pyrox.dev
Merge pull request #120874 from rmcgibbo/astropy
python3Packages.astropy: unbreak multiple modules
authored by
Fabian Affolter
and committed by
GitHub
37c75aaf
c5173fe2
+25
-8
pkgs/development/python-modules/astropy-healpix/default.nix
+25
-8
pkgs/development/python-modules/astropy-healpix/default.nix
···
3
3
, fetchPypi
4
4
, numpy
5
5
, astropy
6
-
, astropy-helpers
6
+
, astropy-extension-helpers
7
+
, setuptools-scm
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+
, pytestCheckHook
9
+
, pytest-doctestplus
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+
, hypothesis
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}:
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buildPythonPackage rec {
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pname = "astropy-healpix";
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version = "0.6";
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-
doCheck = false; # tests require pytest-astropy
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-
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src = fetchPypi {
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-
inherit pname version;
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inherit version;
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pname = lib.replaceStrings ["-"] ["_"] pname;
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sha256 = "409a6621c383641456c074f0f0350a24a4a58e910eaeef14e9bbce3e00ad6690";
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};
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-
propagatedBuildInputs = [ numpy astropy astropy-helpers ];
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+
nativeBuildInputs = [
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+
astropy-extension-helpers
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+
setuptools-scm
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+
];
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+
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+
propagatedBuildInputs = [
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+
numpy
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+
astropy
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+
];
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-
# Disable automatic update of the astropy-helper module
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postPatch = ''
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substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
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+
checkInputs = [
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+
pytestCheckHook
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+
pytest-doctestplus
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+
hypothesis
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+
];
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+
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+
# tests must be run in the build directory
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+
preCheck = ''
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+
cd build/lib*
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'';
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meta = with lib; {
+12
-7
pkgs/development/python-modules/glymur/default.nix
+12
-7
pkgs/development/python-modules/glymur/default.nix
···
2
2
, buildPythonPackage
3
3
, fetchFromGitHub
4
4
, numpy
5
-
, python
6
5
, scikitimage
7
6
, openjpeg
8
7
, procps
8
+
, pytestCheckHook
9
9
, contextlib2
10
10
, mock
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11
, importlib-resources
···
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buildPythonPackage rec {
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pname = "glymur";
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version = "0.8.18";
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+
version = "0.9.3";
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src = fetchFromGitHub {
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owner = "quintusdias";
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repo = pname;
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rev = "v${version}";
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-
sha256 = "1zbghzw1q4fljb019lsrhka9xrnn4425qnxrjbmbv7dssgkkywd7";
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+
sha256 = "1xlpax56qg5qqh0s19xidgvv2483sc684zj7rh6zw1m1z9m37drr";
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};
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propagatedBuildInputs = [
···
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checkInputs = [
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scikitimage
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procps
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+
pytestCheckHook
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];
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postConfigure = ''
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substituteInPlace glymur/config.py \
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-
--replace "path = read_config_file(libname)" "path = '${openjpeg}/lib' + libname + ${if stdenv.isDarwin then "'.dylib'" else "'.so'"}"
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+
--replace "path = read_config_file(libname)" "path = '${openjpeg}/lib/lib' + libname + ${if stdenv.isDarwin then "'.dylib'" else "'.so'"}"
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'';
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-
checkPhase = ''
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${python.interpreter} -m unittest discover
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-
'';
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+
disabledTestPaths = [
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# this test involves glymur's different ways of finding the openjpeg path on
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# fsh systems by reading an .rc file and such, and is obviated by the patch
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# in postConfigure
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"tests/test_config.py"
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];
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+
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meta = with lib; {
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description = "Tools for accessing JPEG2000 files";
+9
-7
pkgs/development/python-modules/pytest-doctestplus/default.nix
+9
-7
pkgs/development/python-modules/pytest-doctestplus/default.nix
···
4
4
, isPy27
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5
, six
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6
, pytest
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+
, pytestCheckHook
7
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, numpy
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+
, setuptools_scm
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}:
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buildPythonPackage rec {
···
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sha256 = "6fe747418461d7b202824a3486ba8f4fa17a9bd0b1eddc743ba1d6d87f03391a";
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};
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-
buildInputs = [ pytest ];
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+
nativeBuildInputs = [
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+
setuptools_scm
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+
];
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+
buildInputs = [
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+
pytest
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+
];
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propagatedBuildInputs = [
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six
···
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];
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checkInputs = [
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-
pytest
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+
pytestCheckHook
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];
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-
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-
# check_distribution incorrectly pulls pytest version
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checkPhase = ''
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pytest -k 'not check_distribution'
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'';
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meta = with lib; {
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description = "Pytest plugin with advanced doctest features";
+6
-14
pkgs/development/python-modules/radio_beam/default.nix
+6
-14
pkgs/development/python-modules/radio_beam/default.nix
···
2
2
, fetchPypi
3
3
, buildPythonPackage
4
4
, astropy
5
-
, pytest
6
-
, pytest-astropy
7
-
, astropy-helpers
5
+
, pytestCheckHook
6
+
, pytest-doctestplus
8
7
, scipy
9
8
}:
10
9
···
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version = "0.3.3";
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src = fetchPypi {
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-
inherit pname version;
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+
inherit version;
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+
pname = "radio-beam";
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sha256 = "e34902d91713ccab9f450b9d3e82317e292cf46a30bd42f9ad3c9a0519fcddcd";
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};
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propagatedBuildInputs = [ astropy ];
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-
nativeBuildInputs = [ astropy-helpers ];
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-
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-
# Disable automatic update of the astropy-helper module
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-
postPatch = ''
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-
substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
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-
'';
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-
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-
checkInputs = [ pytest pytest-astropy scipy ];
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+
checkInputs = [ pytestCheckHook pytest-doctestplus scipy ];
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# Tests must be run in the build directory
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-
checkPhase = ''
25
+
preCheck = ''
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cd build/lib
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-
pytest
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'';
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meta = {
+12
-6
pkgs/development/python-modules/spectral-cube/default.nix
+12
-6
pkgs/development/python-modules/spectral-cube/default.nix
···
1
1
{ lib
2
2
, fetchPypi
3
+
, fetchpatch
3
4
, buildPythonPackage
4
5
, aplpy
5
6
, joblib
6
7
, astropy
7
8
, radio_beam
8
-
, pytest
9
+
, pytestCheckHook
9
10
, pytest-astropy
10
11
, astropy-helpers
11
12
}:
···
20
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sha256 = "17zisr26syfb8kn89xj17lrdycm0hsmy5yp5zrn236wgd8rjriki";
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};
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+
patches = [
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+
# Fix compatibility with radio_beam >= 0.3.3. Will be included
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+
# in the next release of spectral cube > 0.5.0
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+
(fetchpatch {
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+
url = "https://github.com/radio-astro-tools/spectral-cube/commit/bbe4295ebef7dfa6fe4474275a29acd6cb0cb544.patch";
29
+
sha256 = "1qddfm3364kc34yf6wd9nd6rxh4qc2v5pqilvz9adwb4a50z28bf";
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+
})
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+
];
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+
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nativeBuildInputs = [ astropy-helpers ];
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propagatedBuildInputs = [ astropy radio_beam joblib ];
25
-
checkInputs = [ aplpy pytest pytest-astropy ];
26
-
27
-
checkPhase = ''
28
-
pytest spectral_cube
29
-
'';
35
+
checkInputs = [ pytestCheckHook aplpy pytest-astropy ];
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meta = {
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description = "Library for reading and analyzing astrophysical spectral data cubes";