From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Update pandas, numpy, pysnptools, fastlmm Date: Thu, 11 Feb 2016 16:16:50 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:52260) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aTszT-0004UI-8d for guix-devel@gnu.org; Thu, 11 Feb 2016 10:17:08 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aTszO-00056s-OE for guix-devel@gnu.org; Thu, 11 Feb 2016 10:17:07 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:35936) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aTszO-00055l-BR for guix-devel@gnu.org; Thu, 11 Feb 2016 10:17:02 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 5BC90381643 for ; Thu, 11 Feb 2016 16:16:59 +0100 (CET) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id OxU3Y8zZDWgA for ; Thu, 11 Feb 2016 16:16:51 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 11 Feb 2016 16:16:51 +0100 (CET) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel --=-=-= Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Guix, these updates are straight-forward, but I wanted to run them by you anyway, because numpy and pandas seem pretty important. The numpy version is Guix was released in Nov 2014, so I think it=E2=80=99= s time for an update. I needed a later version to upgrade fastlmm (which was my primary goal). (I think both fastlmm and pysnptools should be moved to bioinformatics.scm.) ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-python-pandas-Update-to-0.16.2.patch" >From d052597069c7818ce23b2890aff82d024dda5430 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2016 16:09:07 +0100 Subject: [PATCH 1/4] gnu: python-pandas: Update to 0.16.2. * gnu/packages/python.scm (python-pandas): Update to 0.16.2. --- gnu/packages/python.scm | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 31569f5..cc43c2c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -974,14 +974,13 @@ datetime module, available in Python 2.3+.") (define-public python-pandas (package (name "python-pandas") - (version "0.16.0") + (version "0.16.2") (source (origin - (method url-fetch) - (uri (string-append "https://pypi.python.org/packages/source/p/" - "pandas/pandas-" version ".tar.gz")) - (sha256 - (base32 "1wfrp8dx1zcsry6f09ndza6qm1yr7f163211f4l9vjlnhxpxw4s0")))) + (method url-fetch) + (uri (pypi-uri "pandas" version)) + (sha256 + (base32 "10agmrkps8bi5948vwpipfxds5kj1d076m9i0nhaxwqiw7gm6670")))) (build-system python-build-system) (arguments `(;; Three tests fail: -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-python-numpy-bootstrap-Update-to-1.10.4.patch" >From 1ab9356646527c40fd875e26bfb1cf64b5976728 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2016 16:10:08 +0100 Subject: [PATCH 2/4] gnu: python-numpy-bootstrap: Update to 1.10.4. * gnu/packages/python.scm (python-numpy-bootstrap): Update to 1.10.4. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index cc43c2c..a1da24a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2956,7 +2956,7 @@ writing C extensions for Python as easy as Python itself.") (define python-numpy-bootstrap (package (name "python-numpy-bootstrap") - (version "1.9.1") + (version "1.10.4") (source (origin (method url-fetch) @@ -2964,7 +2964,7 @@ writing C extensions for Python as easy as Python itself.") "/numpy-" version ".tar.gz")) (sha256 (base32 - "070ybfvpgfmiz2hs94x445hvkh9dh52nyi0m8jp5kdihgvhbnx80")))) + "1bjjhvncraka5s6i4lg644jrxij6bvycxy7an20gcz3a0m11iygp")))) (build-system python-build-system) (inputs `(("python-nose" ,python-nose) -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0003-gnu-python2-pysnptools-Update-to-0.3.5.patch" >From 996e39faa14493e3dbdc9f0efc40412b138c0793 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2016 16:10:48 +0100 Subject: [PATCH 3/4] gnu: python2-pysnptools: Update to 0.3.5. * gnu/packages/python.scm (python2-pysnptools): Update to 0.3.5. --- gnu/packages/python.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a1da24a..e18a690 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3386,16 +3386,14 @@ toolkits.") (define-public python2-pysnptools (package (name "python2-pysnptools") - (version "0.2.13") + (version "0.3.5") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/p/pysnptools" - "/pysnptools-" version ".zip")) + (uri (pypi-uri "pysnptools" version ".zip")) (sha256 (base32 - "1rzf5qvwfvd2pp84b14pb2gdvxdk5avnj7rb41ac8gndpkr9g6ib")))) + "15f4j4w5q603i7mlphb5r6mb1mn33pqg81595fpjp158140yqx7b")))) (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2.7 is supported -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0004-gnu-python2-fastlmm-Update-to-0.2.21.patch" >From e7c452734a43445521c66934146358beb757665f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2016 16:11:22 +0100 Subject: [PATCH 4/4] gnu: python2-fastlmm: Update to 0.2.21. * gnu/packages/python.scm (python2-fastlmm): Update to 0.2.21. --- gnu/packages/python.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e18a690..bf046d9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3025,16 +3025,14 @@ capabilities.") (define-public python2-fastlmm (package (name "python2-fastlmm") - (version "0.2.14") + (version "0.2.21") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/f/fastlmm" - "/fastlmm-" version ".zip")) + (uri (pypi-uri "fastlmm" version ".zip")) (sha256 (base32 - "023sydkrc3yxad2bycar02jfswwlh4199kafzhf2bssyx2c3xa0l")))) + "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m")))) (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2.7 is supported -- 2.1.0 --=-=-=--