Merge master into staging

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

@@ -44,7 +44,7 @@ in buildPythonPackage rec {
 
   checkPhase = ''
     export HOME="$NIX_BUILD_TOP"
-    ${python.interpreter} runtests.py \
+    ${python.interpreter} runtests.py -j$NIX_BUILD_CORES \
       ${stdenv.lib.optionalString (builtins.length excludedTests != 0)
         ''--exclude="(${builtins.concatStringsSep "|" excludedTests})"''}
   '';

pkgs/development/python-modules/boto3/default.nix

@@ -13,13 +13,13 @@
 
 buildPythonPackage rec {
   pname =  "boto3";
-  version = "1.7.48";
+  version = "1.7.57";
 
   src = fetchFromGitHub {
     owner = "boto";
     repo  = "boto3";
     rev   = version;
-    sha256 = "0pag37yy6693k8xvlyx4f06asab52i89xljy2ip121i60ih3jfw4";
+    sha256 = "0rp3vclx7mvfl6isa47m7dzlrf33qb9vj53p0gj4cw3mgl14cnbl";
   };
 
   propagatedBuildInputs = [ botocore jmespath s3transfer ] ++ lib.optionals (!isPy3k) [ futures ];

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

@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "botocore";
-  version = "1.10.48";
+  version = "1.10.57";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1432drc7482nwrppwkk1i6ars3wz9w2g9rsxkz5nlxmyf9qm260j";
+    sha256 = "0mif7c12643hac6zxq89gv0wjf4r3vqlmm01bm68psljaj40jnpi";
   };
 
   propagatedBuildInputs = [

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

@@ -1,19 +1,15 @@
-{ stdenv, buildPythonPackage, fetchPypi, fetchpatch, cryptography, boto3, pyyaml, docutils }:
+{ stdenv, buildPythonPackage, fetchPypi, fetchpatch, cryptography, boto3, pyyaml, docutils, nose }:
 
 buildPythonPackage rec {
   pname = "credstash";
-  version = "1.14.0";
+  version = "1.15.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "718b337f7a6fa001e014386071f05c59900525d0507009126d2fe8d75fe0761d";
+    sha256 = "814560f99ae2409e2c6d906d878f9dadada5d1d0a950aafb6b2c0d535291bdfb";
   };
 
-  patches = fetchpatch {
-    url = https://github.com/fugue/credstash/pull/178.patch;
-    sha256 = "15ih4h5v63g7qfmqdl4zca147wkcrx8vnsh4ns33001dipcfb5sc";
-    excludes = [ ".travis.yml" ];
-  };
+  nativeBuildInputs = [ nose ];
 
   propagatedBuildInputs = [ cryptography boto3 pyyaml docutils ];
 

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

@@ -9,11 +9,11 @@ assert pariSupport -> pari != null;
 
 buildPythonPackage rec {
   pname = "cysignals";
-  version = "1.7.1";
+  version = "1.7.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "15nky8siwlc7s8v23vv4m0mnxa1z6jcs2qfr26m2mkw9j9g2na2j";
+    sha256 = "0rzwd9bjw6bj01xcmimqfim1g0njjyyyal0f93frm1la4hcmq96v";
   };
 
   # explicit check:
@@ -23,6 +23,7 @@ buildPythonPackage rec {
   ];
 
   # currently fails, probably because of formatting changes in gdb 8.0
+  # https://trac.sagemath.org/ticket/24692
   doCheck = false;
 
   preCheck = ''

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

@@ -2,11 +2,13 @@
 
 buildPythonPackage rec {
   pname = "geojson";
-  version = "2.3.0";
+  version = "2.4.0";
+
+  format = "wheel";
 
   src = fetchPypi {
-    inherit pname version;
-    sha256 = "06ihcb8839zzgk5jcv18kc6nqld4hhj3nk4f3drzcr8n8893v1y8";
+    inherit pname version format;
+    sha256 = "0r9pc8hgnc5hf5rq98vinbrncn08v4kgzdfmfs14rfypvacsmfpj";
   };
 
   LC_ALL = "en_US.UTF-8";

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

@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "libvirt";
-  version = "4.4.0";
+  version = "4.5.0";
 
   src = assert version == libvirt.version; fetchgit {
     url = git://libvirt.org/libvirt-python.git;
     rev = "v${version}";
-    sha256 = "01kwwwacbq7kbsslb2ac3wwfs4r8nsv7jhn0df2mmff30izbhq34";
+    sha256 = "0w2rzkxv7jsq4670m0j5c6p4hpyi0r0ja6wd3wdvixcwc6hhx407";
   };
 
   nativeBuildInputs = [ pkgconfig ];

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

@@ -0,0 +1,33 @@
+{ stdenv, buildPythonPackage, fetchFromGitHub, pdfminer, chardet, pytest }:
+
+buildPythonPackage rec {
+  pname = "pdfx";
+  version = "1.3.1";
+
+  src = fetchFromGitHub {
+    owner = "metachris";
+    repo = "pdfx";
+    rev = "v${version}";
+    sha256 = "1183k4h5qdf8y0imbir9ja3yzzsvdmqgbv3bi6dnkgr1wy2xfr0v";
+  };
+
+  # Remove after https://github.com/metachris/pdfx/pull/28
+  prePatch = ''
+    sed -i -e "s|pdfminer2|pdfminer.six|" setup.py
+  '';
+
+  propagatedBuildInputs = [ pdfminer chardet ];
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    py.test
+  '';
+
+  meta = with stdenv.lib; {
+    inherit (src.meta) homepage;
+    description = "Extract references (pdf, url, doi, arxiv) and metadata from a PDF";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ marsam ];
+  };
+}