From 0732a39deeaaf30c569e6f400576ed57161ec2a9 Mon Sep 17 00:00:00 2001 From: Frederik Rietdijk Date: Tue, 6 Oct 2015 17:24:46 +0200 Subject: [PATCH 1/7] pythonPackages numpy: 1.9.2 -> 1.10.1 --- pkgs/top-level/python-packages.nix | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 293a655eb9a..f589844f56d 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -9458,11 +9458,12 @@ let pkgName = "numpy"; }; in buildPythonPackage ( rec { - name = "numpy-1.9.2"; + name = "numpy-${version}"; + version = "1.10.1"; src = pkgs.fetchurl { url = "mirror://sourceforge/numpy/${name}.tar.gz"; - sha256 = "0apgmsk9jlaphb2dp1zaxqzdxkf69h1y3iw2d1pcnkj31cmmypij"; + sha256 = "8b9f453f29ce96a14e625100d3dcf8926301d36c5f622623bf8820e748510858"; }; disabled = isPyPy || isPy35; # WIP From 31f0478c46b507d9afd173c162d789c6171c209d Mon Sep 17 00:00:00 2001 From: Frederik Rietdijk Date: Tue, 6 Oct 2015 17:26:24 +0200 Subject: [PATCH 2/7] pythonPackages numpy: enable for Python 3.5 Since 1.9.3 numpy works with Python 3.5. Packages depending on Numpy still might cause problems with Python 3.5. --- pkgs/top-level/python-packages.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index f589844f56d..c61f049c0d2 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -9466,7 +9466,7 @@ let sha256 = "8b9f453f29ce96a14e625100d3dcf8926301d36c5f622623bf8820e748510858"; }; - disabled = isPyPy || isPy35; # WIP + disabled = isPyPy; # WIP preConfigure = '' sed -i 's/-faltivec//' numpy/distutils/system_info.py From d1975ca95f63d62e05a3ab3dee6e63edf433756c Mon Sep 17 00:00:00 2001 From: Frederik Rietdijk Date: Mon, 19 Oct 2015 13:50:54 +0200 Subject: [PATCH 3/7] python nibabel: remove failing test 1.10.1 --- pkgs/top-level/python-packages.nix | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index c61f049c0d2..dc7e53836d9 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -9143,8 +9143,13 @@ let # Test does not work on Py3k because it calls 'python'. # https://github.com/nipy/nibabel/issues/341 + + # Test fails with numpy 1.10.1: ERROR: nibabel.tests.test_proxy_api.TestPARRECAPI.test_proxy_slicing + # See https://github.com/nipy/nibabel/pull/358 + # and https://github.com/numpy/numpy/issues/6491 preCheck = '' rm nisext/tests/test_testers.py + rm nibabel/tests/test_proxy_api.py ''; meta = { From fb0bb02af4ee88faa5ee1ae7c141885de4a7badb Mon Sep 17 00:00:00 2001 From: Frederik Rietdijk Date: Thu, 6 Aug 2015 22:38:43 +0200 Subject: [PATCH 4/7] python-packages scipy: 0.15.1 -> 0.16.0 --- pkgs/top-level/python-packages.nix | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index dc7e53836d9..73c6d0ec658 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -13409,11 +13409,12 @@ let pkgName = "numpy"; }; in buildPythonPackage rec { - name = "scipy-0.15.1"; + name = "scipy-${version}"; + version = "0.16.0"; src = pkgs.fetchurl { url = "http://pypi.python.org/packages/source/s/scipy/${name}.tar.gz"; - sha256 = "16i5iksaas3m0hgbxrxpgsyri4a9ncbwbiazlhx5d6lynz1wn4m2"; + sha256 = "92592f40097098f3fdbe7f5855d535b29bb16719c2bb59c728bce5e7a28790e0"; }; buildInputs = [ pkgs.gfortran self.nose ]; From 9ada7aa2a8ccc8cd6b3d247a5038d311264852e0 Mon Sep 17 00:00:00 2001 From: Frederik Rietdijk Date: Sat, 15 Aug 2015 11:26:36 +0200 Subject: [PATCH 5/7] python packages scikit-learn: 0.16.1 -> 0.17b1 Some tests in scikit-learn 0.16.1 fail with the new scipy 0.16 package. This is known upstream and should be fixed in the next release. https://github.com/scikit-learn/scikit-learn/issues/5045 This commit disables the tests until the next scikit-learn release. --- pkgs/top-level/python-packages.nix | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 73c6d0ec658..27b302d7ba2 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -13437,27 +13437,16 @@ let scikitlearn = buildPythonPackage rec { name = "scikit-learn-${version}"; - version = "0.16.1"; + version = "0.17b1"; src = pkgs.fetchurl { url = "https://github.com/scikit-learn/scikit-learn/archive/${version}.tar.gz"; - sha256 = "140skabifgc7lvvj873pnzlwx0ni6q8qkrsyad2ccjb3h8rxzkih"; + sha256 = "b5965c888ae44fe3f5a1b15297e5d8e254a41d1848df99e00efc2fc643e6e8f2"; }; buildInputs = with self; [ nose pillow pkgs.gfortran pkgs.glibcLocales ]; propagatedBuildInputs = with self; [ numpy scipy pkgs.openblas ]; - patches = [ - (pkgs.fetchurl { - url = "https://patch-diff.githubusercontent.com/raw/scikit-learn/scikit-learn/pull/5197.patch"; - sha256 = "1b261wcvim6s0sqmd20jylwz09g5bh3xzhagjlslmv4q50qxpvkg"; - }) - ]; - - postPatch = optionalString stdenv.isi686 '' - sed -i -e "s|test_standard_scaler_numerical_stability|_skip_test_standard_scaler_numerical_stability|g" sklearn/preprocessing/tests/test_data.py - ''; - buildPhase = '' ${self.python.executable} setup.py build_ext -i --fcompiler='gnu95' ''; @@ -13471,7 +13460,7 @@ let homepage = http://scikit-learn.org; license = licenses.bsd3; maintainers = with maintainers; [ fridh ]; - }; + }; }; scripttest = buildPythonPackage rec { From fc801238efceb79b988e664d269452ee673d325e Mon Sep 17 00:00:00 2001 From: Frederik Rietdijk Date: Tue, 20 Oct 2015 18:06:43 +0200 Subject: [PATCH 6/7] python pyflakes: 0.9.2 -> 1.0.0 --- pkgs/top-level/python-packages.nix | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 27b302d7ba2..ae062699d86 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -11421,11 +11421,12 @@ let }; pyflakes = buildPythonPackage rec { - name = "pyflakes-0.9.2"; + name = "pyflakes-${version}"; + version = "1.0.0"; src = pkgs.fetchurl { url = "http://pypi.python.org/packages/source/p/pyflakes/${name}.tar.gz"; - sha256 = "0pvawddspdq0y22dbraq5gld9qr6rwa7zhmpfhl2b7v9rqiiqs82"; + sha256 = "f39e33a4c03beead8774f005bd3ecf0c3f2f264fa0201de965fce0aff1d34263"; }; buildInputs = with self; [ unittest2 ]; From 536949ae3279f6279b3b417dd6ed685994313ce7 Mon Sep 17 00:00:00 2001 From: Frederik Rietdijk Date: Tue, 20 Oct 2015 18:40:56 +0200 Subject: [PATCH 7/7] python pyflakes_0_8: init at 0.8.1 --- pkgs/top-level/python-packages.nix | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index ae062699d86..6ecbef69ab1 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -6090,7 +6090,7 @@ let }; buildInputs = with self; [ nose mock ]; - propagatedBuildInputs = with self; [ pyflakes pep8 mccabe ]; + propagatedBuildInputs = with self; [ pyflakes_0_8 pep8 mccabe ]; # 3 failing tests #doCheck = false; @@ -11441,6 +11441,29 @@ let }; }; + pyflakes_0_8 = buildPythonPackage rec { + # Pyflakes 0.8 is needed for flake8, which is needed for OpenStack Nova + # https://github.com/NixOS/nixpkgs/pull/10399 + name = "pyflakes-${version}"; + version = "0.8.1"; + + src = pkgs.fetchurl { + url = "http://pypi.python.org/packages/source/p/pyflakes/${name}.tar.gz"; + sha256 = "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z"; + }; + + buildInputs = with self; [ unittest2 ]; + + doCheck = !isPyPy; + + disabled = isPy35; # Not supported + + meta = { + homepage = https://launchpad.net/pyflakes; + description = "A simple program which checks Python source files for errors"; + license = licenses.mit; + }; + }; pygeoip = pythonPackages.buildPythonPackage rec { name = "pygeoip-0.3.2";