Merge remote-tracking branch 'upstream/master' into staging

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

@@ -1,4 +1,5 @@
-{ lib
+{ stdenv
+, lib
 , buildPythonPackage
 , pythonOlder
 , fetchFromGitHub
@@ -37,13 +38,16 @@ buildPythonPackage rec {
 
   # 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 = ''
+  postPatch = ''
     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"
+
+    # Fix pandas >= 1.0 error, #2886
+    substituteInPlace cirq/experiments/t1_decay_experiment.py --replace "del tab.columns.name" 'tab.rename_axis(None, axis="columns", inplace=True)'
   '';
 
   propagatedBuildInputs = [
@@ -76,6 +80,13 @@ buildPythonPackage rec {
     "--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
   ];
+  disabledTests = [
+    "test_convert_to_ion_gates" # fails due to rounding error, 0.75 != 0.750...2
+  ] ++ lib.optionals stdenv.isAarch64 [
+    # Seem to fail due to math issues on aarch64?
+    "expectation_from_wavefunction"
+    "test_single_qubit_op_to_framed_phase_form_output_on_example_case"
+  ];
 
   meta = with lib; {
     description = "A framework for creating, editing, and invoking Noisy Intermediate Scale Quantum (NISQ) circuits.";

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "configshell";
-  version = "1.1.27";
+  version = "1.1.28";
 
   src = fetchFromGitHub {
     owner = "open-iscsi";
-    repo ="${pname}-fb";
+    repo = "${pname}-fb";
     rev = "v${version}";
-    sha256 = "1nldzq3097xqgzd8qxv36ydvx6vj2crwanihz53k46is0myrwcnn";
+    sha256 = "1ym2hkvmmacgy21wnjwzyrcxyl3sx4bcx4hc51vf4lzcnj589l68";
   };
 
   propagatedBuildInputs = [ pyparsing six urwid ];

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

@@ -4,7 +4,7 @@
 , fetchPypi
 , isPyPy
 , python
-, openblasCompat # build segfaults with regular openblas
+, blas, lapack # build segfaults with 64-bit blas
 , suitesparse
 , glpk ? null
 , gsl ? null
@@ -14,6 +14,8 @@
 , withFftw ? true
 }:
 
+assert (!blas.is64bit) && (!lapack.is64bit);
+
 buildPythonPackage rec {
   pname = "cvxopt";
   version = "1.2.4";
@@ -25,12 +27,13 @@ buildPythonPackage rec {
     sha256 = "1h9g79gxpgpy6xciqyypihw5q4ngp322lpkka1nkwk0ysybfsp7s";
   };
 
+  buildInputs = [ blas lapack ];
+
   # similar to Gsl, glpk, fftw there is also a dsdp interface
   # but dsdp is not yet packaged in nixpkgs
   preConfigure = ''
-    export CVXOPT_BLAS_LIB_DIR=${openblasCompat}/lib
-    export CVXOPT_BLAS_LIB=openblas
-    export CVXOPT_LAPACK_LIB=openblas
+    export CVXOPT_BLAS_LIB=blas
+    export CVXOPT_LAPACK_LIB=lapack
     export CVXOPT_SUITESPARSE_LIB_DIR=${lib.getLib suitesparse}/lib
     export CVXOPT_SUITESPARSE_INC_DIR=${lib.getDev suitesparse}/include
   '' + lib.optionalString withGsl ''

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "dkimpy";
-  version = "1.0.2";
+  version = "1.0.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "19rz48pzz1i5cc896khaqx2hkhcj5hwsklnyynrdgdr5818qjyff";
+    sha256 = "14idcs0wiyc0iyi5bz3xqimxf3x6dizcjfn92s2ka5zxp95xdyvd";
 };
 
   checkInputs = [ pytest ];

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "FoxDot";
-  version = "0.8.5";
+  version = "0.8.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1k32fjlmzhhh6hvda71xqis13c3bdn7y3f5z9qqd1q410nfpzf59";
+    sha256 = "0c5iqdn17ip6lkf26xb1cwjvcly0448gvqmkbkvhnqy4birc8cf5";
   };
 
   propagatedBuildInputs = [ tkinter supercollider ];

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

@@ -5,21 +5,23 @@
 , gfortran
 , pytest
 , blas
+, lapack
 , writeTextFile
 , isPyPy
 , cython
 , setuptoolsBuildHook
  }:
 
+assert (!blas.is64bit) && (!lapack.is64bit);
+
 let
-  blasImplementation = lib.nameFromURL blas.name "-";
   cfg = writeTextFile {
     name = "site.cfg";
     text = (lib.generators.toINI {} {
-      ${blasImplementation} = {
-        include_dirs = "${blas}/include";
-        library_dirs = "${blas}/lib";
-      } // lib.optionalAttrs (blasImplementation == "mkl") {
+      ${blas.implementation} = {
+        include_dirs = "${blas}/include:${lapack}/include";
+        library_dirs = "${blas}/lib:${lapack}/lib";
+      } // lib.optionalAttrs (blas.implementation == "mkl") {
         mkl_libs = "mkl_rt";
         lapack_libs = "";
       };
@@ -37,7 +39,7 @@ in buildPythonPackage rec {
   };
 
   nativeBuildInputs = [ gfortran pytest cython setuptoolsBuildHook ];
-  buildInputs = [ blas ];
+  buildInputs = [ blas lapack ];
 
   patches = lib.optionals python.hasDistutilsCxxPatch [
     # We patch cpython/distutils to fix https://bugs.python.org/issue1222585
@@ -68,8 +70,10 @@ in buildPythonPackage rec {
   '';
 
   passthru = {
-    blas = blas;
-    inherit blasImplementation cfg;
+    # just for backwards compatibility
+    blas = blas.provider;
+    blasImplementation = blas.implementation;
+    inherit cfg;
   };
 
   # Disable test

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

@@ -0,0 +1,23 @@
+{ stdenv, buildPythonPackage, fetchPypi, pdfrw }:
+
+buildPythonPackage rec {
+  pname = "pagelabels";
+  version = "1.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "07as5kzyvj66bfgvx8bph8gkyj6cgm4lhgxwb78bpdl4m8y8kpma";
+  };
+
+  buildInputs = [ pdfrw ];
+
+  # upstream doesn't contain tests
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Python library to manipulate PDF page labels.";
+    homepage = "https://github.com/lovasoa/pagelabels-py";
+    maintainers = with maintainers; [ teto ];
+    license = licenses.gpl3;
+  };
+}

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

@@ -0,0 +1,21 @@
+{ stdenv, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "pdfrw";
+  version = "0.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1x1yp63lg3jxpg9igw8lh5rc51q353ifsa1bailb4qb51r54kh0d";
+  };
+
+  # tests require the extra download of github.com/pmaupin/static_pdfs
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "pdfrw is a pure Python library that reads and writes PDFs.";
+    homepage = "https://github.com/pmaupin/pdfrw";
+    maintainers = with maintainers; [ teto ];
+    license =  licenses.mit;
+  };
+}

pkgs/development/python-modules/prox-tv/default.nix

@@ -1,13 +1,11 @@
 { lib
 , blas
+, lapack
 , buildPythonPackage
 , cffi
 , fetchFromGitHub
-, liblapack
 , nose
 , numpy
-, openblas
-, useOpenblas ? true
 }:
 
 buildPythonPackage {
@@ -21,8 +19,6 @@ buildPythonPackage {
     sha256 = "0mlrjbb5rw78dgijkr3bspmsskk6jqs9y7xpsgs35i46dvb327q5";
   };
 
-  patches = lib.optional useOpenblas ./use-openblas.patch;
-
   checkInputs = [
     nose
   ];
@@ -32,12 +28,7 @@ buildPythonPackage {
     cffi
   ];
 
-  buildInputs = (
-    if useOpenblas then
-      [ openblas ]
-    else
-      [ blas liblapack ]
-  );
+  buildInputs = [ blas lapack ];
 
   enableParallelBuilding = true;
 

pkgs/development/python-modules/prox-tv/use-openblas.patch

@@ -1,11 +0,0 @@
-index f100b35..448bbaf 100644
---- a/prox_tv/prox_tv_build.py
-+++ b/prox_tv/prox_tv_build.py
-@@ -109,6 +109,6 @@ ffi.set_source(
-     define_macros=[('NOMATLAB', 1)],
-     extra_compile_args=extra_compile_args,
-     extra_link_args=extra_link_args,
--    libraries=['blas', 'lapack'],
-+    libraries=['openblas'],
-     include_dirs=['/usr/include']
- )

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

@@ -3,7 +3,8 @@
 , fetchFromGitHub
 , numpy
 , setuptools
-, liblapack
+, blas
+, lapack
 , isPy27
 , python
 }:
@@ -24,8 +25,8 @@ buildPythonPackage {
 
   propagatedBuildInputs = [
     numpy
-    numpy.blas
-    liblapack
+    blas
+    lapack
   ];
 
   # Include patches from working version of PySparse 1.3-dev in

pkgs/development/python-modules/python-jsonrpc-server/default.nix

@@ -1,6 +1,6 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, pythonOlder
 , pytest, mock, pytestcov, coverage
-, future, futures, ujson
+, future, futures, ujson, isPy38
 }:
 
 buildPythonPackage rec {
@@ -26,6 +26,8 @@ buildPythonPackage rec {
     pytest
   '';
 
+  disabled = isPy38;
+
   propagatedBuildInputs = [ future ujson ]
     ++ stdenv.lib.optional (pythonOlder "3.2") futures;
 

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "rtslib";
-  version = "2.1.71";
+  version = "2.1.72";
 
   src = fetchFromGitHub {
     owner = "open-iscsi";
-    repo ="${pname}-fb";
+    repo = "${pname}-fb";
     rev = "v${version}";
-    sha256 = "0cn9azi44hf59mp47207igv72kjbkyz4rsvgzmwbpz0s57b0hnab";
+    sha256 = "13kycf9xkyxm1ik8yh3qpd96vird8y65daigyiyb4jvx0lmrd0kv";
   };
 
   propagatedBuildInputs = [ six pyudev pygobject3 ];

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

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , blas
-, liblapack
+, lapack
 , numpy
 , scipy
 , scs
@@ -26,7 +26,7 @@ buildPythonPackage rec {
   '';
 
   buildInputs = [
-    liblapack
+    lapack
     blas
   ];
 

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

@@ -0,0 +1,38 @@
+{ lib
+, isPy3k
+, fetchFromGitHub
+, buildPythonPackage
+, flake8-import-order
+, pyflakes
+, mock
+}:
+
+buildPythonPackage rec {
+  pname = "zimports";
+  version = "0.2.0";
+
+  src = fetchFromGitHub {
+    owner = "sqlalchemyorg";
+    repo = "zimports";
+    rev = version;
+    sha256 = "0a5axflkk0wv0rdnrh8l2rgj8gh2pfkg5lrvr8x4yxxiifawrafc";
+  };
+
+  disabled = !isPy3k;
+
+  propagatedBuildInputs = [
+    pyflakes
+    flake8-import-order
+  ];
+
+  checkInputs = [
+    mock
+  ];
+
+  meta = with lib; {
+    description = "Python import rewriter";
+    homepage = "https://github.com/sqlalchemyorg/zimports";
+    license = licenses.mit;
+    maintainers = with maintainers; [ timokau ];
+  };
+}