pythonPackages.nipype: 0.10.0 -> 0.14.0

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

@@ -0,0 +1,36 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, numpy
+, nose
+, six
+}:
+
+buildPythonPackage rec {
+  pname = "nibabel";
+  version = "2.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1h6nhi1s2ab7sdyyl3qjnvlw0kggcnam7vn4b3z56ay20596kvhw";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    nose
+    six
+  ];
+
+  # Failing tests
+  # nibabel.tests.test_minc1.test_old_namespace
+  # nibabel.gifti.tests.test_parse_gifti_fast.test_parse_dataarrays
+  # nibabel.gifti.tests.test_giftiio.test_read_deprecated
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = http://nipy.org/nibabel/;
+    description = "Access a multitude of neuroimaging data formats";
+    license = licenses.mit;
+    maintainers = with maintainers; [ ashgillman ];
+  };
+}

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

@@ -0,0 +1,68 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, isPy3k
+# python dependencies
+, click
+, configparser ? null
+, dateutil
+, funcsigs
+, future
+, mock
+, networkx
+, nibabel
+, numpy
+, packaging
+, prov
+, psutil
+, pydot
+, pytest
+, scipy
+, simplejson
+, traits
+, xvfbwrapper
+# other dependencies
+, which
+}:
+
+assert !isPy3k -> configparser != null;
+
+buildPythonPackage rec {
+  pname = "nipype";
+  version = "0.14.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0airdrh93vwmbfkqxp5cqfzm0zzqcvjnvphv3zhg197y39xxpl1k";
+  };
+
+  doCheck = false;  # fails with TypeError: None is not callable
+  checkInputs = [ which ];
+  buildInputs = [ pytest mock ];  # required in installPhase
+  propagatedBuildInputs = [
+    click
+    dateutil
+    funcsigs
+    future
+    networkx
+    nibabel
+    numpy
+    packaging
+    prov
+    psutil
+    pydot
+    scipy
+    simplejson
+    traits
+    xvfbwrapper
+  ] ++ stdenv.lib.optional (!isPy3k) [
+    configparser
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = http://nipy.org/nipype/;
+    description = "Neuroimaging in Python: Pipelines and Interfaces";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ ashgillman ];
+  };
+}

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

@@ -0,0 +1,37 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, lxml
+, networkx
+, dateutil
+, six
+, pydotplus
+, rdflib
+}:
+
+buildPythonPackage rec {
+  pname = "prov";
+  version = "1.5.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1vkpayns0mf7i2357vxyvi2n5h5xsyg56ik2yqgrc91k3gx4x9wn";
+  };
+
+  propagatedBuildInputs = [
+    lxml
+    networkx
+    dateutil
+    six
+    pydotplus
+    rdflib
+  ];
+  doCheck = false; # takes ~60 mins
+
+  meta = with stdenv.lib; {
+    description = "A Python library for W3C Provenance Data Model (PROV)";
+    homepage = https://github.com/trungdong/prov;
+    license = licenses.mit;
+    maintainers = with maintainers; [ ashgillman ];
+  };
+}

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

@@ -0,0 +1,28 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pyparsing
+, graphviz
+}:
+
+buildPythonPackage rec {
+  pname = "pydotplus";
+  version = "2.0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1i05cnk3yh722fdyaq0asr7z9xf7v7ikbmnpxa8j6pdqx6g5xs4i";
+  };
+
+  propagatedBuildInputs = [
+    pyparsing
+    graphviz
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/erocarrera/pydot;
+    description = "An improved version of the old pydot project that provides a Python Interface to Graphviz’s Dot language";
+    license = licenses.mit;
+    maintainers = with maintainers; [ ashgillman ];
+  };
+}

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

@@ -0,0 +1,23 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, xorgserver
+}:
+
+buildPythonPackage rec {
+  pname = "xvfbwrapper";
+  version = "0.2.9";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "097wxhvp01ikqpg1z3v8rqhss6f1vwr399zpz9a05d2135bsxx5w";
+  };
+  propagatedBuildInputs = [ xorgserver ];
+
+  meta = with stdenv.lib; {
+    description = "Run headless display inside X virtual framebuffer (Xvfb)";
+    homepage = https://github.com/cgoldberg/xvfbwrapper;
+    license = licenses.mit;
+    maintainers = with maintainers; [ ashgillman ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -6196,6 +6196,8 @@ in {
     };
   };
 
+  prov = callPackage ../development/python-modules/prov { };
+
   pudb = buildPythonPackage rec {
     name = "pudb-2016.2";
 
@@ -6293,6 +6295,8 @@ in {
     inherit (pkgs.stdenv) mkDerivation;
   };
 
+  pydotplus = callPackage ../development/python-modules/pydotplus { };
+
   pyphen = callPackage ../development/python-modules/pyphen {};
 
   pypoppler = buildPythonPackage rec {
@@ -11315,31 +11319,7 @@ in {
     };
   });
 
-  nibabel = buildPythonPackage rec {
-    version = "2.0.2";
-    name = "nibabel-${version}";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/n/nibabel/${name}.tar.gz";
-      sha256 = "0k8mv5zmwb6vc8kwrydl3pp0pnw937rf5mz10figkxczrw6dkk7h";
-    };
-
-    propagatedBuildInputs = with self; [
-      numpy
-      nose
-    ];
-
-    # Failing tests
-    # nibabel.tests.test_minc1.test_old_namespace
-    # nisext.tests.test_testers.test_back_tick
-    doCheck = false;
-
-    meta = {
-      homepage = http://nipy.org/nibabel/;
-      description = "Access a multitude of neuroimaging data formats";
-      license = licenses.mit;
-    };
-  };
+  nibabel = callPackage ../development/python-modules/nibabel {};
 
   nilearn = callPackage ../development/python-modules/nilearn {};
 
@@ -11386,36 +11366,8 @@ in {
     };
   };
 
-  nipype = buildPythonPackage rec {
-    version = "0.10.0";
-    name = "nipype-${version}";
-
-    # Uses python 2 print. Master seems to be Py3 compatible.
-    disabled = isPy3k;
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/n/nipype/${name}.tar.gz";
-      sha256 = "7fb143cd4d05f18db1cb7f0b83dba13d3dcf55b4eb3d16df08c97033ccae507b";
-    };
-
-    # Tests fail due to getcwd returning ENOENT???
-    doCheck = false;
-
-    propagatedBuildInputs = with self; [
-     numpy
-     dateutil
-     nose
-     traits
-     scipy
-     nibabel
-     networkx
-   ];
-
-    meta = {
-      homepage = http://nipy.org/nipype/;
-      description = "Neuroimaging in Python: Pipelines and Interfaces";
-      license = licenses.bsd3;
-    };
+  nipype = callPackage ../development/python-modules/nipype {
+    inherit (pkgs) which;
   };
 
   nose = buildPythonPackage rec {
@@ -15606,11 +15558,11 @@ in {
 
 
   rdflib = buildPythonPackage (rec {
-    name = "rdflib-4.1.2";
+    name = "rdflib-4.2.2";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/r/rdflib/${name}.tar.gz";
-      sha256 = "0kvaf332cqbi47rqzlpdx4mbkvw12mkrzkj8n9l19wk713d4py9w";
+      sha256 = "0398c714znnhaa2x7v51b269hk20iz073knq2mvmqp2ma92z27fs";
     };
 
     # error: invalid command 'test'
@@ -17851,11 +17803,11 @@ in {
 
   traits = buildPythonPackage rec {
     name = "traits-${version}";
-    version = "4.5.0";
+    version = "4.6.0";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/t/traits/${name}.tar.gz";
-      sha256 = "5293a8786030b0b243e059f52004355b6939d7c0f1be2eb5a605b63cca484c84";
+      sha256 = "0w43qv36wnrimlh0nzzgg81315a18yza3vk494wqxf1l19g390jx";
     };
 
     # Use pytest because its easier to discover tests
@@ -17868,7 +17820,7 @@ in {
     # https://github.com/enthought/traits/issues/187
     # https://github.com/enthought/traits/pull/188
     # Furthermore, some tests fail due to being in a chroot
-    doCheck = false;
+    doCheck = isPy33;
 
     propagatedBuildInputs = with self; [ numpy ];
 
@@ -21677,6 +21629,10 @@ EOF
     };
   };
 
+  xvfbwrapper = callPackage ../development/python-modules/xvfbwrapper {
+    inherit (pkgs.xorg) xorgserver;
+  };
+
   hidapi = callPackage ../development/python-modules/hidapi {
     inherit (pkgs) udev libusb1;
   };