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

Conflicts:
	pkgs/applications/version-management/git-and-tools/git/default.nix
	pkgs/top-level/all-packages.nix
	pkgs/top-level/unix-tools.nix

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

@@ -19,12 +19,6 @@ buildPythonPackage rec {
     sha256 = "1y932smng7qx7ybmqw4qh75b0lv9imfs5ak9fd0qhysij8kpmdhi";
   };
 
-  postPatch = ''
-    substituteInPlace alot/defaults/alot.rc.spec \
-      --replace "themes_dir = string(default=None)" \
-                "themes_dir = string(default='$out/share/themes')"
-  '';
-
   nativeBuildInputs = lib.optional withManpage sphinx;
 
   propagatedBuildInputs = [
@@ -50,8 +44,8 @@ buildPythonPackage rec {
     cp -r docs/build/man $out/man
   ''
   + ''
-    mkdir -p $out/share/applications
-    cp -r extra/themes $out/share
+    mkdir -p $out/share/{applications,alot}
+    cp -r extra/themes $out/share/alot
 
     sed "s,/usr/bin,$out/bin,g" extra/alot.desktop > $out/share/applications/alot.desktop
   '';

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

@@ -1,24 +1,24 @@
-{ stdenv, buildPythonPackage, fetchPypi
+{ stdenv, buildPythonPackage, fetchFromGitHub
 , sqlite, isPyPy }:
 
 buildPythonPackage rec {
   pname = "apsw";
-  version = "3.9.2-r1";
+  version = "3.22.0-r1";
 
   disabled = isPyPy;
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "dab96fd164dde9e59f7f27228291498217fa0e74048e2c08c7059d7e39589270";
+  src = fetchFromGitHub {
+    owner = "rogerbinns";
+    repo = "apsw";
+    rev = version;
+    sha256 = "02ldvshcgr4c7c8anp4flfnw8g8ys5bflkb8b51rb618qxhhwyak";
   };
 
   buildInputs = [ sqlite ];
 
-  # python: double free or corruption (fasttop): 0x0000000002fd4660 ***
-#   doCheck = false;
-
   meta = with stdenv.lib; {
     description = "A Python wrapper for the SQLite embedded relational database engine";
-    homepage = http://code.google.com/p/apsw/;
+    homepage = https://github.com/rogerbinns/apsw;
+    license = licenses.zlib;
   };
 }

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

@@ -0,0 +1,69 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isPyPy
+, python
+, openblasCompat # build segfaults with regular openblas
+, suitesparse
+, glpk ? null
+, gsl ? null
+, fftw ? null
+, withGlpk ? true
+, withGsl ? true
+, withFftw ? true
+}:
+
+buildPythonPackage rec {
+  pname = "cvxopt";
+  version = "1.1.9";
+
+  disabled = isPyPy; # hangs at [translation:info]
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0gcqq8ymjxv8qa5ss2pdhsj5bahvdxa6h2rlpp51520mjxrpw5cg";
+  };
+
+  # 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=${openblasCompat}/lib
+    export CVXOPT_BLAS_LIB=openblas
+    export CVXOPT_LAPACK_LIB=openblas
+    export CVXOPT_SUITESPARSE_LIB_DIR=${suitesparse}/lib
+    export CVXOPT_SUITESPARSE_INC_DIR=${suitesparse}/include
+  '' + lib.optionalString withGsl ''
+    export CVXOPT_BUILD_GSL=1
+    export CVXOPT_GSL_LIB_DIR=${gsl}/lib
+    export CVXOPT_GSL_INC_DIR=${gsl}/include
+  '' + lib.optionalString withGlpk ''
+    export CVXOPT_BUILD_GLPK=1
+    export CVXOPT_GLPK_LIB_DIR=${glpk}/lib
+    export CVXOPT_GLPK_INC_DIR=${glpk}/include
+  '' + lib.optionalString withFftw ''
+    export CVXOPT_BUILD_FFTW=1
+    export CVXOPT_FFTW_LIB_DIR=${fftw}/lib
+    export CVXOPT_FFTW_INC_DIR=${fftw.dev}/include
+  '';
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover -s tests
+  '';
+
+  meta = {
+    homepage = http://cvxopt.org/;
+    description = "Python Software for Convex Optimization";
+    longDescription = ''
+      CVXOPT is a free software package for convex optimization based on the
+      Python programming language. It can be used with the interactive
+      Python interpreter, on the command line by executing Python scripts,
+      or integrated in other software via Python extension modules. Its main
+      purpose is to make the development of software for convex optimization
+      applications straightforward by building on Python's extensive
+      standard library and on the strengths of Python as a high-level
+      programming language.
+    '';
+    maintainers = with lib.maintainers; [ edwtjo ];
+    license = lib.licenses.gpl3Plus;
+  };
+}

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

@@ -0,0 +1,41 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, cython
+, sphinx
+}:
+
+buildPythonPackage rec {
+  pname = "cysignals";
+  version = "1.6.9";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "003invnixqy1h4lb358vwrxykxzp15csaddkgq3pqqmswnva5908";
+  };
+
+  hardeningDisable = [
+    "fortify"
+  ];
+
+  # currently fails, probably because of formatting changes in gdb 8.0
+  doCheck = false;
+
+  preCheck = ''
+    # Make sure cysignals-CSI is in PATH
+    export PATH="$out/bin:$PATH"
+  '';
+
+  propagatedBuildInputs = [
+    cython
+  ];
+
+  enableParallelBuilding = true;
+
+  meta = {
+    description = "Interrupt and signal handling for Cython";
+    homepage = https://github.com/sagemath/cysignals/;
+    maintainers = with lib.maintainers; [ timokau ];
+    license = lib.licenses.lgpl3Plus;
+  };
+}

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

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, requests }:
+{ stdenv, buildPythonPackage, fetchPypi, requests, jsonpickle }:
 
 buildPythonPackage rec {
   pname = "python-digitalocean";
@@ -6,10 +6,10 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "06391cf0b253c8b4a5a10b3a4b7b7808b890a1d1e3b43d5ce3b5293a9c77af6b";
+    sha256 = "0h4drpdsmk0b3rlvg6q6cz11k23w0swj1iddk7xdcw4m7r7c52kw";
   };
 
-  propagatedBuildInputs = [ requests ];
+  propagatedBuildInputs = [ requests jsonpickle ];
 
   # Package doesn't distribute tests.
   doCheck = false;

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

@@ -0,0 +1,24 @@
+{ lib, buildPythonPackage, fetchFromGitHub
+, click, jinja2, terminaltables }:
+
+buildPythonPackage rec {
+  pname = "envs";
+  version = "1.2.4";
+
+  # move to fetchPyPi when https://github.com/capless/envs/issues/8 is fixed
+  src = fetchFromGitHub {
+    owner  = "capless";
+    repo   = "envs";
+    rev    = "e1f6cbad7f20316fc44324d2c50826d57c2817a8";
+    sha256 = "0p88a79amj0jxll3ssq1dzg78y7zwgc8yqyr7cf53nv2i7kmpakv";
+  };
+
+  checkInputs = [ click jinja2 terminaltables ];
+
+  meta = with lib; {
+    description = "Easy access to environment variables from Python";
+    homepage = https://github.com/capless/envs;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ peterhoeg ];
+  };
+}

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

@@ -0,0 +1,55 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, pkgconfig
+, gmp
+, pari
+, mpfr
+, fplll
+, cython
+, cysignals
+, numpy
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "fpylll";
+  version = "0.3.0dev";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0bjkh02fnxsrxwjzai8ij12zl2wq319z8y25sn9pvvzla5izgnp9";
+  };
+
+  buildInputs = [
+    gmp
+    pari
+    mpfr
+    fplll
+  ];
+
+  propagatedBuildInputs = [
+    cython
+    cysignals
+    numpy
+  ];
+
+  nativeBuildInputs = [
+    pkgconfig
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    py.test
+  '';
+
+  meta = {
+    description = "A Python interface for fplll";
+    homepage = https://github.com/fplll/fpylll;
+    maintainers = with lib.maintainers; [ timokau ];
+    license = lib.licenses.gpl2Plus;
+  };
+}

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

@@ -0,0 +1,33 @@
+{ lib
+, behave
+, buildPythonPackage
+, fetchPypi
+, lxml
+, pytest
+, pyparsing
+, mock
+}:
+
+buildPythonPackage rec {
+  pname = "python-docx";
+  version = "0.8.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "117i84s6fcdsrfckbvznnqgqwhnf1x0523ps16cki8sg9byydv2m";
+  };
+
+  checkInputs = [ behave mock pyparsing pytest ];
+  propagatedBuildInputs = [ lxml ];
+
+  checkPhase = ''
+    py.test tests
+  '';
+
+  meta = {
+    description = "Create and update Microsoft Word .docx files";
+    homepage = https://python-docx.readthedocs.io/en/latest/;
+    license = lib.licenses.mit;
+    maintainers = [ lib.maintainers.alexchapman ];
+  };
+}

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

@@ -0,0 +1,21 @@
+{ lib, fetchPypi, buildPythonPackage, pytest }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "rlp";
+  version = "0.6.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0d3gx4mp8q4z369s5yk1n9c55sgfw9fidbwqxq67d6s7l45rm1w7";
+  };
+
+  buildInputs = [ pytest ];
+
+  meta = {
+    description = "A package for encoding and decoding data in and from Recursive Length Prefix notation";
+    homepage = "https://github.com/ethereum/pyrlp";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ gebner ];
+  };
+}

pkgs/development/python-modules/rpy2/default.nix

@@ -0,0 +1,54 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isPyPy
+, readline
+, R
+, pcre
+, lzma
+, bzip2
+, zlib
+, icu
+, singledispatch
+, six
+, jinja2
+, pytest
+}:
+
+buildPythonPackage rec {
+    version = "2.8.2";
+    pname = "rpy2";
+    disabled = isPyPy;
+    src = fetchPypi {
+      inherit version pname;
+      sha256 = "0k5jp6n1lfab7a6r5568aq31hg4fgf2cwy0hzvf3chp6yhyk26ic";
+    };
+    buildInputs = [
+      readline
+      R
+      pcre
+      lzma
+      bzip2
+      zlib
+      icu
+    ];
+    propagatedBuildInputs = [
+      singledispatch
+      six
+      jinja2
+    ];
+    checkInputs = [ pytest ];
+    # Tests fail with `assert not _relpath.startswith('..'), "Path must be within the project"`
+    # in the unittest `loader.py`. I don't know what causes this.
+    doCheck = false;
+    # without this tests fail when looking for libreadline.so
+    LD_LIBRARY_PATH = lib.makeLibraryPath buildInputs;
+
+    meta = {
+      homepage = http://rpy.sourceforge.net/rpy2;
+      description = "Python interface to R";
+      license = lib.licenses.gpl2Plus;
+      platforms = lib.platforms.linux;
+      maintainers = with lib.maintainers; [ joelmo ];
+    };
+  }

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

@@ -1,5 +1,5 @@
 { lib, fetchPypi, buildPythonPackage,
-  protobuf, hidapi, ecdsa, mnemonic, requests, pyblake2, click, libusb1
+  protobuf, hidapi, ecdsa, mnemonic, requests, pyblake2, click, libusb1, rlp
 }:
 
 buildPythonPackage rec {
@@ -12,7 +12,7 @@ buildPythonPackage rec {
     sha256 = "a481191011bade98f1e9f1201e7c72a83945050657bbc90dc4ac32dc8b8b46a4";
   };
 
-  propagatedBuildInputs = [ protobuf hidapi ecdsa mnemonic requests pyblake2 click libusb1 ];
+  propagatedBuildInputs = [ protobuf hidapi ecdsa mnemonic requests pyblake2 click libusb1 rlp ];
 
   # There are no actual tests: "ImportError: No module named tests"
   doCheck = false;

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

@@ -0,0 +1,36 @@
+{ lib, buildPythonPackage, fetchFromGitHub, fetchPypi
+, mock
+, boto3, envs, python-jose, requests }:
+
+buildPythonPackage rec {
+  pname = "warrant";
+  version = "0.6.1";
+
+  # move to fetchPyPi when https://github.com/capless/warrant/issues/97 is fixed
+  src = fetchFromGitHub {
+    owner  = "capless";
+    repo   = "warrant";
+    rev    = "ff2e4793d8479e770f2461ef7cbc0c15ee784395";
+    sha256 = "0gw3crg64p1zx3k5js0wh0x5bldgs7viy4g8hld9xbka8q0374hi";
+  };
+
+  # this needs to go when 0.6.2 or later is released
+  postPatch = ''
+    substituteInPlace requirements.txt \
+      --replace "python-jose-cryptodome>=1.3.2" "python-jose>=2.0.0"
+  '';
+
+  checkInputs = [ mock ];
+
+  propagatedBuildInputs = [ boto3 envs python-jose requests ];
+
+  # all the checks are failing
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Python library for using AWS Cognito with support for SRP";
+    homepage = https://github.com/capless/warrant;
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ peterhoeg ];
+  };
+}