Merge branch 'staging-next' (PR #91090)

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

@@ -33,11 +33,11 @@
 
 buildPythonPackage rec {
   pname = "bokeh";
-  version = "2.0.2";
+  version = "2.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d9248bdb0156797abf6d04b5eac581dcb121f5d1db7acbc13282b0609314893a";
+    sha256 = "2dfabf228f55676b88acc464f416e2b13ee06470a8ad1dd3e609bb789425fbad";
   };
 
   patches = [

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

@@ -15,11 +15,11 @@
 
 buildPythonPackage rec {
   pname = "holoviews";
-  version = "1.13.2";
+  version = "1.13.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "00i8732qib86xqa3652vkr178ib3682cls4jcv5g52y0rlkd8bfg";
+    sha256 = "e6753651a8598f21fc2c20e8456865ecec276cfea1519182a76d957506727934";
   };
 
   propagatedBuildInputs = [

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

@@ -22,12 +22,12 @@
 
 buildPythonPackage rec {
   pname = "ipython";
-  version = "7.15.0";
+  version = "7.16.1";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0ef1433879816a960cd3ae1ae1dc82c64732ca75cec8dab5a4e29783fb571d0e";
+    sha256 = "9f4fcb31d3b2c533333893b9172264e4821c1ac91839500f31bd43f2c59b3ccf";
   };
 
   prePatch = lib.optionalString stdenv.isDarwin ''

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

@@ -12,11 +12,11 @@
 
 buildPythonPackage rec {
   pname = "jupyter_client";
-  version = "6.1.3";
+  version = "6.1.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3a32fa4d0b16d1c626b30c3002a62dfd86d6863ed39eaba3f537fade197bb756";
+    sha256 = "5099cda1ac86b27b655a715c51e15bdc8bd9595b2b17adb41a2bd446bbbafc4a";
   };
 
   propagatedBuildInputs = [

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

@@ -11,13 +11,13 @@
 
 buildPythonPackage rec {
   pname = "llvmlite";
-  version = "0.32.1";
+  version = "0.33.0";
 
   disabled = isPyPy || !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "41262a47b8cbba5a09203b15b65fbdf11192f92aa226c81e99115acdee8f3b8d";
+    sha256 = "9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596";
   };
 
   nativeBuildInputs = [ llvm ];

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

@@ -12,11 +12,11 @@
 
 buildPythonPackage rec {
   pname = "nbformat";
-  version = "5.0.6";
+  version = "5.0.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "049af048ed76b95c3c44043620c17e56bc001329e07f83fec4f177f0e3d7b757";
+    sha256 = "54d4d6354835a936bad7e8182dcd003ca3dc0cedfee5a306090e04854343b340";
   };
 
   LC_ALL="en_US.utf8";

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

@@ -13,14 +13,14 @@
 }:
 
 buildPythonPackage rec {
-  version = "0.49.1";
+  version = "0.50.0";
   pname = "numba";
   # uses f-strings
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "89e1ad8215918036b0ffc53501888d44ed44c1f2cb09a9e047d06af5cd7e7a5a";
+    sha256 = "c9e5752821530694294db41ee19a4b00e5826c689821907f6c2ece9a02756b29";
   };
 
   NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isDarwin "-I${libcxx}/include/c++/v1";

pkgs/development/python-modules/numpy/1.16.nix

@@ -0,0 +1,94 @@
+{ lib
+, fetchPypi
+, python
+, buildPythonPackage
+, gfortran
+, pytest
+, blas
+, lapack
+, writeTextFile
+, isPyPy
+, cython
+, setuptoolsBuildHook
+ }:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+let
+  cfg = writeTextFile {
+    name = "site.cfg";
+    text = (lib.generators.toINI {} {
+      ${blas.implementation} = {
+        include_dirs = "${lib.getDev blas}/include:${lib.getDev lapack}/include";
+        library_dirs = "${blas}/lib:${lapack}/lib";
+        libraries = "lapack,lapacke,blas,cblas";
+      };
+      lapack = {
+        include_dirs = "${lib.getDev lapack}/include";
+        library_dirs = "${lapack}/lib";
+      };
+      blas = {
+        include_dirs = "${lib.getDev blas}/include";
+        library_dirs = "${blas}/lib";
+      };
+    });
+  };
+in buildPythonPackage rec {
+  pname = "numpy";
+  version = "1.16.5";
+  format = "pyproject.toml";
+
+  src = fetchPypi {
+    inherit pname version;
+    extension = "zip";
+    sha256 = "8bb452d94e964b312205b0de1238dd7209da452343653ab214b5d681780e7a0c";
+  };
+
+  nativeBuildInputs = [ gfortran pytest cython setuptoolsBuildHook ];
+  buildInputs = [ blas lapack ];
+
+  patches = lib.optionals python.hasDistutilsCxxPatch [
+    # We patch cpython/distutils to fix https://bugs.python.org/issue1222585
+    # Patching of numpy.distutils is needed to prevent it from undoing the
+    # patch to distutils.
+    ./numpy-distutils-C++_1.16.patch
+  ];
+
+  preConfigure = ''
+    sed -i 's/-faltivec//' numpy/distutils/system_info.py
+    export NPY_NUM_BUILD_JOBS=$NIX_BUILD_CORES
+  '';
+
+  preBuild = ''
+    ln -s ${cfg} site.cfg
+  '';
+
+  enableParallelBuilding = true;
+
+  doCheck = !isPyPy; # numpy 1.16+ hits a bug in pypy's ctypes, using either numpy or pypy HEAD fixes this (https://github.com/numpy/numpy/issues/13807)
+
+  checkPhase = ''
+    runHook preCheck
+    pushd dist
+    ${python.interpreter} -c 'import numpy; numpy.test("fast", verbose=10)'
+    popd
+    runHook postCheck
+  '';
+
+  passthru = {
+    # just for backwards compatibility
+    blas = blas.provider;
+    blasImplementation = blas.implementation;
+    inherit cfg;
+  };
+
+  # Disable test
+  # - test_large_file_support: takes a long time and can cause the machine to run out of disk space
+  NOSE_EXCLUDE="test_large_file_support";
+
+  meta = {
+    description = "Scientific tools for Python";
+    homepage = "https://numpy.org/";
+    maintainers = with lib.maintainers; [ fridh ];
+  };
+}

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

@@ -35,13 +35,13 @@ let
   };
 in buildPythonPackage rec {
   pname = "numpy";
-  version = "1.18.5";
+  version = "1.19.0";
   format = "pyproject.toml";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "34e96e9dae65c4839bd80012023aadd6ee2ccb73ce7fdf3074c62f301e63120b";
+    sha256 = "76766cc80d6128750075378d3bb7812cf146415bd29b588616f72c943c00d598";
   };
 
   nativeBuildInputs = [ gfortran pytest cython setuptoolsBuildHook ];

pkgs/development/python-modules/numpy/numpy-distutils-C++.patch

@@ -1,8 +1,7 @@
 diff --git a/numpy/distutils/unixccompiler.py b/numpy/distutils/unixccompiler.py
-index 6ed5eec..82a88b5 100644
 --- a/numpy/distutils/unixccompiler.py
 +++ b/numpy/distutils/unixccompiler.py
-@@ -44,8 +44,6 @@ def UnixCCompiler__compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts
+@@ -37,8 +37,6 @@ def UnixCCompiler__compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts
          if opt not in llink_s:
              self.linker_so = llink_s.split() + opt.split()
  
@@ -11,7 +10,7 @@ index 6ed5eec..82a88b5 100644
      # gcc style automatic dependencies, outputs a makefile (-MF) that lists
      # all headers needed by a c file as a side effect of compilation (-MMD)
      if getattr(self, '_auto_depends', False):
-@@ -54,8 +52,15 @@ def UnixCCompiler__compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts
+@@ -47,8 +45,15 @@ def UnixCCompiler__compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts
          deps = []
  
      try:
@@ -26,6 +25,6 @@ index 6ed5eec..82a88b5 100644
 +            self.spawn(self.compiler_so + cc_args + [src, '-o', obj] + deps +
 +                       extra_postargs, display = display)
 +
-     except DistutilsExecError:
-         msg = str(get_exception())
+     except DistutilsExecError as e:
+         msg = str(e)
          raise CompileError(msg)

pkgs/development/python-modules/numpy/numpy-distutils-C++_1.16.patch

@@ -0,0 +1,30 @@
+diff --git a/numpy/distutils/unixccompiler.py b/numpy/distutils/unixccompiler.py
+--- a/numpy/distutils/unixccompiler.py
++++ b/numpy/distutils/unixccompiler.py
+@@ -44,8 +44,6 @@ def UnixCCompiler__compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts
+         if opt not in llink_s:
+             self.linker_so = llink_s.split() + opt.split()
+ 
+-    display = '%s: %s' % (os.path.basename(self.compiler_so[0]), src)
+-
+     # gcc style automatic dependencies, outputs a makefile (-MF) that lists
+     # all headers needed by a c file as a side effect of compilation (-MMD)
+     if getattr(self, '_auto_depends', False):
+@@ -54,8 +52,15 @@ def UnixCCompiler__compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts
+         deps = []
+ 
+     try:
+-        self.spawn(self.compiler_so + cc_args + [src, '-o', obj] + deps +
+-                   extra_postargs, display = display)
++        if self.detect_language(src) == 'c++':
++            display = '%s: %s' % (os.path.basename(self.compiler_so_cxx[0]), src)
++            self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] + deps +
++                       extra_postargs, display = display)
++        else:
++            display = '%s: %s' % (os.path.basename(self.compiler_so[0]), src)
++            self.spawn(self.compiler_so + cc_args + [src, '-o', obj] + deps +
++                       extra_postargs, display = display)
++
+     except DistutilsExecError:
+         msg = str(get_exception())
+         raise CompileError(msg)

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

@@ -30,11 +30,11 @@ let
 
 in buildPythonPackage rec {
   pname = "pandas";
-  version = "1.0.4";
+  version = "1.0.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b35d625282baa7b51e82e52622c300a1ca9f786711b2af7cbe64f1e6831f4126";
+    sha256 = "69c5d920a0b2a9838e677f78f4dde506b95ea8e4d30da25859db6469ded84fa8";
   };
 
   checkInputs = [ pytest glibcLocales moto hypothesis ];
@@ -95,6 +95,9 @@ in buildPythonPackage rec {
     "order_without_freq"
     # tries to import from pandas.tests post install
     "util_in_top_level"
+    # Fails with 1.0.5
+    "test_constructor_list_frames"
+    "test_constructor_with_embedded_frames"
   ] ++ optionals isDarwin [
     "test_locale"
     "test_clipboard"

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

@@ -12,11 +12,11 @@
 
 buildPythonPackage rec {
   pname = "panel";
-  version = "0.9.5";
+  version = "0.9.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "53340615f30f67f3182793695ebe52bf25e7bbb0751aba6f29763244350d0f42";
+    sha256 = "2e86d82bdd5e7664bf49558eedad62b664d5403ec9e422e5ddfcf69e3bd77318";
   };
 
   propagatedBuildInputs = [

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

@@ -25,6 +25,10 @@ buildPythonPackage rec {
     name = "${pname}-${version}-source";
   };
 
+  # Remove when solved https://github.com/NixOS/nixpkgs/issues/81441
+  # Also update pkgs/development/interpreters/python/hooks/pip-install-hook.sh accordingly
+  patches = [ ./reproducible.patch ];
+
   nativeBuildInputs = [ bootstrapped-pip ];
 
   # pip detects that we already have bootstrapped_pip "installed", so we need

pkgs/development/python-modules/pip/reproducible.patch

@@ -0,0 +1,13 @@
+diff --git a/src/pip/_internal/operations/install/wheel.py b/src/pip/_internal/operations/install/wheel.py
+index e7315ee4..4e36b03d 100644
+--- a/src/pip/_internal/operations/install/wheel.py
++++ b/src/pip/_internal/operations/install/wheel.py
+@@ -615,6 +615,8 @@ def install_wheel(
+     direct_url=None,  # type: Optional[DirectUrl]
+ ):
+     # type: (...) -> None
++    _temp_dir_for_testing = (
++        _temp_dir_for_testing or os.environ.get("NIX_PIP_INSTALL_TMPDIR"))
+     with TempDirectory(
+         path=_temp_dir_for_testing, kind="unpacked-wheel"
+     ) as unpacked_dir, ZipFile(wheel_path, allowZip64=True) as z:

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

@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "pyopencl";
-  version = "2020.1";
+  version = "2020.2";
 
   checkInputs = [ pytest ];
   buildInputs = [ opencl-headers ocl-icd pybind11 ];
@@ -25,7 +25,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7513f7054f4eeb5361de1f5113883145fc67dbabde73a2148f221ae05af4d22c";
+    sha256 = "afd9f22547bcd879b9e54252fc885b45034ebfd1890e630827f1afb408a03d23";
   };
 
   # py.test is not needed during runtime, so remove it from `install_requires`

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

@@ -15,11 +15,11 @@
 
 buildPythonPackage rec {
   pname = "qtconsole";
-  version = "4.7.4";
+  version = "4.7.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1zgm57011kpbh6388p8cqwkcgqwlmb7rc9cy3zn9rrnna48byj7x";
+    sha256 = "f5cb275d30fc8085e2d1d18bc363e5ba0ce6e559bf37d7d6727b773134298754";
   };
 
   checkInputs = [ nose ] ++ lib.optionals isPy27 [mock];

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

@@ -9,11 +9,11 @@ let
   });
 in buildPythonPackage rec {
   pname = "scipy";
-  version = "1.4.1";
+  version = "1.5.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59";
+    sha256 = "4ff72877d19b295ee7f7727615ea8238f2d59159df0bdd98f91754be4a2767f0";
   };
 
   checkInputs = [ nose pytest ];

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

@@ -13,7 +13,7 @@
 
 let
   pname = "setuptools";
-  version = "46.1.3";
+  version = "47.3.1";
 
   # Create an sdist of setuptools
   sdist = stdenv.mkDerivation rec {
@@ -23,7 +23,7 @@ let
       owner = "pypa";
       repo = pname;
       rev = "v${version}";
-      sha256 = "1f6bp3qy5zvykimadk8k11k3629hmnwlw2cfw4vwcsvdarhig673";
+      sha256 = "0sy3p4ibgqx67hzn1f254jh8070a8kl9g2la62p3c74k2x7p0r7f";
       name = "${pname}-${version}-source";
     };
 

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

@@ -14,6 +14,13 @@ buildPythonPackage rec {
     sha256 = "64082ebedf6d36ff409ab2878f1aad5c9035f916c5f15a9a1ec7dffc6dfbbed8";
   };
 
+  patches = [
+    # SOMAXCONN limit of glibc-2.31 has been increased from 128 to 4096:
+    # * https://sourceware.org/git/?p=glibc.git;a=commit;h=96958e2700f5b4f4d1183a0606b2b9848a53ea44
+    # * https://github.com/Supervisor/supervisor/issues/1346
+    ./glibc-2.31.patch
+  ];
+
   # wants to write to /tmp/foo which is likely already owned by another
   # nixbld user on hydra
   doCheck = !stdenv.isDarwin;

pkgs/development/python-modules/supervisor/glibc-2.31.patch

@@ -0,0 +1,13 @@
+diff --git a/supervisor/tests/base.py b/supervisor/tests/base.py
+index 643e609..8aa45e7 100644
+--- a/supervisor/tests/base.py
++++ b/supervisor/tests/base.py
+@@ -358,7 +358,7 @@ class DummySocketConfig:
+         return not self.__eq__(other)
+ 
+     def get_backlog(self):
+-        return 128
++        return 4096
+ 
+     def create_and_bind(self):
+         return DummySocket(self.fd)

pkgs/development/python-modules/tornado/4.nix

@@ -0,0 +1,37 @@
+{ lib
+, python
+, buildPythonPackage
+, fetchPypi
+, backports_abc
+, backports_ssl_match_hostname
+, certifi
+, singledispatch
+, futures
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "tornado";
+  version = "4.5.3";
+
+  propagatedBuildInputs = lib.optionals isPy27 [ backports_abc certifi singledispatch backports_ssl_match_hostname futures ];
+
+  # We specify the name of the test files to prevent
+  # https://github.com/NixOS/nixpkgs/issues/14634
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover *_test.py
+  '';
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "02jzd23l4r6fswmwxaica9ldlyc2p6q8dk6dyff7j58fmdzf853d";
+  };
+
+  __darwinAllowLocalNetworking = true;
+
+  meta = {
+    description = "A web framework and asynchronous networking library";
+    homepage = "https://www.tornadoweb.org/";
+    license = lib.licenses.asl20;
+  };
+}

pkgs/development/python-modules/tornado/5.nix

@@ -0,0 +1,37 @@
+{ lib
+, python
+, buildPythonPackage
+, fetchPypi
+, backports_abc
+, backports_ssl_match_hostname
+, certifi
+, singledispatch
+, futures
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "tornado";
+  version = "5.1.1";
+
+  propagatedBuildInputs = lib.optionals isPy27 [ backports_abc certifi singledispatch backports_ssl_match_hostname futures ];
+
+  # We specify the name of the test files to prevent
+  # https://github.com/NixOS/nixpkgs/issues/14634
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover *_test.py
+  '';
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409";
+  };
+
+  __darwinAllowLocalNetworking = true;
+
+  meta = {
+    description = "A web framework and asynchronous networking library";
+    homepage = "https://www.tornadoweb.org/";
+    license = lib.licenses.asl20;
+  };
+}

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

@@ -2,35 +2,11 @@
 , python
 , buildPythonPackage
 , fetchPypi
-, backports_abc
-, backports_ssl_match_hostname
-, certifi
-, singledispatch
-, pythonOlder
-, futures
-, version ? "5.1"
 }:
 
-let
-  versionMap = {
-    "4.5.3" = {
-      sha256 = "02jzd23l4r6fswmwxaica9ldlyc2p6q8dk6dyff7j58fmdzf853d";
-    };
-    "5.1" = {
-      sha256 = "4f66a2172cb947387193ca4c2c3e19131f1c70fa8be470ddbbd9317fd0801582";
-    };
-  };
-in
-
-with versionMap.${version};
-
 buildPythonPackage rec {
   pname = "tornado";
-  inherit version;
-
-  propagatedBuildInputs = [ backports_abc  certifi singledispatch ]
-    ++ lib.optional (pythonOlder "3.5") backports_ssl_match_hostname
-    ++ lib.optional (pythonOlder "3.2") futures;
+  version = "6.0.4";
 
   # We specify the name of the test files to prevent
   # https://github.com/NixOS/nixpkgs/issues/14634
@@ -39,14 +15,15 @@ buildPythonPackage rec {
   '';
 
   src = fetchPypi {
-    inherit pname sha256 version;
+    inherit pname version;
+    sha256 = "0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc";
   };
 
   __darwinAllowLocalNetworking = true;
 
   meta = {
     description = "A web framework and asynchronous networking library";
-    homepage = "http://www.tornadoweb.org/";
+    homepage = "https://www.tornadoweb.org/";
     license = lib.licenses.asl20;
   };
 }

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

@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "tqdm";
-  version = "4.46.1";
+  version = "4.47.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "cd140979c2bebd2311dfb14781d8f19bd5a9debb92dcab9f6ef899c987fcf71f";
+    sha256 = "63ef7a6d3eb39f80d6b36e4867566b3d8e5f1fe3d6cb50c5e9ede2b3198ba7b7";
   };
 
   checkInputs = [ nose coverage glibcLocales flake8 ];

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

@@ -8,16 +8,18 @@
 , requests_toolbelt
 , setuptools_scm
 , tqdm
+, colorama
+, rfc3986
 }:
 
 buildPythonPackage rec {
   pname = "twine";
-  version = "3.1.1";
+  version = "3.2.0";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d561a5e511f70275e5a485a6275ff61851c16ffcb3a95a602189161112d9f160";
+    sha256 = "34352fd52ec3b9d29837e6072d5a2a7c6fe4290e97bba46bb8d478b5c598f7ab";
   };
 
   nativeBuildInputs = [ setuptools_scm ];
@@ -29,6 +31,8 @@ buildPythonPackage rec {
     requests
     requests_toolbelt
     tqdm
+    colorama
+    rfc3986
   ] ++ lib.optionals (pythonOlder "3.8") [ importlib-metadata ];
 
   # Requires network