--- Begin Message ---
|
Subject: |
python-anndata fails to build |
|
Date: |
Mon, 02 Mar 2020 14:29:44 -0500 |
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.
--- End Message ---
--- Begin Message ---
|
Subject: |
Re: bug#39872: python-anndata fails to build |
|
Date: |
Sat, 07 Mar 2020 21:54:01 -0500 |
|
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) |
Hello Roel,
Roel Janssen <address@hidden> 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 <address@hidden>
> 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 <address@hidden>
> 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 <address@hidden>
> 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 <address@hidden>
> 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 <address@hidden>
> ;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe <address@hidden>
> ;;; Copyright © 2017 José Miguel Sánchez García <address@hidden>
> -;;; Copyright © 2017 Roel Janssen <address@hidden>
> +;;; Copyright © 2017 2020 Roel Janssen <address@hidden>
> ;;; Copyright © 2017, 2018, 2019 Kei Kebreau <address@hidden>
> ;;; Copyright © 2017 Rutger Helling <address@hidden>
> ;;; Copyright © 2017 Muriithi Frederick Muriuki <address@hidden>
> @@ -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
--- End Message ---