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pythonPackages.nipype: 0.10.0 -> 0.14.0 #33916
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,37 @@ | ||
{ stdenv | ||
, buildPythonPackage | ||
, fetchPypi | ||
, numpy | ||
, nose | ||
, six | ||
}: | ||
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buildPythonPackage rec { | ||
name = "${pname}-${version}"; | ||
pname = "nibabel"; | ||
version = "2.2.0"; | ||
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src = fetchPypi { | ||
inherit pname version; | ||
sha256 = "1h6nhi1s2ab7sdyyl3qjnvlw0kggcnam7vn4b3z56ay20596kvhw"; | ||
}; | ||
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propagatedBuildInputs = [ | ||
numpy | ||
nose | ||
six | ||
]; | ||
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# 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; | ||
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meta = with stdenv.lib; { | ||
homepage = http://nipy.org/nibabel/; | ||
description = "Access a multitude of neuroimaging data formats"; | ||
license = licenses.mit; | ||
maintainers = with maintainers; [ ashgillman ]; | ||
}; | ||
} |
Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,69 @@ | ||
{ 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 | ||
}: | ||
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assert !isPy3k -> configparser; | ||
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buildPythonPackage rec { | ||
name = "${pname}-${version}"; | ||
pname = "nipype"; | ||
version = "0.14.0"; | ||
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src = fetchPypi { | ||
inherit pname version; | ||
sha256 = "0airdrh93vwmbfkqxp5cqfzm0zzqcvjnvphv3zhg197y39xxpl1k"; | ||
}; | ||
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doCheck = false; # fails with TypeError: None is not callable | ||
checkInputs = [ which ]; | ||
buildInputs = [ pytest mock ]; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. checkInputs There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. I should move Sorry, I am not aware of a few of these conventions. Are they documented somewhere? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. no, he was asking you to move There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Ah, I see. However, the build fails in installPhase without |
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propagatedBuildInputs = [ | ||
click | ||
dateutil | ||
funcsigs | ||
future | ||
networkx | ||
nibabel | ||
numpy | ||
packaging | ||
prov | ||
psutil | ||
pydot | ||
scipy | ||
simplejson | ||
traits | ||
xvfbwrapper | ||
] ++ stdenv.lib.optional (!isPy3k) [ | ||
configparser | ||
]; | ||
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meta = with stdenv.lib; { | ||
homepage = http://nipy.org/nipype/; | ||
description = "Neuroimaging in Python: Pipelines and Interfaces"; | ||
license = licenses.bsd3; | ||
maintainers = with maintainers; [ ashgillman ]; | ||
}; | ||
} |
Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,38 @@ | ||
{ stdenv | ||
, buildPythonPackage | ||
, fetchPypi | ||
, lxml | ||
, networkx | ||
, dateutil | ||
, six | ||
, pydotplus | ||
, rdflib | ||
}: | ||
|
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buildPythonPackage rec { | ||
name = "${pname}-${version}"; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. no |
||
pname = "prov"; | ||
version = "1.5.0"; | ||
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src = fetchPypi { | ||
inherit pname version; | ||
sha256 = "1vkpayns0mf7i2357vxyvi2n5h5xsyg56ik2yqgrc91k3gx4x9wn"; | ||
}; | ||
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propagatedBuildInputs = [ | ||
lxml | ||
networkx | ||
dateutil | ||
six | ||
pydotplus | ||
rdflib | ||
]; | ||
doCheck = false; # takes forever! | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Please also add a There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. What is "forever"? Test suites of most scientific python packages take some time. There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Looking into this now (I wrote some of these expressions a number of months ago). There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more.
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) |
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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 ]; | ||
}; | ||
} |
Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,29 @@ | ||
{ stdenv | ||
, buildPythonPackage | ||
, fetchPypi | ||
, pyparsing | ||
, graphviz | ||
}: | ||
|
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buildPythonPackage rec { | ||
name = "${pname}-${version}"; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. no |
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pname = "pydotplus"; | ||
version = "2.0.2"; | ||
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src = fetchPypi { | ||
inherit pname version; | ||
sha256 = "1i05cnk3yh722fdyaq0asr7z9xf7v7ikbmnpxa8j6pdqx6g5xs4i"; | ||
}; | ||
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propagatedBuildInputs = [ | ||
pyparsing | ||
graphviz | ||
]; | ||
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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"; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. License is missing; do you want to maintain this package? |
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license = licenses.mit; | ||
maintainers = with maintainers; [ ashgillman ]; | ||
}; | ||
} |
Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,24 @@ | ||
{ stdenv | ||
, buildPythonPackage | ||
, fetchPypi | ||
, xorgserver | ||
}: | ||
|
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buildPythonPackage rec { | ||
name = "${pname}-${version}"; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. no There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. 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 There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. That example should indeed be updated. |
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pname = "xvfbwrapper"; | ||
version = "0.2.9"; | ||
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src = fetchPypi { | ||
inherit pname version; | ||
sha256 = "097wxhvp01ikqpg1z3v8rqhss6f1vwr399zpz9a05d2135bsxx5w"; | ||
}; | ||
propagatedBuildInputs = [ xorgserver ]; | ||
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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 ]; | ||
}; | ||
} |
Original file line number | Diff line number | Diff line change |
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@@ -6196,6 +6196,8 @@ in { | |
}; | ||
}; | ||
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prov = callPackage ../development/python-modules/prov { }; | ||
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pudb = buildPythonPackage rec { | ||
name = "pudb-2016.2"; | ||
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@@ -6293,6 +6295,8 @@ in { | |
inherit (pkgs.stdenv) mkDerivation; | ||
}; | ||
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pydotplus = callPackage ../development/python-modules/pydotplus { }; | ||
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pyphen = callPackage ../development/python-modules/pyphen {}; | ||
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pypoppler = buildPythonPackage rec { | ||
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@@ -11315,31 +11319,7 @@ in { | |
}; | ||
}); | ||
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nibabel = buildPythonPackage rec { | ||
version = "2.0.2"; | ||
name = "nibabel-${version}"; | ||
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src = pkgs.fetchurl { | ||
url = "mirror://pypi/n/nibabel/${name}.tar.gz"; | ||
sha256 = "0k8mv5zmwb6vc8kwrydl3pp0pnw937rf5mz10figkxczrw6dkk7h"; | ||
}; | ||
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propagatedBuildInputs = with self; [ | ||
numpy | ||
nose | ||
]; | ||
|
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# Failing tests | ||
# nibabel.tests.test_minc1.test_old_namespace | ||
# nisext.tests.test_testers.test_back_tick | ||
doCheck = false; | ||
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meta = { | ||
homepage = http://nipy.org/nibabel/; | ||
description = "Access a multitude of neuroimaging data formats"; | ||
license = licenses.mit; | ||
}; | ||
}; | ||
nibabel = callPackage ../development/python-modules/nibabel {}; | ||
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nilearn = callPackage ../development/python-modules/nilearn {}; | ||
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@@ -11386,36 +11366,8 @@ in { | |
}; | ||
}; | ||
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nipype = buildPythonPackage rec { | ||
version = "0.10.0"; | ||
name = "nipype-${version}"; | ||
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# Uses python 2 print. Master seems to be Py3 compatible. | ||
disabled = isPy3k; | ||
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src = pkgs.fetchurl { | ||
url = "mirror://pypi/n/nipype/${name}.tar.gz"; | ||
sha256 = "7fb143cd4d05f18db1cb7f0b83dba13d3dcf55b4eb3d16df08c97033ccae507b"; | ||
}; | ||
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# Tests fail due to getcwd returning ENOENT??? | ||
doCheck = false; | ||
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propagatedBuildInputs = with self; [ | ||
numpy | ||
dateutil | ||
nose | ||
traits | ||
scipy | ||
nibabel | ||
networkx | ||
]; | ||
|
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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; | ||
}; | ||
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nose = buildPythonPackage rec { | ||
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@@ -15606,11 +15558,11 @@ in { | |
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rdflib = buildPythonPackage (rec { | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. We are moving Python expressions out of Please move the expression there, and call it from There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. done |
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name = "rdflib-4.1.2"; | ||
name = "rdflib-4.2.2"; | ||
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src = pkgs.fetchurl { | ||
url = "mirror://pypi/r/rdflib/${name}.tar.gz"; | ||
sha256 = "0kvaf332cqbi47rqzlpdx4mbkvw12mkrzkj8n9l19wk713d4py9w"; | ||
sha256 = "0398c714znnhaa2x7v51b269hk20iz073knq2mvmqp2ma92z27fs"; | ||
}; | ||
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# error: invalid command 'test' | ||
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@@ -17851,11 +17803,11 @@ in { | |
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traits = buildPythonPackage rec { | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. We are moving Python expressions out of Please move the expression there, and call it from There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. done |
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name = "traits-${version}"; | ||
version = "4.5.0"; | ||
version = "4.6.0"; | ||
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src = pkgs.fetchurl { | ||
url = "mirror://pypi/t/traits/${name}.tar.gz"; | ||
sha256 = "5293a8786030b0b243e059f52004355b6939d7c0f1be2eb5a605b63cca484c84"; | ||
sha256 = "0w43qv36wnrimlh0nzzgg81315a18yza3vk494wqxf1l19g390jx"; | ||
}; | ||
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# Use pytest because its easier to discover tests | ||
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@@ -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; | ||
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propagatedBuildInputs = with self; [ numpy ]; | ||
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@@ -21677,6 +21629,10 @@ EOF | |
}; | ||
}; | ||
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xvfbwrapper = callPackage ../development/python-modules/xvfbwrapper { | ||
inherit (pkgs.xorg) xorgserver; | ||
}; | ||
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hidapi = callPackage ../development/python-modules/hidapi { | ||
inherit (pkgs) udev libusb1; | ||
}; | ||
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no name