From: Roel Janssen <roel@roelserve.com>
To: 39904@debbugs.gnu.org
Subject: [bug#39904] Update of python-anndata
Date: Wed, 04 Mar 2020 11:25:33 +0100 [thread overview]
Message-ID: <1eaf5ea7175f71ee190f4b3cf965608c55b5cd83.camel@roelserve.com> (raw)
[-- Attachment #1: Type: text/plain, Size: 585 bytes --]
Dear Guix,
I'd like to update our package for python-anndata. For this I needed to add a
few more packages that are used in the test suite of python-anndata.
I attached the patches. Note that for python-zarr I disabled the tests because
the majority of the tests need external packages. We could add all dependencies
to make the test suite work, but that requires a significant amount of work (for
example, the Azure SDK for Python is one of the external dependencies).
Is it OK to move forward with the disabled test suite for python-zarr?
Thanks!
Kind regards,
Roel Janssen
[-- Attachment #2: 0004-gnu-Update-python-anndata-to-0.7.1.patch --]
[-- Type: text/x-patch, Size: 1534 bytes --]
From 08e25e127b7c19b339c5257d61b6d2c1b9d9a2c9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 4 Mar 2020 11:13:21 +0100
Subject: [PATCH 4/4] gnu: Update python-anndata to 0.7.1.
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.1; Add
dependencies to run the test suite.
---
gnu/packages/python-xyz.scm | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3eabc9e3fa..2ec79404f2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15800,15 +15800,22 @@ compressed, N-dimensional arrays for Python.")
(define-public python-anndata
(package
(name "python-anndata")
- (version "0.6.18")
+ (version "0.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "anndata" version))
(sha256
(base32
- "03x83yjaccbqszj7x4fwwmpil0ai59yx64d1zmf2691za3j03w73"))))
+ "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09"))))
(build-system python-build-system)
+ ;; The following inputs are needed for the test suite.
+ (native-inputs
+ `(("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-packaging" ,python-packaging)
+ ("python-importlib-metadata" ,python-importlib-metadata)
+ ("python-numcodecs" ,python-numcodecs)
+ ("python-zarr" ,python-zarr)))
(propagated-inputs
`(("python-h5py" ,python-h5py)
("python-natsort" ,python-natsort)
--
2.25.1
[-- Attachment #3: 0003-gnu-Add-python-zarr.patch --]
[-- Type: text/x-patch, Size: 1791 bytes --]
From 8a01cc8c797dde47d6e4982f7b8710fc9bf106e1 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 4 Mar 2020 11:12:41 +0100
Subject: [PATCH 3/4] gnu: Add python-zarr.
* gnu/packages/python-xyz.scm (python-zarr): New variable.
---
gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 067756cae8..3eabc9e3fa 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15771,6 +15771,32 @@ codecs for use in data storage and communication applications.")
(description "Draws ASCII trees.")
(license license:expat)))
+(define-public python-zarr
+ (package
+ (name "python-zarr")
+ (version "2.4.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "zarr" version))
+ (sha256
+ (base32
+ "026n3sjzjv2gmwx6y72b8ij0hk42bc8zdbvfj5gdqzd4i6wj3ajk"))))
+ (build-system python-build-system)
+ (arguments
+ ;; The tests import h5py, lmdb, pymongo, bsddb3, and azure.storage.blob from
+ ;; the Azure SDK for python.
+ `(#:tests? #f))
+ (propagated-inputs
+ `(("python-asciitree" ,python-asciitree)
+ ("python-fasteners" ,python-fasteners)
+ ("python-numcodecs" ,python-numcodecs)
+ ("python-numpy" ,python-numpy)))
+ (home-page "https://github.com/zarr-developers/zarr-python")
+ (synopsis "Implementation of chunked, compressed, N-dimensional arrays for Python.")
+ (description "This package provides an implementation of chunked,
+compressed, N-dimensional arrays for Python.")
+ (license license:expat)))
+
(define-public python-anndata
(package
(name "python-anndata")
--
2.25.1
[-- Attachment #4: 0002-gnu-Add-python-asciitree.patch --]
[-- Type: text/x-patch, Size: 1267 bytes --]
From f48903066a6987c3af2b4130dde03ee2c8c9b70e Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 4 Mar 2020 11:12:09 +0100
Subject: [PATCH 2/4] gnu: Add python-asciitree.
* gnu/packages/python-xyz.scm (python-asciitree): New variable.
---
gnu/packages/python-xyz.scm | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index dec41a8c5e..067756cae8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15755,6 +15755,22 @@ tool).")
codecs for use in data storage and communication applications.")
(license license:expat)))
+(define-public python-asciitree
+ (package
+ (name "python-asciitree")
+ (version "0.3.3")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "asciitree" version))
+ (sha256
+ (base32
+ "0vhgri2m2xlnibhz4xwn4hpbc7xacisxjqrk6k5kyppq96vbk92a"))))
+ (build-system python-build-system)
+ (home-page "http://github.com/mbr/asciitree")
+ (synopsis "Draws ASCII trees.")
+ (description "Draws ASCII trees.")
+ (license license:expat)))
+
(define-public python-anndata
(package
(name "python-anndata")
--
2.25.1
[-- Attachment #5: 0001-gnu-Add-python-numcodecs.patch --]
[-- Type: text/x-patch, Size: 2191 bytes --]
From 0fc3b77486289835f28f16a6380c15fd128cab6b Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 4 Mar 2020 11:11:17 +0100
Subject: [PATCH 1/4] gnu: Add python-numcodecs.
* gnu/packages/python-xyz.scm (python-numcodecs): New variable.
---
gnu/packages/python-xyz.scm | 24 +++++++++++++++++++++++-
1 file changed, 23 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f3519b75f6..dec41a8c5e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -40,7 +40,7 @@
;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au>
;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2017 José Miguel Sánchez García <jmi2k@openmailbox.org>
-;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2017 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com>
@@ -15733,6 +15733,28 @@ infrastructure at import time, runtime, or statically (using the included pycc
tool).")
(license license:bsd-3)))
+(define-public python-numcodecs
+ (package
+ (name "python-numcodecs")
+ (version "0.6.4")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "numcodecs" version))
+ (sha256
+ (base32
+ "0kbfr8pl3x9glsypbq8hzim003f16ml1b1cvgrh4w1sdvgal6j7g"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-msgpack" ,python-msgpack)
+ ("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/zarr-developers/numcodecs")
+ (synopsis "Buffer compression and transformation codecs")
+ (description "This package provides buffer compression and transformation
+codecs for use in data storage and communication applications.")
+ (license license:expat)))
+
(define-public python-anndata
(package
(name "python-anndata")
--
2.25.1
next reply other threads:[~2020-03-04 15:01 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-03-04 10:25 Roel Janssen [this message]
[not found] ` <handler.39904.B.15833340305736.ack@debbugs.gnu.org>
2020-03-06 9:44 ` bug#39904: Acknowledgement (Update of python-anndata) Roel Janssen
2020-03-06 22:00 ` [bug#39904] Update of python-anndata Ricardo Wurmus
2020-03-07 8:50 ` Roel Janssen
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=1eaf5ea7175f71ee190f4b3cf965608c55b5cd83.camel@roelserve.com \
--to=roel@roelserve.com \
--cc=39904@debbugs.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.