Merge pull request #71221 from NixOS/staging-next

Staging next

pkgs/development/python-modules/flake8/default.nix

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "flake8";
-  version = "3.7.7";
+  version = "3.7.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "859996073f341f2670741b51ec1e67a01da142831aa1fdc6242dbf88dffbe661";
+    sha256 = "19241c1cbc971b9962473e4438a2ca19749a7dd002dd1a946eaba171b4114548";
   };
 
   checkInputs = [ pytest mock pytestrunner ];

pkgs/development/python-modules/netcdf4/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, isPyPy, pytest
+{ stdenv, lib, buildPythonPackage, fetchPypi, isPyPy, pytest
 , numpy, zlib, netcdf, hdf5, curl, libjpeg, cython, cftime
 }:
 buildPythonPackage rec {
@@ -37,7 +37,7 @@ buildPythonPackage rec {
 
   # Variables used to configure the build process
   USE_NCCONFIG="0";
-  HDF5_DIR=hdf5;
+  HDF5_DIR = lib.getDev hdf5;
   NETCDF4_DIR=netcdf;
   CURL_DIR=curl.dev;
   JPEG_DIR=libjpeg.dev;

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

@@ -6,11 +6,17 @@
 , unzip
 , callPackage
 , bootstrapped-pip
+, lib
+, pipInstallHook
+, setuptoolsBuildHook
 }:
 
 buildPythonPackage rec {
   pname = "setuptools";
   version = "41.2.0";
+  # Because of bootstrapping we don't use the setuptoolsBuildHook that comes with format="setuptools" directly.
+  # Instead, we override it to remove setuptools to avoid a circular dependency.
+  # The same is done for pip and the pipInstallHook.
   format = "other";
 
   src = fetchPypi {
@@ -19,19 +25,18 @@ buildPythonPackage rec {
     sha256 = "66b86bbae7cc7ac2e867f52dc08a6bd064d938bac59dfec71b9b565dd36d6012";
   };
 
-  # There is nothing to build
-  dontBuild = true;
+  nativeBuildInputs = [
+    bootstrapped-pip
+    (pipInstallHook.override{pip=null;})
+    (setuptoolsBuildHook.override{setuptools=null; wheel=null;})
+  ];
 
-  nativeBuildInputs = [ bootstrapped-pip ];
-
-  installPhase = ''
-      dst=$out/${python.sitePackages}
-      mkdir -p $dst
-      export PYTHONPATH="$dst:$PYTHONPATH"
-      ${python.pythonForBuild.interpreter} setup.py install --prefix=$out
-      wrapPythonPrograms
+  preBuild = lib.strings.optionalString (!stdenv.hostPlatform.isWindows) ''
+    export SETUPTOOLS_INSTALL_WINDOWS_SPECIFIC_FILES=0
   '';
 
+  pipInstallFlags = [ "--ignore-installed" ];
+
   # Adds setuptools to nativeBuildInputs causing infinite recursion.
   catchConflicts = false;
 

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

@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "SQLAlchemy";
-  version = "1.3.6";
+  version = "1.3.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1zxhabcgzspwrh9l7b68p57kqx4h664a1dp9xr8mi84r472pyzi1";
+    sha256 = "106digcgx7nwvykdvmnwf3vfxvfkdv6ykwk7sd325afklikgb3rg";
   };
 
   checkInputs = [

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

@@ -1,4 +1,4 @@
-{ stdenv, fetchPypi, python, buildPythonPackage
+{ stdenv, lib, fetchPypi, python, buildPythonPackage
 , cython, bzip2, lzo, numpy, numexpr, hdf5, six, c-blosc, mock }:
 
 with stdenv.lib;
@@ -23,7 +23,6 @@ buildPythonPackage rec {
     "--bzip2=${getDev bzip2}"
     "--blosc=${getDev c-blosc}"
   ];
-
   # Run the test suite.
   # It requires the build path to be in the python search path.
   # These tests take quite some time.

pkgs/development/python-modules/zope-deferredimport/default.nix

@@ -23,6 +23,8 @@ buildPythonPackage rec {
     zope-testrunner --test-path=src []
   '';
 
+  doCheck = false;
+
   meta = with lib; {
     description = "Allows you to perform imports names that will only be resolved when used in the code";
     homepage = https://github.com/zopefoundation/zope.deferredimport;

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

@@ -19,7 +19,7 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ zope_interface zope_exceptions zope_testing six ];
 
-  doCheck = !stdenv.isDarwin;
+  doCheck = false; # custom test modifies sys.path
 
   meta = with stdenv.lib; {
     description = "A flexible test runner with layer support";