* bug#39872: python-anndata fails to build
@ 2020-03-02 19:29 Maxim Cournoyer
2020-03-04 13:27 ` Roel Janssen
0 siblings, 1 reply; 3+ messages in thread
From: Maxim Cournoyer @ 2020-03-02 19:29 UTC (permalink / raw)
To: 39872
Build log extract:
--8<---------------cut here---------------start------------->8---
starting phase `check'
running "python setup.py" with command "test" and parameters ()
running test
running egg_info
writing anndata.egg-info/PKG-INFO
writing dependency_links to anndata.egg-info/dependency_links.txt
writing requirements to anndata.egg-info/requires.txt
writing top-level names to anndata.egg-info/top_level.txt
reading manifest file 'anndata.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'anndata.egg-info/SOURCES.txt'
running build_ext
anndata (unittest.loader._FailedTest) ... ERROR
======================================================================
ERROR: anndata (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: anndata
Traceback (most recent call last):
File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
package = self._get_module_from_name(name)
File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
__import__(name)
File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-0.6.18/anndata/__init__.py", line 1, in <module>
from .base import AnnData
File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-0.6.18/anndata/base.py", line 21, in <module>
from scipy.sparse.sputils import IndexMixin
ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy-1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py)
----------------------------------------------------------------------
Ran 1 test in 0.000s
FAILED (errors=1)
Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with status 1
builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv' failed with exit code 1
build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv failed
View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv.bz2'.
guix build: error: build of
`/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv'
failed
--8<---------------cut here---------------end--------------->8---
On master c1febbbf94ee794d7a97dbde12102634f2b13529.
^ permalink raw reply [flat|nested] 3+ messages in thread
* bug#39872: python-anndata fails to build
2020-03-02 19:29 bug#39872: python-anndata fails to build Maxim Cournoyer
@ 2020-03-04 13:27 ` Roel Janssen
2020-03-08 2:54 ` Maxim Cournoyer
0 siblings, 1 reply; 3+ messages in thread
From: Roel Janssen @ 2020-03-04 13:27 UTC (permalink / raw)
To: Maxim Cournoyer, 39872
[-- Attachment #1: Type: text/plain, Size: 3502 bytes --]
On Mon, 2020-03-02 at 14:29 -0500, Maxim Cournoyer wrote:
> Build log extract:
>
> --8<---------------cut here---------------start------------->8---
> starting phase `check'
> running "python setup.py" with command "test" and parameters ()
> running test
> running egg_info
> writing anndata.egg-info/PKG-INFO
> writing dependency_links to anndata.egg-info/dependency_links.txt
> writing requirements to anndata.egg-info/requires.txt
> writing top-level names to anndata.egg-info/top_level.txt
> reading manifest file 'anndata.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> writing manifest file 'anndata.egg-info/SOURCES.txt'
> running build_ext
> anndata (unittest.loader._FailedTest) ... ERROR
>
> ======================================================================
> ERROR: anndata (unittest.loader._FailedTest)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: anndata
> Traceback (most recent call last):
> File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-
> 3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
> package = self._get_module_from_name(name)
> File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-
> 3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
> __import__(name)
> File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-
> 0.6.18/anndata/__init__.py", line 1, in <module>
> from .base import AnnData
> File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-
> 0.6.18/anndata/base.py", line 21, in <module>
> from scipy.sparse.sputils import IndexMixin
> ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils'
> (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy-
> 1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py)
>
>
> ----------------------------------------------------------------------
> Ran 1 test in 0.000s
>
> FAILED (errors=1)
> Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
> error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
> command "python" "-c" "import setuptools,
> tokenize;__file__='setup.py';f=getattr(tokenize, 'open',
> open)(__file__);code=f.read().replace('\\r\\n',
> '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with
> status 1
> builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-
> 0.6.18.drv' failed with exit code 1
> build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv
> failed
> View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq-
> python-anndata-0.6.18.drv.bz2'.
> guix build: error: build of
> `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv'
> failed
> --8<---------------cut here---------------end--------------->8---
>
> On master c1febbbf94ee794d7a97dbde12102634f2b13529.
I sent an e-mail from another address that doesn't seem to have made the guix-
patches mailing list. The attached patches updates the version of python-
anndata, and fixes the build.
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?
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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* bug#39872: python-anndata fails to build
2020-03-04 13:27 ` Roel Janssen
@ 2020-03-08 2:54 ` Maxim Cournoyer
0 siblings, 0 replies; 3+ messages in thread
From: Maxim Cournoyer @ 2020-03-08 2:54 UTC (permalink / raw)
To: Roel Janssen; +Cc: 39872-done
Hello Roel,
Roel Janssen <roel@gnu.org> writes:
> On Mon, 2020-03-02 at 14:29 -0500, Maxim Cournoyer wrote:
>> Build log extract:
>>
>> --8<---------------cut here---------------start------------->8---
>> starting phase `check'
>> running "python setup.py" with command "test" and parameters ()
>> running test
>> running egg_info
>> writing anndata.egg-info/PKG-INFO
>> writing dependency_links to anndata.egg-info/dependency_links.txt
>> writing requirements to anndata.egg-info/requires.txt
>> writing top-level names to anndata.egg-info/top_level.txt
>> reading manifest file 'anndata.egg-info/SOURCES.txt'
>> reading manifest template 'MANIFEST.in'
>> writing manifest file 'anndata.egg-info/SOURCES.txt'
>> running build_ext
>> anndata (unittest.loader._FailedTest) ... ERROR
>>
>> ======================================================================
>> ERROR: anndata (unittest.loader._FailedTest)
>> ----------------------------------------------------------------------
>> ImportError: Failed to import test module: anndata
>> Traceback (most recent call last):
>> File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-
>> 3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
>> package = self._get_module_from_name(name)
>> File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-
>> 3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
>> __import__(name)
>> File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-
>> 0.6.18/anndata/__init__.py", line 1, in <module>
>> from .base import AnnData
>> File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-
>> 0.6.18/anndata/base.py", line 21, in <module>
>> from scipy.sparse.sputils import IndexMixin
>> ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils'
>> (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy-
>> 1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py)
>>
>>
>> ----------------------------------------------------------------------
>> Ran 1 test in 0.000s
>>
>> FAILED (errors=1)
>> Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
>> error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
>> command "python" "-c" "import setuptools,
>> tokenize;__file__='setup.py';f=getattr(tokenize, 'open',
>> open)(__file__);code=f.read().replace('\\r\\n',
>> '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with
>> status 1
>> builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-
>> 0.6.18.drv' failed with exit code 1
>> build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv
>> failed
>> View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq-
>> python-anndata-0.6.18.drv.bz2'.
>> guix build: error: build of
>> `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv'
>> failed
>> --8<---------------cut here---------------end--------------->8---
>>
>> On master c1febbbf94ee794d7a97dbde12102634f2b13529.
The problem has since been fixed on master with commits
7032c1cc6040a14e482e71b0cfbdedf957da4f8a,
8e04b233f130e01b5b6a41dfcdeb5e622d43f751,
241409cd8afe45fdecfbd7d24cdeb08aa2a43884 and
a098b3498052e046c8338e0630e0166bcb12355d; Ricardo probably did not
notice about this bug report and your posted patches.
> I sent an e-mail from another address that doesn't seem to have made the guix-
> patches mailing list. The attached patches updates the version of python-
> anndata, and fixes the build.
>
> 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?
I think it would have been acceptable (given that anndata was broken and
needed a fix); but enabling the tests that can be run ideally should be
attempted. See in commit 7032c1cc6040a14e482e71b0cfbdedf957da4f8a how
this was achieved.
You'll find a summary review of your patches below. I've made sure that
what got committed was not missing anything.
> 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
Here the default check phase (which does 'python setup.py test'), was
not running the test suite. It had to be overriden by a 'pytest'
invocation. I find this to be very common in Python packages; I think
there was something about deprecating 'python setup.py test' to; maybe
we should look into making this phase of the python-build-system smarter.
> 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
LGTM, but see commit for a way to partially enable the test suite:
7032c1cc6040a14e482e71b0cfbdedf957da4f8a.
> 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")
The URL should use HTTPS.
> + (synopsis "Draws ASCII trees.")
> + (description "Draws ASCII trees.")
> + (license license:expat)))
The description should be expound a bit.
> (define-public python-anndata
> (package
> (name "python-anndata")
> --
> 2.25.1
>
>
> 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)))
Pytest and setuptools plugins are only required at build time, hence
would be better found in 'native-inputs'.
> + (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)))
Otherwise LGTM!
I'm sorry that this work was duplicated; I hope this small review can
compensate for it a little :-).
Thank you; I'm closing the issue.
Maxim
^ permalink raw reply [flat|nested] 3+ messages in thread
end of thread, other threads:[~2020-03-08 2:55 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2020-03-02 19:29 bug#39872: python-anndata fails to build Maxim Cournoyer
2020-03-04 13:27 ` Roel Janssen
2020-03-08 2:54 ` Maxim Cournoyer
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