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
|
{
lib,
buildPythonPackage,
fetchFromGitHub,
substituteAll,
cmdstan,
setuptools,
pandas,
numpy,
tqdm,
stanio,
xarray,
pytestCheckHook,
stdenv,
}:
buildPythonPackage rec {
pname = "cmdstanpy";
version = "1.2.4";
pyproject = true;
src = fetchFromGitHub {
owner = "stan-dev";
repo = "cmdstanpy";
rev = "refs/tags/v${version}";
hash = "sha256-SKDqLvWbzaBcL13E87kcphBJNIZfdkPp2g4SIDEKA0U=";
};
patches = [
(substituteAll {
src = ./use-nix-cmdstan-path.patch;
cmdstan = "${cmdstan}/opt/cmdstan";
})
];
postPatch = ''
# conftest.py would have used git to clean up, which is unnecessary here
rm test/conftest.py
'';
nativeBuildInputs = [
setuptools
];
propagatedBuildInputs = [
pandas
numpy
tqdm
stanio
];
passthru.optional-dependencies = {
all = [ xarray ];
};
pythonRelaxDeps = [ "stanio" ];
preCheck = ''
export HOME=$(mktemp -d)
'';
nativeCheckInputs = [ pytestCheckHook ] ++ passthru.optional-dependencies.all;
disabledTestPaths = [
# No need to test these when using Nix
"test/test_install_cmdstan.py"
"test/test_cxx_installation.py"
];
disabledTests =
[
"test_serialization" # Pickle class mismatch errors
# These tests use the flag -DSTAN_THREADS which doesn't work in cmdstan (missing file)
"test_multi_proc_threads"
"test_compile_force"
# These tests require a writeable cmdstan source directory
"test_pathfinder_threads"
"test_save_profile"
]
++ lib.optionals stdenv.isDarwin [
"test_init_types" # CmdStan error: error during processing Operation not permitted
];
pythonImportsCheck = [ "cmdstanpy" ];
meta = {
homepage = "https://github.com/stan-dev/cmdstanpy";
description = "Lightweight interface to Stan for Python users";
changelog = "https://github.com/stan-dev/cmdstanpy/releases/tag/v${version}";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ tomasajt ];
};
}
|
