Merge staging-next into staging

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

@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "aiorun";
-  version = "2019.11.1";
+  version = "2020.1.3";
   format = "flit";
 
   disabled = isPy27;
@@ -18,7 +18,7 @@ buildPythonPackage rec {
     owner = "cjrh";
     repo = pname;
     rev = "v${version}";
-    sha256 = "04p3sci6af6qqfkcqamsqhmqqrigcwvl4bmx8yv5ppvkyq39pxi7";
+    sha256 = "0ka0pj6xr47j7rw6kd5mkrr5jyhn631pfpd95ig7vbln4434qnb4";
   };
 
   checkInputs = [

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

@@ -18,12 +18,12 @@
 
 buildPythonPackage rec {
   pname = "altair";
-  version = "4.0.0";
+  version = "4.0.1";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "92dcd7b84c715f8e02bbdf37e36193a4af8138b5b064c05f237e6ed41573880a";
+    sha256 = "145gjad415zjfp0ciq1b19i97ibavj8fki1vzhjppqz55k4704nk";
   };
 
   propagatedBuildInputs = [

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

@@ -1,6 +1,6 @@
 { stdenv, buildPythonPackage, pythonOlder, fetchFromGitHub, async-timeout, pytest, pytest-asyncio }:
 buildPythonPackage rec {
-  version = "3.2.2";
+  version = "3.2.3";
   pname = "asgiref";
 
   disabled = pythonOlder "3.5";
@@ -10,7 +10,7 @@ buildPythonPackage rec {
     owner = "django";
     repo = pname;
     rev = version;
-    sha256 = "11lnynspgdi5zp3hd8piy8h9fq0s3ck6lzyl7h0fn2mxxyx83yh2";
+    sha256 = "1b8h50wvvby9m17q39kc0ql8a2yvg2f89ii7zrl2phaw0vb9i109";
   };
 
   propagatedBuildInputs = [ async-timeout ];

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

@@ -3,12 +3,12 @@
 
 buildPythonPackage rec {
   pname = "asyncpg";
-  version = "0.20.0";
+  version = "0.20.1";
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0yjszgg1zbbsfxj1gv17ymc2hcfvymkvg69dvpvwy0dqspjxq0ma";
+    sha256 = "1c4mcjrdbvvq5crrfc3b9m221qb6pxp55yynijihgfnvvndz2jrr";
   };
 
   checkInputs = [

pkgs/development/python-modules/azure-mgmt-iothub/default.nix

@@ -10,12 +10,12 @@
 
 buildPythonPackage rec {
   pname = "azure-mgmt-iothub";
-  version = "0.9.0";
+  version = "0.10.0";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "19gcvmcd0r9xi2i3m800h3ak0mkf9yj64d55z7nrk25v3ksx0wrl";
+    sha256 = "1xms5wf21z9i28xl0p515xb08mrlsqnzhxcwv7pjlf26lwxadfi0";
   };
 
   propagatedBuildInputs = [

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

@@ -34,7 +34,6 @@ in buildPythonPackage rec {
     six
   ];
 
-  # Tests are in nixos/tests/blivet.nix.
   doCheck = false;
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/cbor2/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "cbor2";
-  version = "4.1.2";
+  version = "5.0.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1bp9l3wdj0wm15xlmlcwbgv6hc6vcfx39nssikj8fkwnd7d1bdhp";
+    sha256 = "1fid6li95jx9c3v83v8c2c8lb03jgirkk9mjmck30yxcwmlxp6a2";
   };
 
   nativeBuildInputs = [ setuptools_scm ];

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

@@ -0,0 +1,86 @@
+{ lib
+, buildPythonPackage
+, pythonOlder
+, fetchFromGitHub
+, google_api_python_client
+, matplotlib
+, networkx
+, numpy
+, pandas
+, pythonProtobuf  # pythonPackages.protobuf
+, requests
+, scipy
+, sortedcontainers
+, sympy
+, typing-extensions
+  # test inputs
+, pytestCheckHook
+, pytest-benchmark
+, ply
+, pydot
+, pyyaml
+, pygraphviz
+}:
+
+buildPythonPackage rec {
+  pname = "cirq";
+  version = "0.6.1";
+
+  disabled = pythonOlder "3.5";
+
+  src = fetchFromGitHub {
+    owner = "quantumlib";
+    repo = "cirq";
+    rev = "v${version}";
+    sha256 = "0lhr2dka7vpz9xd6akxphrcv2b3ni2cgjywpc1r7qpqa5mrq1q7f";
+  };
+
+  # Cirq 0.6 requires networkx==2.3 only for optional qiskit dependency/test, disable this to avoid networkx version conflicts. https://github.com/quantumlib/Cirq/issues/2368
+  # Cirq locks protobuf==3.8.0, but tested working with default pythonPackages.protobuf (3.7). This avoids overrides/pythonPackages.protobuf conflicts
+  prePatch = ''
+    substituteInPlace requirements.txt --replace "networkx==2.3" "networkx" \
+      --replace "protobuf==3.8.0" "protobuf"
+
+    # Fix sympy 1.5 test failures. Should be fixed in v0.7
+    substituteInPlace cirq/optimizers/eject_phased_paulis_test.py --replace "phase_exponent=0.125 + x / 8" "phase_exponent=0.125 + x * 0.125"
+    substituteInPlace cirq/contrib/quirk/cells/parse_test.py --replace "parse_formula('5t') == 5 * t" "parse_formula('5t') == 5.0 * t"
+  '';
+
+  propagatedBuildInputs = [
+    google_api_python_client
+    numpy
+    matplotlib
+    networkx
+    pandas
+    pythonProtobuf
+    requests
+    scipy
+    sortedcontainers
+    sympy
+    typing-extensions
+  ];
+
+  doCheck = true;
+  # pythonImportsCheck = [ "cirq" "cirq.Ciruit" ];  # cirq's importlib hook doesn't work here
+  dontUseSetuptoolsCheck = true;
+  checkInputs = [
+    pytestCheckHook
+    pytest-benchmark
+    ply
+    pydot
+    pyyaml
+    pygraphviz
+  ];
+  # TODO: enable op_serializer_test. Error is type checking, for some reason wants bool instead of numpy.bool_. Not sure if protobuf or internal issue
+  pytestFlagsArray = [
+    "--ignore=dev_tools"  # Only needed when developing new code, which is out-of-scope
+    "--ignore=cirq/google/op_serializer_test.py"  # investigating in https://github.com/quantumlib/Cirq/issues/2727
+  ];
+
+  meta = with lib; {
+    description = "A framework for creating, editing, and invoking Noisy Intermediate Scale Quantum (NISQ) circuits.";
+    homepage = "http://github.com/quantumlib/cirq";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ drewrisinger ];
+  };
+}

pkgs/development/python-modules/django-picklefield/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "django-picklefield";
-  version = "2.0";
+  version = "2.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f1733a8db1b6046c0d7d738e785f9875aa3c198215de11993463a9339aa4ea24";
+    sha256 = "0imncys5s3vsy2q79nn7k5d670da1xgmcr9gmhn06fry6ibf39b7";
   };
 
   propagatedBuildInputs = [ django ];

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

@@ -1,4 +1,4 @@
-{ buildPythonPackage, fetchFromGitHub, fetchpatch, isPyPy, lib
+{ stdenv, buildPythonPackage, fetchFromGitHub, fetchpatch, isPyPy, lib
 , psutil, setuptools, bottle, batinfo, pysnmp
 , hddtemp, future
 # Optional dependencies:
@@ -20,19 +20,38 @@ buildPythonPackage rec {
   };
 
   # Some tests fail in the sandbox (they e.g. require access to /sys/class/power_supply):
-  patches = lib.optional doCheck ./skip-failing-tests.patch
-    ++ [ (fetchpatch {
-      # Correct unitest
-      url = "https://github.com/nicolargo/glances/commit/abf64ffde31113f5f46ef286703ff061fc57395f.patch";
-      sha256 = "00krahqq89jvbgrqx2359cndmvq5maffhpj163z10s1n7q80kxp1";
-    }) ];
+  patches = lib.optional (doCheck && stdenv.isLinux) ./skip-failing-tests.patch
+    ++ [
+      (fetchpatch {
+        # Correct unitest
+        url = "https://github.com/nicolargo/glances/commit/abf64ffde31113f5f46ef286703ff061fc57395f.patch";
+        sha256 = "00krahqq89jvbgrqx2359cndmvq5maffhpj163z10s1n7q80kxp1";
+      })
+
+      (fetchpatch {
+        # Fix IP plugin initialization issue
+        url = "https://github.com/nicolargo/glances/commit/48cb5ef8053d823302e7e53490fb22cec2fabb0f.patch";
+        sha256 = "1590qgcr8w3d9ddpgd9mk5j6q6aq29341vr8bi202yjwwiv2bia9";
+      })
+    ];
+
+  # On Darwin this package segfaults due to mismatch of pure and impure
+  # CoreFoundation. This issues was solved for binaries but for interpreted
+  # scripts a workaround below is still required.
+  # Relevant: https://github.com/NixOS/nixpkgs/issues/24693
+  makeWrapperArgs = lib.optionals stdenv.isDarwin [
+    "--set" "DYLD_FRAMEWORK_PATH" "/System/Library/Frameworks"
+  ];
 
   doCheck = true;
   checkInputs = [ unittest2 ];
+  preCheck = lib.optional stdenv.isDarwin ''
+    export DYLD_FRAMEWORK_PATH=/System/Library/Frameworks
+  '';
 
-  propagatedBuildInputs = [ psutil setuptools bottle batinfo pysnmp hddtemp future
+  propagatedBuildInputs = [ psutil setuptools bottle batinfo pysnmp future
     netifaces
-  ];
+  ] ++ lib.optional stdenv.isLinux hddtemp;
 
   preConfigure = ''
     sed -i 's/data_files\.append((conf_path/data_files.append(("etc\/glances"/' setup.py;
@@ -43,5 +62,6 @@ buildPythonPackage rec {
     description = "Cross-platform curses-based monitoring tool";
     license = licenses.lgpl3;
     maintainers = with maintainers; [ primeos koral ];
+    platforms = platforms.linux ++ platforms.darwin;
   };
 }

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

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "josepy";
-  version = "1.2.0";
+  version = "1.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1lq2s1649zinfii9ccl1wk6aqpaj35r8xwz44020ylp9ky1rmv4w";
+    sha256 = "068nkdbag049cjs9q3rrs5j5f1239202y0g9xblii6rr0fjgyhf3";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/nest-asyncio/default.nix

@@ -5,16 +5,16 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.2.1";
+  version = "1.2.2";
   pname = "nest_asyncio";
   disabled = !(pythonAtLeast "3.5");
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7d4d7c1ca2aad0e5c2706d0222c8ff006805abfd05caa97e6127c8811d0f6adc";
+    sha256 = "06hw495yqg60j738jp3qaxryhyrs36lpgmblf1sm2m2c3mgm92p5";
   };
 
-  # tests not packaged with source dist as of 1.2.1/1.2.2, and
+  # tests not packaged with source dist as of 1.2.2/1.2.2, and
   # can't check tests out of GitHub easily without specific commit IDs (no tagged releases)
   doCheck = false;
   pythonImportsCheck = [ "nest_asyncio" ];

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pdftotext";
-  version = "2.1.2";
+  version = "2.1.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c8bdc47b08baa17b8e03ba1f960fc6335b183d2644eaf7300e088516758a6090";
+    sha256 = "00xf3jmpb4m3q758wvk4khpcmiys4gmd88vvrz6i7yw1jl268y6k";
   };
 
   buildInputs = [ poppler ];

pkgs/development/python-modules/pre-commit/default.nix

@@ -7,6 +7,7 @@
 , importlib-metadata
 , importlib-resources
 , nodeenv
+, python
 , six
 , toml
 , virtualenv
@@ -22,6 +23,10 @@ buildPythonApplication rec {
     sha256 = "0l5qg1cw4a0670m96s0ryy5mqz5aslfrrnwpriqgmrnsgdixhj4g";
   };
 
+  patches = [
+    ./hook-tmpl-use-the-hardcoded-path-to-pre-commit.patch
+  ];
+
   propagatedBuildInputs = [
     aspy-yaml
     cached-property
@@ -38,6 +43,11 @@ buildPythonApplication rec {
   # slow and impure
   doCheck = false;
 
+  preFixup = ''
+    substituteInPlace $out/${python.sitePackages}/pre_commit/resources/hook-tmpl \
+      --subst-var-by pre-commit $out
+  '';
+
   meta = with lib; {
     description = "A framework for managing and maintaining multi-language pre-commit hooks";
     homepage = https://pre-commit.com/;

pkgs/development/python-modules/pre-commit/hook-tmpl-use-the-hardcoded-path-to-pre-commit.patch

@@ -0,0 +1,25 @@
+From d9e6999e32112602ec276634cb004eda3ca64ec3 Mon Sep 17 00:00:00 2001
+From: "Wael M. Nasreddine" <wael.nasreddine@gmail.com>
+Date: Mon, 13 Jan 2020 11:04:58 -0800
+Subject: [PATCH] hook-tmpl: use the hardcoded path to pre-commit, if found
+
+---
+ pre_commit/resources/hook-tmpl | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/pre_commit/resources/hook-tmpl b/pre_commit/resources/hook-tmpl
+index 213d16e..3a99211 100755
+--- a/pre_commit/resources/hook-tmpl
++++ b/pre_commit/resources/hook-tmpl
+@@ -107,6 +107,8 @@ def _exe() -> Tuple[str, ...]:
+             except OSError:
+                 pass
+ 
++    if os.path.isfile('@pre-commit@/bin/pre-commit') and os.access('@pre-commit@/bin/pre-commit', os.X_OK):
++        return ('@pre-commit@/bin/pre-commit', 'run')
+     if distutils.spawn.find_executable('pre-commit'):
+         return ('pre-commit', 'run')
+ 
+-- 
+2.23.1
+

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

@@ -1,7 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
-, pkgs
+, enchant2
 }:
 
 buildPythonPackage rec {
@@ -13,15 +13,21 @@ buildPythonPackage rec {
     sha256 = "fc31cda72ace001da8fe5d42f11c26e514a91fa8c70468739216ddd8de64e2a0";
   };
 
-  propagatedBuildInputs = [ pkgs.enchant1 ];
+  propagatedBuildInputs = [ enchant2 ];
 
-  patchPhase = let
-    path_hack_script = "s|LoadLibrary(e_path)|LoadLibrary('${pkgs.enchant1}/lib/' + e_path)|";
+  postPatch = let
+    libext = stdenv.hostPlatform.extensions.sharedLibrary;
   in ''
-    sed -i "${path_hack_script}" enchant/_enchant.py
-
-    # They hardcode a bad path for Darwin in their library search code
-    substituteInPlace enchant/_enchant.py --replace '/opt/local/lib/' ""
+    # Use the $PYENCHANT_LIBRARY_PATH envvar lookup line to hard-code the
+    # location of the nix enchant-2 library into _enchant.py.
+    #
+    # Also, they hardcode a bad path for Darwin in their library search code;
+    # This code should never be hit, but in case it does, we don't want to have
+    # it "accidentally" work by pulling something from /opt.
+    substituteInPlace enchant/_enchant.py                  \
+      --replace 'os.environ.get("PYENCHANT_LIBRARY_PATH")' \
+                "'${enchant2}/lib/libenchant-2${libext}'"  \
+      --replace '/opt/local/lib/' ""
   '';
 
   # dictionaries needed for tests
@@ -31,7 +37,6 @@ buildPythonPackage rec {
     description = "pyenchant: Python bindings for the Enchant spellchecker";
     homepage = https://github.com/pyenchant/pyenchant;
     license = licenses.lgpl21;
-    badPlatforms = [ "x86_64-darwin" ];
   };
 
 }

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "python-sql";
-  version = "1.0.0";
+  version = "1.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "05ni936y0ia9xmryl7mlhbj9i80nnvq1bi4zxhb96rv7yvpb3fqb";
+    sha256 = "0f0g10y0whvax8yv0rfs7b4yd68lbxbss1za0mvbvr65b8r3pdxz";
   };
 
   meta = {

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "quantities";
-  version = "0.12.3";
+  version = "0.12.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "582f3c7aeba897846761e966615e01202a5e5d06add304492931b05085d19883";
+    sha256 = "12qx6cgib3wxmm2cvann4zw4jnhhn24ms61ifq9f3jbh31nn6gd3";
   };
 
   propagatedBuildInputs = [ numpy ];

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "relatorio";
-  version = "0.9.0";
+  version = "0.9.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0q93sl7ppfvjxylgq9m5n4xdgv4af7d69yxd84zszq10vjmpsg6k";
+    sha256 = "0an1yiy4pxfazrbaw4sm8ybhxqn46yzsakkl9qjklafn1j69lnza";
   };
 
   propagatedBuildInputs = [

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

@@ -7,13 +7,13 @@
 
 buildPythonPackage rec {
   pname = "rpyc";
-  version = "4.1.2";
+  version = "4.1.3";
 
   src = fetchFromGitHub {
     owner = "tomerfiliba";
     repo = pname;
     rev = version;
-    sha256 = "1xvrcik1650r1412fg79va0kd0fgg1ml241y1ai429qwy87dil1k";
+    sha256 = "145mi8p37x9cbfm5117g4ng7b5rmghjjwgm319qqhwgzvqg3y4j9";
   };
 
   propagatedBuildInputs = [ plumbum ];

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

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "sqlmap";
-  version = "1.3.12";
+  version = "1.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3bad3275e2f29ffa54d4013a2ac2c77e87d01a1d745065d54ed5e60bc68dfbf0";
+    sha256 = "0s6lgp66bn0l4a5mwxiv9h04sa7braqvjskns315lb93lyb4y092";
   };
 
   # No tests in archive

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

@@ -14,14 +14,14 @@
 
 buildPythonPackage rec {
   pname = "uvicorn";
-  version = "0.10.4";
+  version = "0.11.2";
   disabled = isPy27;
 
   src = fetchFromGitHub {
     owner = "encode";
     repo = pname;
     rev = version;
-    sha256 = "0z4h04mbkzqgpk698bac6f50jxkf02ils6khzl7zbw7yvi6gkkc8";
+    sha256 = "145c569j4511zw3wglyv9qgd7g1757ypi2blcckpcmahqw11l5p2";
   };
 
   propagatedBuildInputs = [