forked from pool/python-xarray
Accepting request 872458 from home:bnavigator:branches:devel:languages:python:numeric
- Disable python36 build: python36-numpy is no longer in Tumbleweed xarray will follow to drop Python 3.6 support on next release. (NEP 29) - Add xarray-pr4884-dask2021.patch gh#pydata/xarray#4884 - Enable parralel testing with pytest-xdist - Recommend/Suggest the extras OBS-URL: https://build.opensuse.org/request/show/872458 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-xarray?expand=0&rev=43
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@ -1,3 +1,13 @@
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-------------------------------------------------------------------
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Mon Feb 15 12:30:53 UTC 2021 - Ben Greiner <code@bnavigator.de>
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- Disable python36 build: python36-numpy is no longer in Tumbleweed
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xarray will follow to drop Python 3.6 support on next release.
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(NEP 29)
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- Add xarray-pr4884-dask2021.patch gh#pydata/xarray#4884
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- Enable parralel testing with pytest-xdist
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- Recommend/Suggest the extras
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-------------------------------------------------------------------
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Sun Dec 20 16:09:14 UTC 2020 - Sebastian Wagner <sebix+novell.com@sebix.at>
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@ -1,7 +1,7 @@
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#
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# spec file for package python-xarray
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#
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# Copyright (c) 2020 SUSE LLC
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# Copyright (c) 2021 SUSE LLC
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#
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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@ -18,6 +18,8 @@
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%{?!python_module:%define python_module() python-%{**} python3-%{**}}
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%define skip_python2 1
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# NEP 29: Numpy 1.20 dropped support for Python 3.6, python36-numpy is removed from Tumbleweed. xarray will follow on next release
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%define skip_python36 1
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Name: python-xarray
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Version: 0.16.2
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Release: 0
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@ -25,6 +27,8 @@ Summary: N-D labeled arrays and datasets in Python
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License: Apache-2.0
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URL: https://github.com/pydata/xarray
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Source: https://files.pythonhosted.org/packages/source/x/xarray/xarray-%{version}.tar.gz
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# PATCH-FIX-UPSTREAM xarray-pr4884-dask2021.patch gh#pydata/xarray#4884
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Patch0: xarray-pr4884-dask2021.patch
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BuildRequires: %{python_module numpy >= 1.15}
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BuildRequires: %{python_module numpy-devel >= 1.14}
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BuildRequires: %{python_module pandas >= 0.25}
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@ -34,15 +38,35 @@ BuildRequires: fdupes
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BuildRequires: python-rpm-macros
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Requires: python-numpy >= 1.15
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Requires: python-pandas >= 0.25
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Recommends: python-scipy >= 1.3
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Suggests: python-dask >= 2.2
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Provides: python-xray = %{version}
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Obsoletes: python-xray < %{version}
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BuildArch: noarch
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Suggests: python-dask-all
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# SECTION extras accel
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Recommends: python-scipy >= 1.3
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Recommends: python-bottleneck
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Recommends: python-numbagg
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# /SECTION
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# SECTION extras viz
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Suggests: python-matplotlib
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Suggests: python-seaborn
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Suggests: python-nc-time-axis
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#/SECTION
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# SECTION extras io
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Suggests: python-netCDF4
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Suggests: python-h5netcdf
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Suggests: python-scipy
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Suggests: python-pydap
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Suggests: python-zarr
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Suggests: python-fsspec
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Suggests: python-cftime
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Suggests: python-rasterio
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Suggests: python-cfgrib
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#/SECTION
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# SECTION tests
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# dask tests currently failing
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# BuildRequires: %%{python_module dask-dataframe}
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BuildRequires: %{python_module pytest >= 2.7.1}
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BuildRequires: %{python_module dask-dataframe}
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BuildRequires: %{python_module pytest-xdist}
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BuildRequires: %{python_module pytest}
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BuildRequires: %{python_module scipy}
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# /SECTION
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%python_subpackages
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@ -57,7 +81,7 @@ The Common Data Model for self-describing scientific data is used.
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The dataset is an in-memory representation of a netCDF file.
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%prep
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%setup -q -n xarray-%{version}
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%autosetup -p1 -n xarray-%{version}
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chmod -x xarray/util/print_versions.py
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%build
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@ -68,12 +92,16 @@ chmod -x xarray/util/print_versions.py
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%python_expand %fdupes %{buildroot}%{$python_sitelib}
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%check
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# test_no_warning_from_dask_effective_get fails due to upstream scipy warning
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%pytest -k "not test_download_from_github and not test_no_warning_from_dask_effective_get" xarray
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if [ $(getconf LONG_BIT) -eq 32 ]; then
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# precision errors on 32-bit
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donttest="(test_interpolate_chunk_advanced and linear)"
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fi
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%pytest -n auto ${donttest:+ -k "not ($donttest)"} xarray
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%files %{python_files}
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%doc README.rst
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%license LICENSE licenses/
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%{python_sitelib}/xarray*
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%{python_sitelib}/xarray
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%{python_sitelib}/xarray-%{version}*-info
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%changelog
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119
xarray-pr4884-dask2021.patch
Normal file
119
xarray-pr4884-dask2021.patch
Normal file
@ -0,0 +1,119 @@
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From a825faaf60dc75e0365f18a0f24acb0fe288b263 Mon Sep 17 00:00:00 2001
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From: crusaderky <crusaderky@gmail.com>
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Date: Tue, 9 Feb 2021 16:03:14 +0000
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Subject: [PATCH 1/2] Compatibility with dask 2021.02.0
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---
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ci/requirements/environment-windows.yml | 2 +-
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ci/requirements/environment.yml | 2 +-
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xarray/core/dataset.py | 32 +++++++++++++++++++------
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3 files changed, 27 insertions(+), 9 deletions(-)
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Index: xarray-0.16.2/xarray/core/dataset.py
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===================================================================
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--- xarray-0.16.2.orig/xarray/core/dataset.py
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+++ xarray-0.16.2/xarray/core/dataset.py
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@@ -809,13 +809,12 @@ class Dataset(Mapping, ImplementsDataset
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import dask
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info = [
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- (True, k, v.__dask_postcompute__())
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+ (k, None) + v.__dask_postcompute__()
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if dask.is_dask_collection(v)
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- else (False, k, v)
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+ else (k, v, None, None)
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for k, v in self._variables.items()
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]
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- args = (
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- info,
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+ construct_direct_args = (
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self._coord_names,
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self._dims,
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self._attrs,
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@@ -823,19 +822,18 @@ class Dataset(Mapping, ImplementsDataset
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self._encoding,
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self._file_obj,
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)
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- return self._dask_postcompute, args
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+ return self._dask_postcompute, (info, construct_direct_args)
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def __dask_postpersist__(self):
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import dask
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info = [
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- (True, k, v.__dask_postpersist__())
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+ (k, None, v.__dask_keys__()) + v.__dask_postpersist__()
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if dask.is_dask_collection(v)
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- else (False, k, v)
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+ else (k, v, None, None, None)
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for k, v in self._variables.items()
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]
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- args = (
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- info,
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+ construct_direct_args = (
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self._coord_names,
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self._dims,
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self._attrs,
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@@ -843,45 +841,37 @@ class Dataset(Mapping, ImplementsDataset
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self._encoding,
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self._file_obj,
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)
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- return self._dask_postpersist, args
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+ return self._dask_postpersist, (info, construct_direct_args)
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@staticmethod
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- def _dask_postcompute(results, info, *args):
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+ def _dask_postcompute(results, info, construct_direct_args):
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variables = {}
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- results2 = list(results[::-1])
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- for is_dask, k, v in info:
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- if is_dask:
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- func, args2 = v
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- r = results2.pop()
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- result = func(r, *args2)
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+ results_iter = iter(results)
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+ for k, v, rebuild, rebuild_args in info:
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+ if v is None:
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+ variables[k] = rebuild(next(results_iter), *rebuild_args)
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else:
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- result = v
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- variables[k] = result
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+ variables[k] = v
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- final = Dataset._construct_direct(variables, *args)
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+ final = Dataset._construct_direct(variables, *construct_direct_args)
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return final
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@staticmethod
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- def _dask_postpersist(dsk, info, *args):
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+ def _dask_postpersist(dsk, info, construct_direct_args):
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+ from dask.optimization import cull
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+
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variables = {}
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# postpersist is called in both dask.optimize and dask.persist
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# When persisting, we want to filter out unrelated keys for
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# each Variable's task graph.
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- is_persist = len(dsk) == len(info)
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- for is_dask, k, v in info:
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- if is_dask:
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- func, args2 = v
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- if is_persist:
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- name = args2[1][0]
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- dsk2 = {k: v for k, v in dsk.items() if k[0] == name}
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- else:
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- dsk2 = dsk
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- result = func(dsk2, *args2)
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+ for k, v, dask_keys, rebuild, rebuild_args in info:
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+ if v is None:
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+ dsk2, _ = cull(dsk, dask_keys)
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+ variables[k] = rebuild(dsk2, *rebuild_args)
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else:
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- result = v
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- variables[k] = result
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+ variables[k] = v
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- return Dataset._construct_direct(variables, *args)
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+ return Dataset._construct_direct(variables, *construct_direct_args)
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def compute(self, **kwargs) -> "Dataset":
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"""Manually trigger loading and/or computation of this dataset's data
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