mirror of
https://github.com/SebastianWendel/nixpkgs.git
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Merge pull request #120874 from rmcgibbo/astropy
python3Packages.astropy: unbreak multiple modules
This commit is contained in:
commit
37c75aaf3e
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@ -3,25 +3,42 @@
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, fetchPypi
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, fetchPypi
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, numpy
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, numpy
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, astropy
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, astropy
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, astropy-helpers
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, astropy-extension-helpers
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, setuptools-scm
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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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buildPythonPackage rec {
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buildPythonPackage rec {
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pname = "astropy-healpix";
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pname = "astropy-healpix";
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version = "0.6";
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version = "0.6";
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doCheck = false; # tests require pytest-astropy
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src = fetchPypi {
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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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sha256 = "409a6621c383641456c074f0f0350a24a4a58e910eaeef14e9bbce3e00ad6690";
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};
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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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# Disable automatic update of the astropy-helper module
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propagatedBuildInputs = [
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postPatch = ''
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numpy
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substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
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astropy
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];
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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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# 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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'';
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meta = with lib; {
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meta = with lib; {
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@ -2,10 +2,10 @@
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, buildPythonPackage
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, buildPythonPackage
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, fetchFromGitHub
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, fetchFromGitHub
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, numpy
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, numpy
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, python
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, scikitimage
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, scikitimage
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, openjpeg
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, openjpeg
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, procps
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, procps
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, pytestCheckHook
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, contextlib2
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, contextlib2
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, mock
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, mock
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, importlib-resources
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, importlib-resources
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@ -14,13 +14,13 @@
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buildPythonPackage rec {
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buildPythonPackage rec {
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pname = "glymur";
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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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src = fetchFromGitHub {
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owner = "quintusdias";
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owner = "quintusdias";
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repo = pname;
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repo = pname;
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rev = "v${version}";
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rev = "v${version}";
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sha256 = "1zbghzw1q4fljb019lsrhka9xrnn4425qnxrjbmbv7dssgkkywd7";
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sha256 = "1xlpax56qg5qqh0s19xidgvv2483sc684zj7rh6zw1m1z9m37drr";
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};
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};
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propagatedBuildInputs = [
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propagatedBuildInputs = [
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@ -30,16 +30,21 @@ buildPythonPackage rec {
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checkInputs = [
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checkInputs = [
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scikitimage
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scikitimage
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procps
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procps
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pytestCheckHook
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];
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];
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postConfigure = ''
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postConfigure = ''
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substituteInPlace glymur/config.py \
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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 + ${if stdenv.isDarwin then "'.dylib'" else "'.so'"}"
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'';
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'';
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checkPhase = ''
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disabledTestPaths = [
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${python.interpreter} -m unittest discover
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# this test involves glymur's different ways of finding the openjpeg path on
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'';
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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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meta = with lib; {
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meta = with lib; {
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description = "Tools for accessing JPEG2000 files";
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description = "Tools for accessing JPEG2000 files";
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@ -4,7 +4,9 @@
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, isPy27
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, isPy27
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, six
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, six
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, pytest
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, pytest
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, pytestCheckHook
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, numpy
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, numpy
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, setuptools_scm
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}:
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}:
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buildPythonPackage rec {
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buildPythonPackage rec {
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@ -17,7 +19,12 @@ buildPythonPackage rec {
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sha256 = "6fe747418461d7b202824a3486ba8f4fa17a9bd0b1eddc743ba1d6d87f03391a";
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sha256 = "6fe747418461d7b202824a3486ba8f4fa17a9bd0b1eddc743ba1d6d87f03391a";
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};
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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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propagatedBuildInputs = [
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six
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six
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@ -25,14 +32,9 @@ buildPythonPackage rec {
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];
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];
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checkInputs = [
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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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meta = with lib; {
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description = "Pytest plugin with advanced doctest features";
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description = "Pytest plugin with advanced doctest features";
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homepage = "https://astropy.org";
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homepage = "https://astropy.org";
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@ -2,9 +2,8 @@
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, fetchPypi
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, fetchPypi
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, buildPythonPackage
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, buildPythonPackage
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, astropy
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, astropy
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, pytest
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, pytestCheckHook
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, pytest-astropy
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, pytest-doctestplus
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, astropy-helpers
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, scipy
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, scipy
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}:
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}:
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@ -13,25 +12,18 @@ buildPythonPackage rec {
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version = "0.3.3";
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version = "0.3.3";
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src = fetchPypi {
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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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sha256 = "e34902d91713ccab9f450b9d3e82317e292cf46a30bd42f9ad3c9a0519fcddcd";
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};
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};
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propagatedBuildInputs = [ astropy ];
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propagatedBuildInputs = [ astropy ];
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nativeBuildInputs = [ astropy-helpers ];
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checkInputs = [ pytestCheckHook pytest-doctestplus scipy ];
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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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checkInputs = [ pytest pytest-astropy scipy ];
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# Tests must be run in the build directory
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# Tests must be run in the build directory
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checkPhase = ''
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preCheck = ''
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cd build/lib
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cd build/lib
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pytest
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'';
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'';
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meta = {
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meta = {
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@ -1,11 +1,12 @@
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{ lib
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{ lib
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, fetchPypi
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, fetchPypi
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, fetchpatch
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, buildPythonPackage
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, buildPythonPackage
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, aplpy
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, aplpy
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, joblib
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, joblib
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, astropy
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, astropy
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, radio_beam
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, radio_beam
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, pytest
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, pytestCheckHook
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, pytest-astropy
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, pytest-astropy
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, astropy-helpers
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, astropy-helpers
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}:
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}:
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@ -20,13 +21,18 @@ buildPythonPackage rec {
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sha256 = "17zisr26syfb8kn89xj17lrdycm0hsmy5yp5zrn236wgd8rjriki";
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sha256 = "17zisr26syfb8kn89xj17lrdycm0hsmy5yp5zrn236wgd8rjriki";
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};
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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";
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sha256 = "1qddfm3364kc34yf6wd9nd6rxh4qc2v5pqilvz9adwb4a50z28bf";
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})
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];
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nativeBuildInputs = [ astropy-helpers ];
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nativeBuildInputs = [ astropy-helpers ];
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propagatedBuildInputs = [ astropy radio_beam joblib ];
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propagatedBuildInputs = [ astropy radio_beam joblib ];
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checkInputs = [ aplpy pytest pytest-astropy ];
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checkInputs = [ pytestCheckHook aplpy pytest-astropy ];
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checkPhase = ''
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pytest spectral_cube
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'';
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meta = {
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meta = {
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description = "Library for reading and analyzing astrophysical spectral data cubes";
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description = "Library for reading and analyzing astrophysical spectral data cubes";
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@ -11,6 +11,7 @@
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, beautifulsoup4
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, beautifulsoup4
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, drms
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, drms
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, glymur
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, glymur
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, h5netcdf
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, hypothesis
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, hypothesis
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, matplotlib
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, matplotlib
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, numpy
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, numpy
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@ -50,6 +51,7 @@ buildPythonPackage rec {
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pandas
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pandas
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astropy
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astropy
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astropy-helpers
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astropy-helpers
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h5netcdf
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parfive
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parfive
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sqlalchemy
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sqlalchemy
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scikitimage
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scikitimage
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