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
From 08e25e127b7c19b339c5257d61b6d2c1b9d9a2c9 Mon Sep 17 00:00:00 2001 From: Roel Janssen <r...@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
From 8a01cc8c797dde47d6e4982f7b8710fc9bf106e1 Mon Sep 17 00:00:00 2001 From: Roel Janssen <r...@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
From f48903066a6987c3af2b4130dde03ee2c8c9b70e Mon Sep 17 00:00:00 2001 From: Roel Janssen <r...@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
From 0fc3b77486289835f28f16a6380c15fd128cab6b Mon Sep 17 00:00:00 2001 From: Roel Janssen <r...@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 <b...@sturm.com.au> ;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe <m.othac...@gmail.com> ;;; Copyright © 2017 José Miguel Sánchez García <jm...@openmailbox.org> -;;; Copyright © 2017 Roel Janssen <r...@gnu.org> +;;; Copyright © 2017 2020 Roel Janssen <r...@gnu.org> ;;; Copyright © 2017, 2018, 2019 Kei Kebreau <kkebr...@posteo.net> ;;; Copyright © 2017 Rutger Helling <rhell...@mykolab.com> ;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmang...@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