[PATCH] Update pandas, numpy, pysnptools, fastlmm

[PATCH] Update pandas, numpy, pysnptools, fastlmm

[Ricardo Wurmus]

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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’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


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From d052597069c7818ce23b2890aff82d024dda5430 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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


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From 1ab9356646527c40fd875e26bfb1cf64b5976728 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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


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From 996e39faa14493e3dbdc9f0efc40412b138c0793 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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


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From e7c452734a43445521c66934146358beb757665f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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

Re: [PATCH] Update pandas, numpy, pysnptools, fastlmm

[Efraim Flashner]

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On Thu, 11 Feb 2016 16:16:50 +0100
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> wrote:

> 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’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
> 

Looks good to me. As for fastlmm and pysnptools, they look like scary bio
packages, the type I stay away from when I'm doing updating :)

-- 
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Re: [PATCH] Update pandas, numpy, pysnptools, fastlmm

[Andreas Enge]

Hello,

it looks like the python2-numpy update has broken vigra:
   http://hydra.gnu.org/build/1008323/nixlog/1/tail-reload
I could confirm it on my own machine.

This is quite annoying, as vigra is an input to libreoffice.

Could one of you have a look?

Andreas

Re: [PATCH] Update pandas, numpy, pysnptools, fastlmm

[Ricardo Wurmus]

Andreas Enge <andreas@enge.fr> writes:

> it looks like the python2-numpy update has broken vigra:
>    http://hydra.gnu.org/build/1008323/nixlog/1/tail-reload
> I could confirm it on my own machine.
>
> This is quite annoying, as vigra is an input to libreoffice.
>
> Could one of you have a look?

I had a look but couldn’t find anything obvious, so I reported a bug:

  https://github.com/ukoethe/vigra/issues/326

Seems that Debian people have also run into this bug:

  https://www.mail-archive.com/debian-bugs-dist@lists.debian.org/msg1391368.html

~~ Ricardo