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
|
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class PyMdanalysis(PythonPackage):
"""MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation
packages including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and
Gromacs. (See the lists of supported trajectory formats and
topology formats.)"""
homepage = "https://www.mdanalysis.org"
pypi = "MDAnalysis/MDAnalysis-2.4.2.tar.gz"
maintainers("RMeli")
license("CC-BY-ND-3.0")
version("2.6.1", sha256="9cc69b94bddd026f26ffcaf5bdbed6d568c1c10e19a341d84f8d37a2a70222f2")
version("2.6.0", sha256="210b198a115165004c36fbbbe5eb83a13323f52b10ccaef30dd40bfe25ba3e61")
version("2.5.0", sha256="06ce4efab6ca1dbd2ee2959fc668049e1d574a8fe94ab948a4608244da1d016b")
version("2.4.3", sha256="c4fbdc414e4fdda69052fff2a6e412180fe6fa90a42c24793beee04123648c92")
version("2.4.2", sha256="ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636")
variant(
"analysis",
default=True,
description="Enable analysis packages: matplotlib, scipy, seaborn",
)
variant("extra_formats", default=False, description="Support extra formats")
depends_on("python@3.9:", type=("build", "run"), when="@2.5.0:")
depends_on("python@3.8:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-cython@0.28:", type="build")
# MDAnalysis required dependencies (install_requires)
depends_on("py-numpy@1.22.3:1", when="@2.6.0:", type=("build", "run"))
depends_on("py-numpy@1.21.0:", when="@2.5.0:", type=("build", "run"))
depends_on("py-numpy@1.20.0:", type=("build", "run"))
depends_on("py-biopython@1.80:", type=("build", "run"))
depends_on("py-networkx@2.0:", type=("build", "run"))
depends_on("py-griddataformats@0.4.0:", type=("build", "run"))
depends_on("py-mmtf-python@1.0.0:", type=("build", "run"))
depends_on("py-joblib@0.12:", type=("build", "run"))
depends_on("py-scipy@1.5.0:", type=("build", "run"))
depends_on("py-matplotlib@1.5.1:", type=("build", "run"))
depends_on("py-tqdm@4.43.0:", type=("build", "run"))
depends_on("py-threadpoolctl", type=("build", "run"))
depends_on("py-packaging", type=("build", "run"))
depends_on("py-fasteners", type=("build", "run"))
depends_on("py-gsd@1.9.3:", when="@:2.5.0", type=("build", "run"))
# extra_format (extras_require)
depends_on("py-netcdf4@1.0:", when="+extra_formats", type=("build", "run"))
depends_on("py-h5py@2.10:", when="+extra_formats", type=("build", "run"))
depends_on("py-pytng@0.2.3:", when="+extra_formats", type=("build", "run"))
depends_on("py-chemfiles@0.10:", when="+extra_formats", type=("build", "run"))
depends_on("py-pyedr@0.7.0:", when="+extra_formats", type=("build", "run"))
# py-gsd is now an optional dependency and requires >3.0.0
# gsd>=2.9.0 requires setuptools>=64 and can't be concretised with py-numpy
# depends_on("py-gsd@3.0.1:", when="+extra_formats @2.6.0:", type=("build", "run"))
depends_on(
"rdkit@2020.03.1: +python ~coordgen ~maeparser ~yaehmop ~descriptors3d",
when="+extra_formats @2.6.0:",
type=("build", "run"),
)
depends_on("py-parmed", when="+extra_formats @2.6.0:", type=("build", "run"))
# analysis (extras_require)
depends_on("py-seaborn", when="+analysis", type=("build", "run"))
depends_on("py-scikit-learn", when="+analysis", type=("build", "run"))
depends_on("py-tidynamics@1:", when="+analysis", type=("build", "run"))
|
