2
      - mako
      - pybind11
      - pytest-forked
      - pytest-repeat
      - pytest-sugar
      - pytest-xdist
      - snowballstemmer
      - soupsieve
      - sphinx
      - sphinxcontrib-applehelp
      - sphinxcontrib-devhelp
      - sphinxcontrib-htmlhelp
      - sphinxcontrib-jsmath
      - sphinxcontrib-qthelp
      - sphinxcontrib-serializinghtml
      - tabulate
      - termcolor
      - toml
      - tqdm
      - traittypes
      - yapf
      - homog==0.1.14
      - xbin==0.1.7