Merge master into staging-next

pkgs/applications/science/logic/poly/default.nix

@@ -12,6 +12,13 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-E2lHo8Bt4ujoGQ623fjkQbqRnDYJYilXdRt4lnF4wJk=";
   };
 
+  # https://github.com/SRI-CSL/libpoly/pull/52
+  postPatch = lib.optionalString stdenv.isDarwin ''
+    substituteInPlace src/CMakeLists.txt --replace \
+      '"utils/open_memstream.c ''${poly_SOURCES}"' \
+      'utils/open_memstream.c ''${poly_SOURCES}'
+  '';
+
   nativeBuildInputs = [ cmake ];
 
   buildInputs = [ gmp python3 ];

pkgs/applications/version-management/git-and-tools/gh/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "gh";
-  version = "1.10.2";
+  version = "1.10.3";
 
   src = fetchFromGitHub {
     owner = "cli";
     repo = "cli";
     rev = "v${version}";
-    sha256 = "sha256-hI4kV7Xj0oMEfD6SzZ+KWHmMp9yGtr18HPPwkOpr5JA=";
+    sha256 = "sha256-hwqnINygXycd9W6tPjXsRcGbdTyULGL31aRl5NUxGtc=";
   };
 
-  vendorSha256 = "sha256-A7Bo0HQ5Z2SXY32jWCYgwvvInD3xYLSXvipzeaQTDiM=";
+  vendorSha256 = "sha256-acFN/StOMu8RSN/wvJsf4vSnjsmRnkrjuDb9cDMnXRs=";
 
   nativeBuildInputs = [ installShellFiles ];
 

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

@@ -1,15 +1,16 @@
 { lib, buildPythonPackage, fetchPypi, fetchFromGitHub
-, wheel, pytestCheckHook, pytestrunner }:
+, wheel, pytestCheckHook, pytestrunner, pythonAtLeast }:
 
 buildPythonPackage rec {
-  version = "0.18.1";
+  version = "0.18.4";
   pname = "bacpypes";
+  disabled = pythonAtLeast "3.9";
 
   src = fetchFromGitHub {
     owner = "JoelBender";
     repo = "bacpypes";
     rev = version;
-    sha256 = "1fxrh57z3fjl95db8jh71grkv5id8qk65g6k5jqcs9v3dgkg8jkl";
+    sha256 = "1z5v0i7ms8na062wxd5ki43yy5z2d9cns0p4vdmkx2drwsbzlav2";
   };
 
   propagatedBuildInputs = [ wheel ];

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

@@ -1,7 +1,7 @@
 { lib, buildPythonPackage, fetchFromGitHub, isPy27 }:
 
 buildPythonPackage rec {
-  version = "2.2.1";
+  version = "2.2.2";
   pname = "elementpath";
   disabled = isPy27; # uses incompatible class syntax
 
@@ -9,7 +9,7 @@ buildPythonPackage rec {
     owner = "sissaschool";
     repo = "elementpath";
     rev = "v${version}";
-    sha256 = "15yjl18n81zddd27789mcy12gnja3cqycjdykybwgd9i0ysj96gl";
+    sha256 = "sha256-n4zIn2WmFHaVaah2J0mz7Q6G4Ptb8Ms0dwQYbh0Ofcs=";
   };
 
   # avoid circular dependency with xmlschema which directly depends on this

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

@@ -53,6 +53,9 @@ buildPythonPackage {
   ] ++ lib.optionals stdenv.isAarch64 [
     # https://github.com/pydicom/pydicom/issues/1386
     "test_array"
+  ] ++ lib.optionals stdenv.isDarwin [
+    # flaky, hard to reproduce failure outside hydra
+    "test_time_check"
   ];
 
   meta = with lib; {

pkgs/development/python-modules/pyside/shiboken.nix

@@ -1,8 +1,6 @@
 { lib, fetchFromGitHub, buildPythonPackage
 , cmake
-, isPy35
-, isPy36
-, isPy37
+, fetchurl
 , isPy3k
 , libxml2
 , libxslt
@@ -10,6 +8,7 @@
 , pysideApiextractor
 , pysideGeneratorrunner
 , python
+, pythonAtLeast
 , qt4
 , sphinx
 }:
@@ -39,8 +38,17 @@ buildPythonPackage rec {
       \"$\{GENERATORRUNNER_PLUGIN_DIR}\" lib/generatorrunner/
   '';
 
-  # gcc6 patch was also sent upstream: https://github.com/pyside/Shiboken/pull/86
-  patches = [ ./gcc6.patch ] ++ (lib.optional (isPy35 || isPy36 || isPy37) ./shiboken_py35.patch);
+  patches = [
+    # gcc6 patch was also sent upstream: https://github.com/pyside/Shiboken/pull/86
+    ./gcc6.patch
+    (lib.optional (pythonAtLeast "3.5") ./shiboken_py35.patch)
+    (fetchurl {
+      # https://github.com/pyside/Shiboken/pull/90
+      name = "fix-build-with-python-3.9.patch";
+      url = "https://github.com/pyside/Shiboken/commit/d1c901d4c0af581003553865360ba964cda041e8.patch";
+      sha256 = "1f7slz8n8rps5r67hz3hi4rr82igc3l166shfy6647ivsb2fnxwy";
+    })
+  ];
 
   cmakeFlags = lib.optionals isPy3k [
     "-DUSE_PYTHON3=TRUE"

pkgs/development/python-modules/pyvisa-py/default.nix

@@ -0,0 +1,48 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, setuptools-scm
+, pyserial
+, pyusb
+, pyvisa
+, typing-extensions
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "pyvisa-py";
+  version = "0.5.1";
+
+  src = fetchFromGitHub {
+    owner = "pyvisa";
+    repo = "pyvisa-py";
+    rev = version;
+    hash = "sha256-V1BS+BvHVI8h/rynLnOHvQdIR6RwQrNa2p2S6GQug98=";
+  };
+
+  nativeBuildInputs = [
+    setuptools-scm
+  ];
+
+  propagatedBuildInputs = [
+    pyserial
+    pyusb
+    pyvisa
+    typing-extensions
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  postConfigure = ''
+    export SETUPTOOLS_SCM_PRETEND_VERSION="v${version}"
+  '';
+
+  meta = with lib; {
+    description = "PyVISA backend that implements a large part of the Virtual Instrument Software Architecture in pure Python";
+    homepage = "https://github.com/pyvisa/pyvisa-py";
+    license = licenses.mit;
+    maintainers = with maintainers; [ mvnetbiz ];
+  };
+}

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

@@ -0,0 +1,49 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, setuptools-scm
+, setuptools
+, typing-extensions
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "pyvisa";
+  version = "1.11.3";
+
+  src = fetchFromGitHub {
+    owner = "pyvisa";
+    repo = "pyvisa";
+    rev = version;
+    hash = "sha256-Qe7W1zPI1aedLDnhkLTDPTa/lsNnCGik5Hu+jLn+meA=";
+  };
+
+  nativeBuildInputs = [
+    setuptools-scm
+  ];
+
+  propagatedBuildInputs = [
+    typing-extensions
+    setuptools
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  # Test can't find cli tool bin path correctly
+  disabledTests = [
+    "test_visa_info"
+  ];
+
+  postConfigure = ''
+    export SETUPTOOLS_SCM_PRETEND_VERSION="v${version}"
+  '';
+
+  meta = with lib; {
+    description = "Python package for support of the Virtual Instrument Software Architecture (VISA)";
+    homepage = "https://github.com/pyvisa/pyvisa";
+    license = licenses.mit;
+    maintainers = with maintainers; [ mvnetbiz ];
+  };
+}

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

@@ -5,25 +5,20 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.5.3";
+  version = "1.6.2";
   pname = "xmlschema";
 
   src = fetchFromGitHub {
     owner = "sissaschool";
     repo = "xmlschema";
     rev = "v${version}";
-    sha256 = "0pv8zdz03wjnjwrgjr5pc3q69h7zh51h0iwgwxwl65qi1r6ydk54";
+    sha256 = "sha256-GL2PlHxKDSEsZwHPBAy+tjBSbKyvlbXUWwXakKPmzSs=";
   };
 
   propagatedBuildInputs = [ elementpath ];
 
   checkInputs = [ lxml pytest ];
 
-  postPatch = ''
-    substituteInPlace setup.py \
-      --replace "elementpath~=2.0.0" "elementpath~=2.0"
-  '';
-
   # Ignore broken fixtures, and tests for files which don't exist.
   # For darwin, we need to explicity say we can't reach network
   checkPhase = ''

pkgs/tools/games/ajour/default.nix

@@ -34,16 +34,16 @@ let
 
 in rustPlatform.buildRustPackage rec {
   pname = "Ajour";
-  version = "1.1.0";
+  version = "1.2.0";
 
   src = fetchFromGitHub {
     owner = "casperstorm";
     repo = "ajour";
     rev = version;
-    sha256 = "1xzsgxkdwdqcr8xs9ajr1ykfjjz95z9k7b7l644yijg31xf1lbq6";
+    sha256 = "0xmjr8brjmkk13dsn3yvcl5ss6b214hpka0idk072n46qsyhg2wh";
   };
 
-  cargoSha256 = "02g25wr0f2bjr7zmpll3iicc6i8wk1j9iavagg1vhbpynp6z013x";
+  cargoSha256 = "06d1h2c2abg56567znxh65d4ddpi6wvxip9rbzkmdnzgy3b3y2wl";
 
   nativeBuildInputs = [
     autoPatchelfHook

pkgs/top-level/python-packages.nix

@@ -6927,6 +6927,10 @@ in {
 
   pyvicare = callPackage ../development/python-modules/pyvicare { };
 
+  pyvisa = callPackage ../development/python-modules/pyvisa { };
+
+  pyvisa-py = callPackage ../development/python-modules/pyvisa-py { };
+
   pyviz-comms = callPackage ../development/python-modules/pyviz-comms { };
 
   pyvizio = callPackage ../development/python-modules/pyvizio { };