From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] Update pandas, numpy, pysnptools, fastlmm
Date: Thu, 11 Feb 2016 16:16:50 +0100 [thread overview]
Message-ID: <idjfuwz6zvh.fsf@bimsb-sys02.mdc-berlin.net> (raw)
[-- Attachment #1: Type: text/plain, Size: 404 bytes --]
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-python-pandas-Update-to-0.16.2.patch --]
[-- Type: text/x-patch, Size: 1252 bytes --]
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0002-gnu-python-numpy-bootstrap-Update-to-1.10.4.patch --]
[-- Type: text/x-patch, Size: 1217 bytes --]
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #4: 0003-gnu-python2-pysnptools-Update-to-0.3.5.patch --]
[-- Type: text/x-patch, Size: 1246 bytes --]
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
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #5: 0004-gnu-python2-fastlmm-Update-to-0.2.21.patch --]
[-- Type: text/x-patch, Size: 1232 bytes --]
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
next reply other threads:[~2016-02-11 15:17 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-02-11 15:16 Ricardo Wurmus [this message]
2016-02-11 21:13 ` [PATCH] Update pandas, numpy, pysnptools, fastlmm Efraim Flashner
2016-02-13 10:07 ` Andreas Enge
2016-02-16 21:34 ` Ricardo Wurmus
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=idjfuwz6zvh.fsf@bimsb-sys02.mdc-berlin.net \
--to=ricardo.wurmus@mdc-berlin.de \
--cc=guix-devel@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.