Merge pull request #107770 from rmcgibbo/astropy

python3Packages.astropy: unbreak

pkgs/development/python-modules/aplpy/default.nix

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , numpy
 , astropy
 , astropy-helpers
@@ -18,6 +19,7 @@
 buildPythonPackage rec {
   pname = "aplpy";
   version = "2.0.3";
+  format = "pyproject";
 
   src = fetchPypi {
     pname = "APLpy";
@@ -25,6 +27,15 @@ buildPythonPackage rec {
     sha256 = "239f3d83635ca4251536aeb577df7c60df77fc4d658097b92094719739aec3f3";
   };
 
+  patches = [ (fetchpatch {
+      # Can be removed in next release after 2.0.3
+      url = "https://github.com/aplpy/aplpy/pull/448.patch";
+      sha256 = "1pnzh7ykjc8hwahzbzyryrzv5a8fddgd1bmzbhagkrn6lmvhhpvq";
+      excludes = [ "tox.ini" "azure-pipelines.yml" ".circleci/config.yml" "MANIFEST.in" ".gitignore"
+       "setup.cfg" "appveyor.yml" "readthedocs.yml" "CHANGES.rst" ".gitmodules" ".travis.yml" "astropy_helpers" ];
+    })
+  ];
+
   propagatedBuildInputs = [
     numpy
     astropy
@@ -38,18 +49,10 @@ buildPythonPackage rec {
   ];
 
   nativeBuildInputs = [ astropy-helpers ];
-
   checkInputs = [ pytest pytest-astropy ];
 
-  # Disable automatic update of the astropy-helper module
-  postPatch = ''
-    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
-  '';
-
-  # Tests must be run in the build directory
   checkPhase = ''
-    cd build/lib
+    OPENMP_EXPECTED=0 pytest aplpy
-    pytest
   '';
 
   meta = with lib; {

pkgs/development/python-modules/asdf/default.nix

@@ -17,18 +17,13 @@ buildPythonPackage rec {
   pname = "asdf";
   version = "2.7.1";
   disabled = isPy27;
+  format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "4ba2e31cb24b974a10dfae3edee23db2e6bea2d00608604d062366aa3af6e81a";
   };
 
-  postPatch = ''
-    substituteInPlace setup.cfg \
-      --replace "semantic_version>=2.3.1,<=2.6.0" "semantic_version>=2.3.1" \
-      --replace "doctest_plus = enabled" ""
-  '';
-
   checkInputs = [
     pytest-astropy
     astropy
@@ -45,7 +40,7 @@ buildPythonPackage rec {
   ];
 
   checkPhase = ''
-    pytest
+    PY_IGNORE_IMPORTMISMATCH=1 pytest
   '';
 
   meta = with lib; {

pkgs/development/python-modules/astropy-extension-helpers/default.nix

@@ -0,0 +1,31 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "extension-helpers";
+  version = "0.1";
+  format = "pyproject";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "10iqjzmya2h4sk765dlm1pbqypwlqyh8rw59a5m9i63d3klnz2mc";
+  };
+
+  patches = [ ./permissions.patch ];
+
+  checkInputs = [ pytestCheckHook ];
+
+  pythonImportsCheck = [
+    "extension_helpers"
+  ];
+
+  meta = with lib; {
+    description = "Utilities for building and installing packages in the Astropy ecosystem";
+    homepage = "https://github.com/astropy/extension-helpers";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.rmcgibbo ];
+  };
+}

pkgs/development/python-modules/astropy-extension-helpers/permissions.patch

@@ -0,0 +1,20 @@
+diff --git a/extension_helpers/_setup_helpers.py b/extension_helpers/_setup_helpers.py
+index ec3e547..e2419f7 100644
+--- a/extension_helpers/_setup_helpers.py
++++ b/extension_helpers/_setup_helpers.py
+@@ -79,8 +79,13 @@ def get_extensions(srcdir='.'):
+     if len(ext_modules) > 0:
+         main_package_dir = min(packages, key=len)
+         src_path = os.path.join(os.path.dirname(__file__), 'src')
+-        shutil.copy(os.path.join(src_path, 'compiler.c'),
+-                    os.path.join(srcdir, main_package_dir, '_compiler.c'))
++        a = os.path.join(src_path, 'compiler.c')
++        b = os.path.join(srcdir, main_package_dir, '_compiler.c')
++        try:
++            os.unlink(b)
++        except OSError:
++            pass
++        shutil.copy(a, b)
+         ext = Extension(main_package_dir + '.compiler_version',
+                         [os.path.join(main_package_dir, '_compiler.c')])
+         ext_modules.append(ext)

pkgs/development/python-modules/astropy/default.nix

@@ -1,5 +1,6 @@
 { lib
 , fetchPypi
+, setuptools_scm
 , buildPythonPackage
 , isPy3k
 , cython
@@ -8,11 +9,14 @@
 , pytest
 , pytest-astropy
 , astropy-helpers
+, astropy-extension-helpers
+, pyerfa
 }:
 
 buildPythonPackage rec {
   pname = "astropy";
   version = "4.2";
+  format = "pyproject";
 
   disabled = !isPy3k; # according to setup.py
 
@@ -21,15 +25,12 @@ buildPythonPackage rec {
     sha256 = "2c194f8a429b8399de64a413a06881ea49f0525cabaa2d78fc132b9e970adc6a";
   };
 
-  nativeBuildInputs = [ astropy-helpers cython jinja2 ];
+  nativeBuildInputs = [ setuptools_scm astropy-helpers astropy-extension-helpers cython jinja2 ];
-
+  propagatedBuildInputs = [ numpy pyerfa ];
-  propagatedBuildInputs = [ numpy pytest ]; # yes it really has pytest in install_requires
-
   checkInputs = [ pytest pytest-astropy ];
 
-  # Disable automatic update of the astropy-helper module
+  preBuild = ''
-  postPatch = ''
+    export SETUPTOOLS_SCM_PRETEND_VERSION="${version}"
-    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
   '';
 
   # Tests must be run from the build directory.  astropy/samp tests
@@ -42,15 +43,14 @@ buildPythonPackage rec {
   '';
 
   # 368 failed, 10889 passed, 978 skipped, 69 xfailed in 196.24s
+  # doCheck = false;
   doCheck = false;
 
-  meta = {
+  meta = with lib; {
     description = "Astronomy/Astrophysics library for Python";
     homepage = "https://www.astropy.org";
-    license = lib.licenses.bsd3;
+    license = licenses.bsd3;
-    platforms = lib.platforms.all;
+    platforms = platforms.all;
-    maintainers = with lib.maintainers; [ kentjames ];
+    maintainers = [ maintainers.kentjames ];
   };
 }
-
-

pkgs/development/python-modules/astroquery/default.nix

@@ -15,6 +15,7 @@
 buildPythonPackage rec {
   pname = "astroquery";
   version = "0.4.1";
+  format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;
@@ -31,11 +32,6 @@ buildPythonPackage rec {
   doCheck = false;
   checkInputs = [ pytest pytest-astropy ];
 
-  # Disable automatic update of the astropy-helper module
-  postPatch = ''
-    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
-  '';
-
   # Tests must be run in the build directory. The tests create files
   # in $HOME/.astropy so we need to set HOME to $TMPDIR.
   checkPhase = ''

pkgs/development/python-modules/drms/default.nix

@@ -4,13 +4,15 @@
 , numpy
 , pandas
 , six
-, pytest
+, astropy
-, python
+, pytestCheckHook
+, pytest-doctestplus
 }:
 
 buildPythonPackage rec {
   pname = "drms";
   version = "0.6.0";
+  format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;
@@ -24,13 +26,11 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
-    pytest
+    astropy
+    pytestCheckHook
+    pytest-doctestplus
   ];
 
-  checkPhase = ''
-    ${python.interpreter} -m drms.tests
-  '';
-
   meta = with lib; {
     description = "Access HMI, AIA and MDI data with Python";
     homepage = "https://github.com/sunpy/drms";

pkgs/development/python-modules/extension-helpers/default.nix

@@ -1,41 +0,0 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
-, isPy27
-, pytestCheckHook
-, setuptools_scm
-}:
-
-buildPythonPackage rec {
-  pname = "extension-helpers";
-  version = "0.1";
-  disabled = isPy27;
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "10iqjzmya2h4sk765dlm1pbqypwlqyh8rw59a5m9i63d3klnz2mc";
-  };
-
-  nativeBuildInputs = [
-    setuptools_scm
-  ];
-
-  propagatedBuildInputs = [
-    pytestCheckHook
-  ];
-
-  # avoid importing local module
-  preCheck = ''
-    cd extension_helpers
-  '';
-
-  # assumes setup.py is in pwd
-  disabledTests = [ "compiler_module" ];
-
-  meta = with lib; {
-    description = "Helpers to assist with building packages with compiled C/Cython extensions";
-    homepage = "https://github.com/astropy/extension-helpers";
-    license = licenses.bsd3;
-    maintainers = [ ];
-  };
-}

pkgs/development/python-modules/pyerfa/default.nix

@@ -0,0 +1,42 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isPy3k
+, liberfa
+, packaging
+, numpy
+}:
+
+buildPythonPackage rec {
+  pname = "pyerfa";
+  format = "pyproject";
+  version = "1.7.1.1";
+
+  doCheck = false;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "09i2qcsvxd3q04a5yaf6fwzg79paaslpksinan9d8smj7viql15i";
+  };
+
+  nativeBuildInputs = [ packaging ];
+  propagatedBuildInputs = [ liberfa numpy ];
+  preBuild = ''
+    export PYERFA_USE_SYSTEM_LIBERFA=1
+  '';
+
+  meta = with lib; {
+    description = "Python bindings for ERFA routines";
+    longDescription = ''
+        PyERFA is the Python wrapper for the ERFA library (Essential Routines
+        for Fundamental Astronomy), a C library containing key algorithms for
+        astronomy, which is based on the SOFA library published by the
+        International Astronomical Union (IAU). All C routines are wrapped as
+        Numpy universal functions, so that they can be called with scalar or
+        array inputs.
+    '';
+    homepage = "https://github.com/liberfa/pyerfa";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.rmcgibbo ];
+  };
+}

pkgs/development/python-modules/pytest-astropy-header/default.nix

@@ -1,21 +1,36 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , pytest
 , pytestcov
 , pytestCheckHook
 , numpy
 , astropy
+, scipy
+, h5py
+, scikitimage
 }:
 
 buildPythonPackage rec {
   pname = "pytest-astropy-header";
   version = "0.1.2";
+  format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "1y87agr324p6x5gvhziymxjlw54pyn4gqnd49papbl941djpkp5g";
   };
+  patches = [ (fetchpatch {
+      url = "https://github.com/astropy/pytest-astropy-header/pull/16.patch";
+      sha256 = "11ln63zq0kgsdx1jw3prlzpcdbxmc99p9cwr18s0x6apy0k6df31";
+    })
+    (fetchpatch {
+      url = "https://github.com/astropy/pytest-astropy-header/pull/29.patch";
+      sha256 = "18l434c926r5z1iq3b6lpnp0lrssszars9y1y9hs6216r60jgjpl";
+    })
+  ];
+
 
   propagatedBuildInputs = [
     pytest
@@ -25,6 +40,9 @@ buildPythonPackage rec {
     pytestCheckHook
     pytestcov
     numpy
+    scipy
+    h5py
+    scikitimage
     astropy
   ];
 

pkgs/development/python-modules/reproject/default.nix

@@ -6,7 +6,7 @@
 , astropy
 , astropy-healpix
 , astropy-helpers
-, extension-helpers
+, astropy-extension-helpers
 , scipy
 , pytest
 , pytest-astropy
@@ -23,15 +23,16 @@ buildPythonPackage rec {
     sha256 = "1jsc3ad518vyys5987fr1achq8qvnz8rm80zp5an9qxlwr4zmh4m";
   };
 
+  patches = [ (fetchpatch {
+      # Can be removed in next release after 0.7.1
+      # See https://github.com/astropy/reproject/issues/246
+      url = "https://github.com/astropy/reproject/pull/243.patch";
+      sha256 = "0dq3ii39hsrks0b9v306dlqf07dx0hqad8rwajmzw6rfda9m3c2a";
+    })
+  ];
+
   propagatedBuildInputs = [ numpy astropy astropy-healpix astropy-helpers scipy ];
-
+  nativeBuildInputs = [ astropy-helpers cython astropy-extension-helpers setuptools_scm ];
-  nativeBuildInputs = [ astropy-helpers cython extension-helpers setuptools_scm ];
-
-  # Disable automatic update of the astropy-helper module
-  postPatch = ''
-    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
-  '';
-
   checkInputs = [ pytest pytest-astropy ];
 
   # Tests must be run in the build directory

pkgs/development/python-modules/spectral-cube/default.nix

@@ -1,7 +1,8 @@
 { lib
-, fetchFromGitHub
+, fetchPypi
 , buildPythonPackage
 , aplpy
+, joblib
 , astropy
 , radio_beam
 , pytest
@@ -11,31 +12,20 @@
 
 buildPythonPackage rec {
   pname = "spectral-cube";
-  version = "0.4.5";
+  version = "0.5.0";
+  format = "pyproject";
 
-  # Fetch from GitHub instead of PyPi, as 0.4.5 isn't available in PyPi
+  src = fetchPypi {
-  src = fetchFromGitHub {
+    inherit pname version;
-    owner = "radio-astro-tools";
+    sha256 = "17zisr26syfb8kn89xj17lrdycm0hsmy5yp5zrn236wgd8rjriki";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "1xc1m6vpl0bm600fx9vypa7zcvwg7yvhgn0w89y6v9d1vl0qcs7z";
   };
 
-  propagatedBuildInputs = [ astropy radio_beam ];
-
   nativeBuildInputs = [ astropy-helpers ];
-
+  propagatedBuildInputs = [ astropy radio_beam joblib ];
   checkInputs = [ aplpy pytest pytest-astropy ];
 
-  # Disable automatic update of the astropy-helper module
-  postPatch = ''
-    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
-  '';
-
-  # Tests must be run in the build directory
   checkPhase = ''
-    cd build/lib
+    pytest spectral_cube
-    pytest
   '';
 
   meta = {

pkgs/development/python-modules/sunpy/default.nix

@@ -1,12 +1,12 @@
 { stdenv
 , lib
 , buildPythonPackage
-, fetchFromGitHub
+, fetchPypi
 , pythonOlder
-
 , asdf
 , astropy
 , astropy-helpers
+, astropy-extension-helpers
 , beautifulsoup4
 , drms
 , glymur
@@ -29,16 +29,18 @@
 
 buildPythonPackage rec {
   pname = "sunpy";
-  version = "1.0.6";
+  version = "2.0.6";
   disabled = pythonOlder "3.6";
 
-  src = fetchFromGitHub {
+  src = fetchPypi {
-    owner = "sunpy";
+    inherit pname version;
-    repo = pname;
+    sha256 = "109flghca42yhsm2w5xicqhyx1mc8c3vlwvadbn65fz3lhysqj67";
-    rev = "v${version}";
-    sha256 = "0j2yfhfxgi95rig8cfp9lvszb7694gq90jvs0xrb472hwnzgh2sk";
   };
 
+  nativeBuildInputs = [
+    astropy-extension-helpers
+  ];
+
   propagatedBuildInputs = [
     numpy
     scipy
@@ -66,16 +68,11 @@ buildPythonPackage rec {
     pytest-mock
   ];
 
-  preBuild = ''
-    export SETUPTOOLS_SCM_PRETEND_VERSION="${version}"
-    export HOME=$(mktemp -d)
-  '';
-
   # darwin has write permission issues
   doCheck = stdenv.isLinux;
   # ignore documentation tests
   checkPhase = ''
-    pytest sunpy -k 'not rst'
+    PY_IGNORE_IMPORTMISMATCH=1 HOME=$(mktemp -d) pytest sunpy -k 'not rst'
   '';
 
   meta = with lib; {

pkgs/top-level/python-packages.nix

@@ -421,6 +421,8 @@ in {
 
   astropy-helpers = callPackage ../development/python-modules/astropy-helpers { };
 
+  astropy-extension-helpers = callPackage ../development/python-modules/astropy-extension-helpers { };
+
   astroquery = callPackage ../development/python-modules/astroquery { };
 
   asttokens = callPackage ../development/python-modules/asttokens { };
@@ -1999,8 +2001,6 @@ in {
 
   exifread = callPackage ../development/python-modules/exifread { };
 
-  extension-helpers = callPackage ../development/python-modules/extension-helpers { };
-
   extras = callPackage ../development/python-modules/extras { };
 
   eyeD3 = callPackage ../development/python-modules/eyed3 { };
@@ -5121,6 +5121,8 @@ in {
 
   pyepsg = callPackage ../development/python-modules/pyepsg { };
 
+  pyerfa = callPackage ../development/python-modules/pyerfa { };
+
   pyexcel = callPackage ../development/python-modules/pyexcel { };
 
   pyexcelerator = callPackage ../development/python-modules/pyexcelerator { };