[bug#39904] Update of python-anndata

[bug#39904] Update of python-anndata

[Roel Janssen]

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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 --]
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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 --]
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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


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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 --]
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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

bug#39904: Acknowledgement (Update of python-anndata)

[Roel Janssen]

On Wed, 2020-03-04 at 15:01 +0000, GNU bug Tracking System wrote:
> Thank you for filing a new bug report with debbugs.gnu.org.
> 
> This is an automatically generated reply to let you know your message
> has been received.
> 
> Your message is being forwarded to the package maintainers and other
> interested parties for their attention; they will reply in due
> course.
> 
> Your message has been sent to the package maintainer(s):
>  guix-patches@gnu.org
> 
> If you wish to submit further information on this problem, please
> send it to 39904@debbugs.gnu.org.
> 
> Please do not send mail to help-debbugs@gnu.org unless you wish
> to report a problem with the Bug-tracking system.
> 

So, Ricardo has pushed similar patches in the meantime. Closing this
one.

Kind regards,
Roel Janssen

[bug#39904] Update of python-anndata

[Ricardo Wurmus]

Hi Roel,

> 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’m sorry I missed this patch series.  I noticed that scanpy failed to
build, so I worked on upgrading it together with anndata.  I must have
started the work right before your patches came in.

> 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).

These tests that use external services (such as Azure Storage Blob,
Redis, etc) can be disabled with environment variables, which is what I
did in my version of the package definition.

--
Ricardo

[bug#39904] Update of python-anndata

[Roel Janssen]

On Fri, 2020-03-06 at 23:00 +0100, Ricardo Wurmus wrote:
> Hi Roel,
> 
> > 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’m sorry I missed this patch series.  I noticed that scanpy failed
> to
> build, so I worked on upgrading it together with anndata.  I must
> have
> started the work right before your patches came in.
> 
> > 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).
> 
> These tests that use external services (such as Azure Storage Blob,
> Redis, etc) can be disabled with environment variables, which is what
> I
> did in my version of the package definition.

Thanks.