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pythonPackages.nipype: 0.10.0 -> 0.14.0 #33916

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pythonPackages.nipype: 0.10.0 -> 0.14.0 #33916

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cc72c60
pythonPackages.rdflib: 4.1.2 -> 4.2.2
ashgillman Jan 16, 2018
ab59e9d
pythonPackages.traits: 4.5.0 -> 4.6.0
ashgillman Jan 16, 2018
1b69f23
pythonPackages.xvfbwrapper: init at 0.2.9
ashgillman Jan 16, 2018
7b0e038
pythonPackages.nibabel: 2.0.2 -> 2.2.0
ashgillman Jan 16, 2018
0133d1e
pythonPackages.pydotplus: init at 2.0.2
ashgillman Jan 16, 2018
2c9b615
pythonPackages.prov: init at 1.5.0
ashgillman Jan 16, 2018
f34d818
pythonPackages.nipype: 0.10.0 -> 0.14.0
ashgillman Jan 16, 2018
d272782
pythonPackages.prov: Add meta
ashgillman Jan 16, 2018
4b0d9b3
pythonPackages.pydotplus: Update homepage, add license and maintainers.
ashgillman Jan 16, 2018
6f9e372
pythonPackages.nipype: Check phase requires which, but still fails
ashgillman Jan 16, 2018
265e9be
pythonPackages.nibabel: Move to separate file.
ashgillman Jan 16, 2018
5a6148f
pythonPackages.nipype: To separate file.
ashgillman Jan 16, 2018
56cd80d
pythonPackages.{nibabel,nipype,prov,pydotplus,xvfbwrapper}: Remove name
ashgillman Jan 17, 2018
4f6283d
pythonPackages.prov: More descriptive reason for skipping check phase
ashgillman Jan 17, 2018
c3c6559
pythonPackages.nipype: Fix bad definition for py27.
ashgillman Jan 17, 2018
04c960c
pythonPackages.nipype: Document reason for buildInputs.
ashgillman Jan 17, 2018
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38 changes: 38 additions & 0 deletions pkgs/development/python-modules/prov/default.nix
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Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
{ stdenv
, buildPythonPackage
, fetchPypi
, lxml
, networkx
, dateutil
, six
, pydotplus
, rdflib
}:

buildPythonPackage rec {
name = "${pname}-${version}";
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no name

pname = "prov";
version = "1.5.0";

src = fetchPypi {
inherit pname version;
sha256 = "1vkpayns0mf7i2357vxyvi2n5h5xsyg56ik2yqgrc91k3gx4x9wn";
};

propagatedBuildInputs = [
lxml
networkx
dateutil
six
pydotplus
rdflib
];
doCheck = false; # takes forever!
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@Mic92 Mic92 Jan 16, 2018 •
edited
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Please also add a meta attributes here.

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What is "forever"? Test suites of most scientific python packages take some time.

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Looking into this now (I wrote some of these expressions a number of months ago).

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Ran 956 tests in 3594.012s

FAILED (failures=22, expected failures=17)
Test failed: <unittest.runner.TextTestResult run=956 errors=0 failures=22>

So about an hour (total build time was about an hour and 10).

I am investigating whether the errors are present in 1.5.1 before reporting upstream. (NB: Nipype currently requires exactly 1.5.0, this is being dealt with)


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 ];
};
}
29 changes: 29 additions & 0 deletions pkgs/development/python-modules/pydotplus/default.nix
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@@ -0,0 +1,29 @@
{ stdenv
, buildPythonPackage
, fetchPypi
, pyparsing
, graphviz
}:

buildPythonPackage rec {
name = "${pname}-${version}";
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no name

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";
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License is missing; do you want to maintain this package?

license = licenses.mit;
maintainers = with maintainers; [ ashgillman ];
};
}
24 changes: 24 additions & 0 deletions pkgs/development/python-modules/xvfbwrapper/default.nix
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@@ -0,0 +1,24 @@
{ stdenv
, buildPythonPackage
, fetchPypi
, xorgserver
}:

buildPythonPackage rec {
name = "${pname}-${version}";
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no name

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Not sure what you mean sorry. There should be no name attr? https://github.com/NixOS/nixpkgs/blob/master/doc/languages-frameworks/python.md recommends this

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That example should indeed be updated. buildPython* functions fill in name when given pname and version.

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 ];
};
}
63 changes: 40 additions & 23 deletions pkgs/top-level/python-packages.nix
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Expand Up @@ -6196,6 +6196,8 @@ in {
};
};

prov = callPackage ../development/python-modules/prov { };

pudb = buildPythonPackage rec {
name = "pudb-2016.2";

Expand Down Expand Up @@ -6293,6 +6295,8 @@ in {
inherit (pkgs.stdenv) mkDerivation;
};

pydotplus = callPackage ../development/python-modules/pydotplus { };

pyphen = callPackage ../development/python-modules/pyphen {};

pypoppler = buildPythonPackage rec {
Expand Down Expand Up @@ -11316,17 +11320,18 @@ in {
});

nibabel = buildPythonPackage rec {
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We are moving Python expressions out of pkgs/top-level/python-packages.nix into pkgs/development/python-modules/<module>/default.nix.

Please move the expression there, and call it from pkgs/top-level/python-packages.nix using callPackage ../development/python-modules/<package> { };.

version = "2.0.2";
version = "2.2.0";
name = "nibabel-${version}";

src = pkgs.fetchurl {
url = "mirror://pypi/n/nibabel/${name}.tar.gz";
sha256 = "0k8mv5zmwb6vc8kwrydl3pp0pnw937rf5mz10figkxczrw6dkk7h";
sha256 = "1h6nhi1s2ab7sdyyl3qjnvlw0kggcnam7vn4b3z56ay20596kvhw";
};

propagatedBuildInputs = with self; [
numpy
nose
six
];

# Failing tests
Expand Down Expand Up @@ -11387,34 +11392,42 @@ in {
};

nipype = buildPythonPackage rec {
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We are moving Python expressions out of pkgs/top-level/python-packages.nix into pkgs/development/python-modules/<module>/default.nix.

Please move the expression there, and call it from pkgs/top-level/python-packages.nix using callPackage ../development/python-modules/<package> { };.

version = "0.10.0";
version = "0.14.0";
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";
sha256 = "0airdrh93vwmbfkqxp5cqfzm0zzqcvjnvphv3zhg197y39xxpl1k";
};

# Tests fail due to getcwd returning ENOENT???
doCheck = false;

doCheck = false; # fails with TypeError: None is not callable
checkInputs = [ pkgs.which ];
buildInputs = with self; [ pytest mock ];
propagatedBuildInputs = with self; [
numpy
dateutil
nose
traits
scipy
nibabel
networkx
];
click
dateutil
funcsigs
future
networkx
nibabel
numpy
packaging
prov
psutil
pydot
scipy
simplejson
traits
xvfbwrapper
] ++ stdenv.lib.optional (!isPy3k) [
configparser
];

meta = {
homepage = http://nipy.org/nipype/;
description = "Neuroimaging in Python: Pipelines and Interfaces";
license = licenses.bsd3;
maintainers = with maintainers; [ ashgillman ];
};
};

Expand Down Expand Up @@ -15606,11 +15619,11 @@ in {


rdflib = buildPythonPackage (rec {
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We are moving Python expressions out of pkgs/top-level/python-packages.nix into pkgs/development/python-modules/<module>/default.nix.

Please move the expression there, and call it from pkgs/top-level/python-packages.nix using callPackage ../development/python-modules/<package> { };.

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done

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'
Expand Down Expand Up @@ -17851,11 +17864,11 @@ in {

traits = buildPythonPackage rec {
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We are moving Python expressions out of pkgs/top-level/python-packages.nix into pkgs/development/python-modules/<module>/default.nix.

Please move the expression there, and call it from pkgs/top-level/python-packages.nix using callPackage ../development/python-modules/<package> { };.

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done

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
Expand All @@ -17868,7 +17881,7 @@ 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 ];

Expand Down Expand Up @@ -21677,6 +21690,10 @@ EOF
};
};

xvfbwrapper = callPackage ../development/python-modules/xvfbwrapper {
inherit (pkgs.xorg) xorgserver;
};

hidapi = callPackage ../development/python-modules/hidapi {
inherit (pkgs) udev libusb1;
};
Expand Down