Merge pull request #255124 from doronbehar/pkg/astropy

python3.pkgs.astropy: 5.2.1 -> 5.3.3 & more

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

@@ -94,5 +94,7 @@ buildPythonPackage rec {
     homepage = "https://github.com/asdf-format/asdf";
     license = licenses.bsd3;
     maintainers = with maintainers; [ ];
+    # Many tests fail, according to Hydra
+    broken = true;
   };
 }

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , findutils
 , pytestCheckHook
 , pythonOlder
@@ -11,23 +12,31 @@
 
 buildPythonPackage rec {
   pname = "extension-helpers";
-  version = "1.0.0";
+  version = "1.1.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6";
+    hash = "sha256-SUYMeKP40fjOwXRHn16FrURZSMzEFgM8WqPm3fLFAik=";
   };
 
+  patches = [
+    # Not needed to allow this package to build, but meant for it's dependent
+    # packages, like astropy. See explanation at:
+    # https://github.com/astropy/extension-helpers/pull/59
+    (fetchpatch {
+      url = "https://github.com/astropy/extension-helpers/commit/796f3e7831298df2d26b6d994b13fd57061a56d1.patch";
+      hash = "sha256-NnqK9HQq1hQ66RUJf9gTCuLyA0BVqVtL292mSXJ9860=";
+    })
+  ];
+
   nativeBuildInputs = [
     setuptools-scm
     wheel
   ];
 
-  patches = [ ./permissions.patch ];
-
   nativeCheckInputs = [
     findutils
     pip

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

@@ -1,20 +0,0 @@
-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
+, fetchpatch
 , buildPythonPackage
 , pythonOlder
 
@@ -10,6 +11,11 @@
 , oldest-supported-numpy
 , setuptools-scm
 , wheel
+# testing
+, pytestCheckHook
+, pytest-xdist
+, pytest-astropy
+, python
 
 # runtime
 , numpy
@@ -18,21 +24,30 @@
 , pyyaml
 }:
 
-let
+buildPythonPackage rec {
   pname = "astropy";
-  version = "5.2.1";
-in
-buildPythonPackage {
-  inherit pname version;
+  version = "5.3.3";
   format = "pyproject";
 
   disabled = pythonOlder "3.8"; # according to setup.cfg
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-9q4noHf46oSQPvp2x5C5hWFzQaAISw0hw5H3o/MyrCM=";
+    hash = "sha256-AzDfn116IlQ2fpuM9EJVuhBwsGEjGIxqcu3BgEk/k7s=";
   };
+  patches = [
+    # Fixes running tests in parallel issue
+    # https://github.com/astropy/astropy/issues/15316. Fix from
+    # https://github.com/astropy/astropy/pull/15327
+    (fetchpatch {
+      url = "https://github.com/astropy/astropy/commit/1042c0fb06a992f683bdc1eea2beda0b846ed356.patch";
+      hash = "sha256-bApAcGBRrJ94thhByoYvdqw2e6v77+FmTfgmGcE6MMk=";
+    })
+  ];
 
+  # Relax cython dependency to allow this to build, upstream only doesn't
+  # support cython 3 as of writing. See:
+  # https://github.com/astropy/astropy/issues/15315
   postPatch = ''
     substituteInPlace pyproject.toml \
       --replace 'cython==' 'cython>='
@@ -54,14 +69,28 @@ buildPythonPackage {
     pyyaml
   ];
 
-  # infinite recursion with pytest-astropy (pytest-astropy-header depends on astropy itself)
-  doCheck = false;
+  nativeCheckInputs = [
+    pytestCheckHook
+    pytest-xdist
+    pytest-astropy
+  ];
 
-  meta = with lib; {
+  # Not running it inside the build directory. See:
+  # https://github.com/astropy/astropy/issues/15316#issuecomment-1722190547
+  preCheck = ''
+    cd "$out"
+    export HOME="$(mktemp -d)"
+    export OMP_NUM_THREADS=$(( $NIX_BUILD_CORES / 4 ))
+  '';
+  pythonImportsCheck = [
+    "astropy"
+  ];
+
+  meta = {
     description = "Astronomy/Astrophysics library for Python";
     homepage = "https://www.astropy.org";
-    license = licenses.bsd3;
-    platforms = platforms.all;
-    maintainers = [ maintainers.kentjames ];
+    license = lib.licenses.bsd3;
+    platforms = lib.platforms.all;
+    maintainers = with lib.maintainers; [ kentjames doronbehar ];
   };
 }

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

@@ -66,6 +66,8 @@ buildPythonPackage rec {
     description = "Functions and classes to access online data resources";
     homepage = "https://astroquery.readthedocs.io/";
     license = licenses.bsd3;
+    # Broken since a certain astropy update, due to API incompatibility
+    broken = true;
     maintainers = [ maintainers.smaret ];
   };
 }

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , jinja2
 , oldest-supported-numpy
 , setuptools-scm
@@ -8,20 +9,28 @@
 , liberfa
 , packaging
 , numpy
+, pytestCheckHook
+, pytest-doctestplus
 }:
 
 buildPythonPackage rec {
   pname = "pyerfa";
   format = "pyproject";
-  version = "2.0.0.1";
-
-  doCheck = false;
+  version = "2.0.0.3";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-L9Rjf/4sHm7edILBP1g7p8cxGdeL75AXVEjOUGoO3jA=";
+    hash = "sha256-13+7+lg1DBlMy5nl2TqgXTwrFNWq2LZi2Txq2f/0Hzk=";
   };
 
+  patches = [
+    # Sort of helps maybe for https://github.com/liberfa/pyerfa/issues/112
+    (fetchpatch {
+      url = "https://github.com/liberfa/pyerfa/commit/4866342b94c5e7344711146f1186a4c3e7534da8.patch";
+      hash = "sha256-uPFFdLYfRweQdeEApBAw6Ulqh31NTQwwmnaU+x/M+C0=";
+    })
+  ];
+
   nativeBuildInputs = [
     jinja2
     oldest-supported-numpy
@@ -31,14 +40,32 @@ buildPythonPackage rec {
   ];
 
   propagatedBuildInputs = [
-    liberfa
     numpy
   ];
+  buildInputs = [
+    liberfa
+  ];
 
   preBuild = ''
     export PYERFA_USE_SYSTEM_LIBERFA=1
   '';
 
+  # See https://github.com/liberfa/pyerfa/issues/112#issuecomment-1721197483
+  NIX_CFLAGS_COMPILE = "-O2";
+  nativeCheckInputs = [
+    pytestCheckHook
+    pytest-doctestplus
+  ];
+  # Getting circular import errors without this, not clear yet why. This was mentioned to
+  # upstream at: https://github.com/liberfa/pyerfa/issues/112 and downstream at
+  # https://github.com/NixOS/nixpkgs/issues/255262
+  preCheck = ''
+    cd $out
+  '';
+  pythonImportsCheck = [
+    "erfa"
+  ];
+
   meta = with lib; {
     description = "Python bindings for ERFA routines";
     longDescription = ''

pkgs/development/python-modules/qcodes-loop/default.nix

@@ -1,4 +1,5 @@
 { lib
+, stdenv
 , fetchpatch
 , fetchPypi
 , pythonOlder
@@ -97,5 +98,7 @@ buildPythonPackage rec {
     homepage = "https://github.com/QCoDeS/Qcodes_loop";
     license = licenses.mit;
     maintainers = with maintainers; [ evilmav ];
+    # Some tests fail on this platform
+    broken = stdenv.isDarwin;
   };
 }

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

@@ -63,5 +63,7 @@ buildPythonPackage rec {
     changelog = "https://github.com/radio-astro-tools/spectral-cube/releases/tag/v${version}";
     license = licenses.bsd3;
     maintainers = with maintainers; [ smaret ];
+    # Tests fail to start, according to Hydra
+    broken = true;
   };
 }