forked from pool/python-xarray
Accepting request 1179054 from home:bnavigator:branches:devel:languages:python:numeric
- Update to 2024.5.0
* Update reference to 'Weighted quantile estimators' by
@AndreyAkinshin in #8898
* Update docstring for compute and persist by @saschahofmann in
#8903
* Stateful tests with Dataset by @dcherian in #8658
* Trigger hypothesis stateful tests nightly by @dcherian in #8907
* Don't access data when creating DataArray from Variable. by
@dcherian in #8754
* Add typing to test_plot.py by @Illviljan in #8889
* Update hypothesis action to always save the cache by @dcherian
in #8913
* Add typing to some functions in indexing.py by @Illviljan in
#8922
* Enhance the ugly error in constructor when no data passed by
@aimtsou in #8920
* Migrate iterators.py for datatree. by @owenlittlejohns in #8879
* use pd.to_timedelta instead of TimedeltaIndex by @keewis in
#8938
* adapt more tests to the copy-on-write behavior of pandas by
@keewis in #8940
* Correct save_mfdataset docstring by @TomNicholas in #8934
* Convert 360_day calendars by choosing random dates to drop or
add by @aulemahal in #8603
* Migrate datatree mapping.py by @owenlittlejohns in #8948
* (feat): Support for pandas ExtensionArray by @ilan-gold in
#8723
* Migrate formatting_html.py into xarray core by @eni-awowale in
#8930
* use nan instead of NaN by @keewis in #8961
* stop pruning datatree_ directory from distribution by
@flamingbear in #8953
* Delete pynio backend. by @dcherian in #8971
* Migrate datatreee assertions/extensions/formatting by
@owenlittlejohns in #8967
* Bump dependencies incl pandas>=2 by @dcherian in #8968
* Option to not auto-create index during expand_dims by
@TomNicholas in #8960
* Raise errors on new warnings from within xarray by @max-sixty
in #8974
* more engine environment tricks in preparation for numpy>=2 by
@keewis in #8978
* Switch all methods to dim by @max-sixty in #8982
* Docstring and documentation improvement for the Dataset class
by @noahbenson in #8973
* Add notes on when to add ignores to warnings by @max-sixty in
#8987
* Remove .drop warning allow by @max-sixty in #8988
* Skip flaky test_open_mfdataset_manyfiles test by @max-sixty in
#8989
* avoid a couple of warnings in polyfit by @keewis in #8939
* Migration of datatree/ops.py -> datatree_ops.py by @flamingbear
in #8976
* Mark test_use_cftime_false_standard_calendar_in_range as an
expected failure by @spencerkclark in #8996
* call np.cross with 3D vectors only by @keewis in #8993
* Fix syntax error in test related to cupy by @hmaarrfk in #9000
* Add argument check_dims to assert_allclose to allow transposed
inputs (#5733) by @ignamv in #8991
* Faster fastpath by @hmaarrfk in #9001
* Speed up localize by @Illviljan in #8536
* Port negative frequency fix for pandas.date_range to
cftime_range by @spencerkclark in #8999
* Zarr: Optimize region="auto" detection by @dcherian in #8997
* Add a benchmark to monitor performance for large dataset
indexing by @hmaarrfk in #9012
* Avoid extra read from disk when creating Pandas Index. by
@dcherian in #8893
* Avoid auto creation of indexes in concat by @TomNicholas in
#8872
* Zarr: Optimize appending by @dcherian in #8998
- Drop xarray-pr8953-nodatatreeprune.patch
- Add xarray-pr8854-np2.patch gh#pydata/xarray#8854
- Add xarray-pr9305-cftime.patch gh#pydata/xarray#9305
OBS-URL: https://build.opensuse.org/request/show/1179054
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-xarray?expand=0&rev=97
This commit is contained in:
Sebastian Wagner
Git OBS Bridge
parent
69cc45c6ae
commit
4042c8f6d5
@ -2,11 +2,11 @@
|
|||||||
xarray/tutorial.py | 5 ++++-
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xarray/tutorial.py | 5 ++++-
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1 file changed, 4 insertions(+), 1 deletion(-)
|
1 file changed, 4 insertions(+), 1 deletion(-)
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|
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Index: xarray-2023.8.0/xarray/tutorial.py
|
Index: xarray-2024.05.0/xarray/tutorial.py
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===================================================================
|
===================================================================
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--- xarray-2023.8.0.orig/xarray/tutorial.py
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--- xarray-2024.05.0.orig/xarray/tutorial.py
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+++ xarray-2023.8.0/xarray/tutorial.py
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+++ xarray-2024.05.0/xarray/tutorial.py
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@@ -157,7 +157,10 @@ def open_dataset(
|
@@ -158,7 +158,10 @@ def open_dataset(
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url = f"{base_url}/raw/{version}/{path.name}"
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url = f"{base_url}/raw/{version}/{path.name}"
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# retrieve the file
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# retrieve the file
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@ -1,3 +1,81 @@
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|
-------------------------------------------------------------------
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Wed Jun 5 15:00:43 UTC 2024 - Ben Greiner <code@bnavigator.de>
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- Update to 2024.5.0
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|
* Update reference to 'Weighted quantile estimators' by
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|
@AndreyAkinshin in #8898
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|
* Update docstring for compute and persist by @saschahofmann in
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|
#8903
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|
* Stateful tests with Dataset by @dcherian in #8658
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||||||
|
* Trigger hypothesis stateful tests nightly by @dcherian in #8907
|
||||||
|
* Don't access data when creating DataArray from Variable. by
|
||||||
|
@dcherian in #8754
|
||||||
|
* Add typing to test_plot.py by @Illviljan in #8889
|
||||||
|
* Update hypothesis action to always save the cache by @dcherian
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|
in #8913
|
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|
* Add typing to some functions in indexing.py by @Illviljan in
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||||||
|
#8922
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|
* Enhance the ugly error in constructor when no data passed by
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|
@aimtsou in #8920
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|
* Migrate iterators.py for datatree. by @owenlittlejohns in #8879
|
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|
* use pd.to_timedelta instead of TimedeltaIndex by @keewis in
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|
#8938
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* adapt more tests to the copy-on-write behavior of pandas by
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|
@keewis in #8940
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|
* Correct save_mfdataset docstring by @TomNicholas in #8934
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|
* Convert 360_day calendars by choosing random dates to drop or
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|
add by @aulemahal in #8603
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|
* Migrate datatree mapping.py by @owenlittlejohns in #8948
|
||||||
|
* (feat): Support for pandas ExtensionArray by @ilan-gold in
|
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|
#8723
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|
* Migrate formatting_html.py into xarray core by @eni-awowale in
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|
#8930
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|
* use nan instead of NaN by @keewis in #8961
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|
* stop pruning datatree_ directory from distribution by
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|
@flamingbear in #8953
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* Delete pynio backend. by @dcherian in #8971
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|
* Migrate datatreee assertions/extensions/formatting by
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|
@owenlittlejohns in #8967
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* Bump dependencies incl pandas>=2 by @dcherian in #8968
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|
* Option to not auto-create index during expand_dims by
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|
@TomNicholas in #8960
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* Raise errors on new warnings from within xarray by @max-sixty
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in #8974
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|
* more engine environment tricks in preparation for numpy>=2 by
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|
@keewis in #8978
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* Switch all methods to dim by @max-sixty in #8982
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* Docstring and documentation improvement for the Dataset class
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by @noahbenson in #8973
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* Add notes on when to add ignores to warnings by @max-sixty in
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|
#8987
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* Remove .drop warning allow by @max-sixty in #8988
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* Skip flaky test_open_mfdataset_manyfiles test by @max-sixty in
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|
#8989
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* avoid a couple of warnings in polyfit by @keewis in #8939
|
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* Migration of datatree/ops.py -> datatree_ops.py by @flamingbear
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in #8976
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* Mark test_use_cftime_false_standard_calendar_in_range as an
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expected failure by @spencerkclark in #8996
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|
* call np.cross with 3D vectors only by @keewis in #8993
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|
* Fix syntax error in test related to cupy by @hmaarrfk in #9000
|
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|
* Add argument check_dims to assert_allclose to allow transposed
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|
inputs (#5733) by @ignamv in #8991
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* Faster fastpath by @hmaarrfk in #9001
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* Speed up localize by @Illviljan in #8536
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* Port negative frequency fix for pandas.date_range to
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cftime_range by @spencerkclark in #8999
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* Zarr: Optimize region="auto" detection by @dcherian in #8997
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* Add a benchmark to monitor performance for large dataset
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indexing by @hmaarrfk in #9012
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* Avoid extra read from disk when creating Pandas Index. by
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@dcherian in #8893
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|
* Avoid auto creation of indexes in concat by @TomNicholas in
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|
#8872
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* Zarr: Optimize appending by @dcherian in #8998
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- Drop xarray-pr8953-nodatatreeprune.patch
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- Add xarray-pr8854-np2.patch gh#pydata/xarray#8854
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- Add xarray-pr9305-cftime.patch gh#pydata/xarray#9305
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-------------------------------------------------------------------
|
-------------------------------------------------------------------
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Fri May 3 13:02:26 UTC 2024 - Ben Greiner <code@bnavigator.de>
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Fri May 3 13:02:26 UTC 2024 - Ben Greiner <code@bnavigator.de>
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@ -25,11 +25,11 @@
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%define psuffix %{nil}
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%define psuffix %{nil}
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%endif
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%endif
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%define ghversion 2024.03.0
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%define ghversion 2024.05.0
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%{?sle15_python_module_pythons}
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%{?sle15_python_module_pythons}
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Name: python-xarray%{psuffix}
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Name: python-xarray%{psuffix}
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Version: 2024.3.0
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Version: 2024.5.0
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Release: 0
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Release: 0
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Summary: N-D labeled arrays and datasets in Python
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Summary: N-D labeled arrays and datasets in Python
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License: Apache-2.0
|
License: Apache-2.0
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@ -38,8 +38,10 @@ Source: https://github.com/pydata/xarray/archive/refs/tags/v%{ghversion}
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# PATCH-FEATURE-UPSTREAM local_dataset.patch gh#pydata/xarray#5377 mcepl@suse.com
|
# PATCH-FEATURE-UPSTREAM local_dataset.patch gh#pydata/xarray#5377 mcepl@suse.com
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# fix xr.tutorial.open_dataset to work with the preloaded cache.
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# fix xr.tutorial.open_dataset to work with the preloaded cache.
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Patch0: local_dataset.patch
|
Patch0: local_dataset.patch
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# PATCH-FIX-UPSTREAM xarray-pr8953-nodatatreeprune.patch gh#pydata/xarray#8953
|
# PATCH-FIX-UPSTREAM xarray-pr8854-np2.patch gh#pydata/xarray#8854
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Patch1: xarray-pr8953-nodatatreeprune.patch
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Patch1: xarray-pr8854-np2.patch
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# PATCH-FIX-UPSTREAM xarray-pr9305-cftime.patch gh#pydata/xarray#9305
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Patch2: xarray-pr9305-cftime.patch
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BuildRequires: %{python_module base >= 3.9}
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BuildRequires: %{python_module base >= 3.9}
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BuildRequires: %{python_module pip}
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BuildRequires: %{python_module pip}
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BuildRequires: %{python_module setuptools_scm}
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BuildRequires: %{python_module setuptools_scm}
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@ -48,8 +50,8 @@ BuildRequires: %{python_module wheel}
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BuildRequires: fdupes
|
BuildRequires: fdupes
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BuildRequires: python-rpm-macros
|
BuildRequires: python-rpm-macros
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Requires: python-numpy >= 1.23
|
Requires: python-numpy >= 1.23
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Requires: python-packaging >= 22
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Requires: python-packaging >= 23.1
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Requires: python-pandas >= 1.5
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Requires: python-pandas >= 2
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Obsoletes: python-xray <= 0.7
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Obsoletes: python-xray <= 0.7
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BuildArch: noarch
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BuildArch: noarch
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%if %{with test}
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%if %{with test}
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@ -175,6 +177,7 @@ if [ $(getconf LONG_BIT) -eq 32 ]; then
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donttest="$donttest or (test_interpolate_chunk_advanced and linear)"
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donttest="$donttest or (test_interpolate_chunk_advanced and linear)"
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# tests for 64bit types
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# tests for 64bit types
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donttest="$donttest or TestZarrDictStore or TestZarrDirectoryStore or TestZarrWriteEmpty"
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donttest="$donttest or TestZarrDictStore or TestZarrDirectoryStore or TestZarrWriteEmpty"
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donttest="$donttest or test_repr_multiindex or test_array_repr_dtypes_unix"
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fi
|
fi
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# h5py was built without ROS3 support, can't use ros3 driver
|
# h5py was built without ROS3 support, can't use ros3 driver
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donttest="$donttest or TestH5NetCDFDataRos3Driver"
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donttest="$donttest or TestH5NetCDFDataRos3Driver"
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@ -1,3 +0,0 @@
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version https://git-lfs.github.com/spec/v1
|
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oid sha256:c4cc63dd850fe5a0b62d6805147b64947f6df81a876de31e563558be0543d3a6
|
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size 3722922
|
|
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3
xarray-2024.05.0-gh.tar.gz
Normal file
3
xarray-2024.05.0-gh.tar.gz
Normal file
@ -0,0 +1,3 @@
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|
version https://git-lfs.github.com/spec/v1
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|
oid sha256:604a801c7bba96524b09b993b159ae998e0987627949b667c884f65895939f11
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|
size 3739324
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772
xarray-pr8854-np2.patch
Normal file
772
xarray-pr8854-np2.patch
Normal file
@ -0,0 +1,772 @@
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From e066a6c559e9d7f31c359ea95da42d0e45c585ce Mon Sep 17 00:00:00 2001
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|
From: Justus Magin <keewis@posteo.de>
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Date: Tue, 19 Mar 2024 11:32:32 +0100
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Subject: [PATCH 01/65] replace the use of `numpy.array_api` with
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`array_api_strict`
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This would make it a dependency of `namedarray`, and not allow
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behavior that is allowed but not required by the array API standard. Otherwise we can:
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- use the main `numpy` namespace
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- use `array_api_compat` (would also be a new dependency) to allow
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optional behavior
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---
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xarray/namedarray/_array_api.py | 9 ---------
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1 file changed, 9 deletions(-)
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Index: xarray-2024.05.0/xarray/namedarray/_array_api.py
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===================================================================
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--- xarray-2024.05.0.orig/xarray/namedarray/_array_api.py
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+++ xarray-2024.05.0/xarray/namedarray/_array_api.py
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@@ -1,6 +1,5 @@
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from __future__ import annotations
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-import warnings
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from types import ModuleType
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from typing import Any
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@@ -21,14 +20,6 @@ from xarray.namedarray._typing import (
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)
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from xarray.namedarray.core import NamedArray
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-with warnings.catch_warnings():
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- warnings.filterwarnings(
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- "ignore",
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- r"The numpy.array_api submodule is still experimental",
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- category=UserWarning,
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- )
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- import numpy.array_api as nxp # noqa: F401
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-
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def _get_data_namespace(x: NamedArray[Any, Any]) -> ModuleType:
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if isinstance(x._data, _arrayapi):
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@@ -68,13 +59,13 @@ def astype(
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|
Examples
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|
--------
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- >>> narr = NamedArray(("x",), nxp.asarray([1.5, 2.5]))
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+ >>> narr = NamedArray(("x",), np.asarray([1.5, 2.5]))
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>>> narr
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<xarray.NamedArray (x: 2)> Size: 16B
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- Array([1.5, 2.5], dtype=float64)
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+ array([1.5, 2.5])
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>>> astype(narr, np.dtype(np.int32))
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<xarray.NamedArray (x: 2)> Size: 8B
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- Array([1, 2], dtype=int32)
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+ array([1, 2], dtype=int32)
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"""
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if isinstance(x._data, _arrayapi):
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xp = x._data.__array_namespace__()
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@@ -109,7 +100,7 @@ def imag(
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|
Examples
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|
--------
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- >>> narr = NamedArray(("x",), np.asarray([1.0 + 2j, 2 + 4j])) # TODO: Use nxp
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+ >>> narr = NamedArray(("x",), np.asarray([1.0 + 2j, 2 + 4j]))
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>>> imag(narr)
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<xarray.NamedArray (x: 2)> Size: 16B
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array([2., 4.])
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@@ -141,7 +132,7 @@ def real(
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Examples
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--------
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- >>> narr = NamedArray(("x",), np.asarray([1.0 + 2j, 2 + 4j])) # TODO: Use nxp
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+ >>> narr = NamedArray(("x",), np.asarray([1.0 + 2j, 2 + 4j]))
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>>> real(narr)
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<xarray.NamedArray (x: 2)> Size: 16B
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array([1., 2.])
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@@ -179,15 +170,15 @@ def expand_dims(
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Examples
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--------
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- >>> x = NamedArray(("x", "y"), nxp.asarray([[1.0, 2.0], [3.0, 4.0]]))
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+ >>> x = NamedArray(("x", "y"), np.asarray([[1.0, 2.0], [3.0, 4.0]]))
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>>> expand_dims(x)
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<xarray.NamedArray (dim_2: 1, x: 2, y: 2)> Size: 32B
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- Array([[[1., 2.],
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- [3., 4.]]], dtype=float64)
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+ array([[[1., 2.],
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+ [3., 4.]]])
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>>> expand_dims(x, dim="z")
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<xarray.NamedArray (z: 1, x: 2, y: 2)> Size: 32B
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- Array([[[1., 2.],
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- [3., 4.]]], dtype=float64)
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+ array([[[1., 2.],
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+ [3., 4.]]])
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"""
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xp = _get_data_namespace(x)
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dims = x.dims
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Index: xarray-2024.05.0/xarray/tests/__init__.py
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===================================================================
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--- xarray-2024.05.0.orig/xarray/tests/__init__.py
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+++ xarray-2024.05.0/xarray/tests/__init__.py
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@@ -147,9 +147,10 @@ has_numbagg_or_bottleneck = has_numbagg
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requires_numbagg_or_bottleneck = pytest.mark.skipif(
|
||||||
|
not has_scipy_or_netCDF4, reason="requires scipy or netCDF4"
|
||||||
|
)
|
||||||
|
-has_numpy_array_api, requires_numpy_array_api = _importorskip("numpy", "1.26.0")
|
||||||
|
has_numpy_2, requires_numpy_2 = _importorskip("numpy", "2.0.0")
|
||||||
|
|
||||||
|
+has_array_api_strict, requires_array_api_strict = _importorskip("array_api_strict")
|
||||||
|
+
|
||||||
|
|
||||||
|
def _importorskip_h5netcdf_ros3():
|
||||||
|
try:
|
||||||
|
Index: xarray-2024.05.0/xarray/tests/test_array_api.py
|
||||||
|
===================================================================
|
||||||
|
--- xarray-2024.05.0.orig/xarray/tests/test_array_api.py
|
||||||
|
+++ xarray-2024.05.0/xarray/tests/test_array_api.py
|
||||||
|
@@ -6,20 +6,9 @@ import xarray as xr
|
||||||
|
from xarray.testing import assert_equal
|
||||||
|
|
||||||
|
np = pytest.importorskip("numpy", minversion="1.22")
|
||||||
|
+xp = pytest.importorskip("array_api_strict")
|
||||||
|
|
||||||
|
-try:
|
||||||
|
- import warnings
|
||||||
|
-
|
||||||
|
- with warnings.catch_warnings():
|
||||||
|
- warnings.simplefilter("ignore")
|
||||||
|
-
|
||||||
|
- import numpy.array_api as xp
|
||||||
|
- from numpy.array_api._array_object import Array
|
||||||
|
-except ImportError:
|
||||||
|
- # for `numpy>=2.0`
|
||||||
|
- xp = pytest.importorskip("array_api_strict")
|
||||||
|
-
|
||||||
|
- from array_api_strict._array_object import Array # type: ignore[no-redef]
|
||||||
|
+from array_api_strict._array_object import Array # isort:skip # type: ignore[no-redef]
|
||||||
|
|
||||||
|
|
||||||
|
@pytest.fixture
|
||||||
|
@@ -65,8 +54,8 @@ def test_aggregation_skipna(arrays) -> N
|
||||||
|
def test_astype(arrays) -> None:
|
||||||
|
np_arr, xp_arr = arrays
|
||||||
|
expected = np_arr.astype(np.int64)
|
||||||
|
- actual = xp_arr.astype(np.int64)
|
||||||
|
- assert actual.dtype == np.int64
|
||||||
|
+ actual = xp_arr.astype(xp.int64)
|
||||||
|
+ assert actual.dtype == xp.int64
|
||||||
|
assert isinstance(actual.data, Array)
|
||||||
|
assert_equal(actual, expected)
|
||||||
|
|
||||||
|
@@ -118,8 +107,10 @@ def test_indexing(arrays: tuple[xr.DataA
|
||||||
|
|
||||||
|
def test_properties(arrays: tuple[xr.DataArray, xr.DataArray]) -> None:
|
||||||
|
np_arr, xp_arr = arrays
|
||||||
|
- assert np_arr.nbytes == np_arr.data.nbytes
|
||||||
|
- assert xp_arr.nbytes == np_arr.data.nbytes
|
||||||
|
+
|
||||||
|
+ expected = np_arr.data.nbytes
|
||||||
|
+ assert np_arr.nbytes == expected
|
||||||
|
+ assert xp_arr.nbytes == expected
|
||||||
|
|
||||||
|
|
||||||
|
def test_reorganizing_operation(arrays: tuple[xr.DataArray, xr.DataArray]) -> None:
|
||||||
|
Index: xarray-2024.05.0/xarray/tests/test_namedarray.py
|
||||||
|
===================================================================
|
||||||
|
--- xarray-2024.05.0.orig/xarray/tests/test_namedarray.py
|
||||||
|
+++ xarray-2024.05.0/xarray/tests/test_namedarray.py
|
||||||
|
@@ -1,7 +1,6 @@
|
||||||
|
from __future__ import annotations
|
||||||
|
|
||||||
|
import copy
|
||||||
|
-import warnings
|
||||||
|
from abc import abstractmethod
|
||||||
|
from collections.abc import Mapping
|
||||||
|
from typing import TYPE_CHECKING, Any, Generic, cast, overload
|
||||||
|
@@ -79,6 +78,17 @@ class CustomArrayIndexable(
|
||||||
|
return np
|
||||||
|
|
||||||
|
|
||||||
|
+def check_duck_array_typevar(a: duckarray[Any, _DType]) -> duckarray[Any, _DType]:
|
||||||
|
+ # Mypy checks a is valid:
|
||||||
|
+ b: duckarray[Any, _DType] = a
|
||||||
|
+
|
||||||
|
+ # Runtime check if valid:
|
||||||
|
+ if isinstance(b, _arrayfunction_or_api):
|
||||||
|
+ return b
|
||||||
|
+ else:
|
||||||
|
+ raise TypeError(f"a ({type(a)}) is not a valid _arrayfunction or _arrayapi")
|
||||||
|
+
|
||||||
|
+
|
||||||
|
class NamedArraySubclassobjects:
|
||||||
|
@pytest.fixture
|
||||||
|
def target(self, data: np.ndarray[Any, Any]) -> Any:
|
||||||
|
@@ -328,48 +338,27 @@ class TestNamedArray(NamedArraySubclasso
|
||||||
|
named_array.dims = new_dims
|
||||||
|
assert named_array.dims == tuple(new_dims)
|
||||||
|
|
||||||
|
- def test_duck_array_class(
|
||||||
|
- self,
|
||||||
|
- ) -> None:
|
||||||
|
- def test_duck_array_typevar(
|
||||||
|
- a: duckarray[Any, _DType],
|
||||||
|
- ) -> duckarray[Any, _DType]:
|
||||||
|
- # Mypy checks a is valid:
|
||||||
|
- b: duckarray[Any, _DType] = a
|
||||||
|
-
|
||||||
|
- # Runtime check if valid:
|
||||||
|
- if isinstance(b, _arrayfunction_or_api):
|
||||||
|
- return b
|
||||||
|
- else:
|
||||||
|
- raise TypeError(
|
||||||
|
- f"a ({type(a)}) is not a valid _arrayfunction or _arrayapi"
|
||||||
|
- )
|
||||||
|
-
|
||||||
|
+ def test_duck_array_class(self) -> None:
|
||||||
|
numpy_a: NDArray[np.int64]
|
||||||
|
numpy_a = np.array([2.1, 4], dtype=np.dtype(np.int64))
|
||||||
|
- test_duck_array_typevar(numpy_a)
|
||||||
|
+ check_duck_array_typevar(numpy_a)
|
||||||
|
|
||||||
|
masked_a: np.ma.MaskedArray[Any, np.dtype[np.int64]]
|
||||||
|
masked_a = np.ma.asarray([2.1, 4], dtype=np.dtype(np.int64)) # type: ignore[no-untyped-call]
|
||||||
|
- test_duck_array_typevar(masked_a)
|
||||||
|
+ check_duck_array_typevar(masked_a)
|
||||||
|
|
||||||
|
custom_a: CustomArrayIndexable[Any, np.dtype[np.int64]]
|
||||||
|
custom_a = CustomArrayIndexable(numpy_a)
|
||||||
|
- test_duck_array_typevar(custom_a)
|
||||||
|
+ check_duck_array_typevar(custom_a)
|
||||||
|
|
||||||
|
+ def test_duck_array_class_array_api(self) -> None:
|
||||||
|
# Test numpy's array api:
|
||||||
|
- with warnings.catch_warnings():
|
||||||
|
- warnings.filterwarnings(
|
||||||
|
- "ignore",
|
||||||
|
- r"The numpy.array_api submodule is still experimental",
|
||||||
|
- category=UserWarning,
|
||||||
|
- )
|
||||||
|
- import numpy.array_api as nxp
|
||||||
|
+ nxp = pytest.importorskip("array_api_strict", minversion="1.0")
|
||||||
|
|
||||||
|
# TODO: nxp doesn't use dtype typevars, so can only use Any for the moment:
|
||||||
|
arrayapi_a: duckarray[Any, Any] # duckarray[Any, np.dtype[np.int64]]
|
||||||
|
- arrayapi_a = nxp.asarray([2.1, 4], dtype=np.dtype(np.int64))
|
||||||
|
- test_duck_array_typevar(arrayapi_a)
|
||||||
|
+ arrayapi_a = nxp.asarray([2.1, 4], dtype=nxp.int64)
|
||||||
|
+ check_duck_array_typevar(arrayapi_a)
|
||||||
|
|
||||||
|
def test_new_namedarray(self) -> None:
|
||||||
|
dtype_float = np.dtype(np.float32)
|
||||||
|
Index: xarray-2024.05.0/xarray/tests/test_strategies.py
|
||||||
|
===================================================================
|
||||||
|
--- xarray-2024.05.0.orig/xarray/tests/test_strategies.py
|
||||||
|
+++ xarray-2024.05.0/xarray/tests/test_strategies.py
|
||||||
|
@@ -1,6 +1,9 @@
|
||||||
|
+import warnings
|
||||||
|
+
|
||||||
|
import numpy as np
|
||||||
|
import numpy.testing as npt
|
||||||
|
import pytest
|
||||||
|
+from packaging.version import Version
|
||||||
|
|
||||||
|
pytest.importorskip("hypothesis")
|
||||||
|
# isort: split
|
||||||
|
@@ -19,7 +22,6 @@ from xarray.testing.strategies import (
|
||||||
|
unique_subset_of,
|
||||||
|
variables,
|
||||||
|
)
|
||||||
|
-from xarray.tests import requires_numpy_array_api
|
||||||
|
|
||||||
|
ALLOWED_ATTRS_VALUES_TYPES = (int, bool, str, np.ndarray)
|
||||||
|
|
||||||
|
@@ -199,7 +201,6 @@ class TestVariablesStrategy:
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
- @requires_numpy_array_api
|
||||||
|
@given(st.data())
|
||||||
|
def test_make_strategies_namespace(self, data):
|
||||||
|
"""
|
||||||
|
@@ -208,16 +209,24 @@ class TestVariablesStrategy:
|
||||||
|
We still want to generate dtypes not in the array API by default, but this checks we don't accidentally override
|
||||||
|
the user's choice of dtypes with non-API-compliant ones.
|
||||||
|
"""
|
||||||
|
- from numpy import (
|
||||||
|
- array_api as np_array_api, # requires numpy>=1.26.0, and we expect a UserWarning to be raised
|
||||||
|
- )
|
||||||
|
+ if Version(np.__version__) >= Version("2.0.0.dev0"):
|
||||||
|
+ nxp = np
|
||||||
|
+ else:
|
||||||
|
+ # requires numpy>=1.26.0, and we expect a UserWarning to be raised
|
||||||
|
+ with warnings.catch_warnings():
|
||||||
|
+ warnings.filterwarnings(
|
||||||
|
+ "ignore", category=UserWarning, message=".+See NEP 47."
|
||||||
|
+ )
|
||||||
|
+ from numpy import ( # type: ignore[no-redef,unused-ignore]
|
||||||
|
+ array_api as nxp,
|
||||||
|
+ )
|
||||||
|
|
||||||
|
- np_array_api_st = make_strategies_namespace(np_array_api)
|
||||||
|
+ nxp_st = make_strategies_namespace(nxp)
|
||||||
|
|
||||||
|
data.draw(
|
||||||
|
variables(
|
||||||
|
- array_strategy_fn=np_array_api_st.arrays,
|
||||||
|
- dtype=np_array_api_st.scalar_dtypes(),
|
||||||
|
+ array_strategy_fn=nxp_st.arrays,
|
||||||
|
+ dtype=nxp_st.scalar_dtypes(),
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
Index: xarray-2024.05.0/xarray/core/duck_array_ops.py
|
||||||
|
===================================================================
|
||||||
|
--- xarray-2024.05.0.orig/xarray/core/duck_array_ops.py
|
||||||
|
+++ xarray-2024.05.0/xarray/core/duck_array_ops.py
|
||||||
|
@@ -142,17 +142,25 @@ around.__doc__ = str.replace(
|
||||||
|
|
||||||
|
def isnull(data):
|
||||||
|
data = asarray(data)
|
||||||
|
- scalar_type = data.dtype.type
|
||||||
|
- if issubclass(scalar_type, (np.datetime64, np.timedelta64)):
|
||||||
|
+
|
||||||
|
+ xp = get_array_namespace(data)
|
||||||
|
+ scalar_type = data.dtype
|
||||||
|
+ if dtypes.is_datetime_like(scalar_type):
|
||||||
|
# datetime types use NaT for null
|
||||||
|
# note: must check timedelta64 before integers, because currently
|
||||||
|
# timedelta64 inherits from np.integer
|
||||||
|
return isnat(data)
|
||||||
|
- elif issubclass(scalar_type, np.inexact):
|
||||||
|
+ elif dtypes.isdtype(scalar_type, ("real floating", "complex floating"), xp=xp):
|
||||||
|
# float types use NaN for null
|
||||||
|
xp = get_array_namespace(data)
|
||||||
|
return xp.isnan(data)
|
||||||
|
- elif issubclass(scalar_type, (np.bool_, np.integer, np.character, np.void)):
|
||||||
|
+ elif dtypes.isdtype(scalar_type, ("bool", "integral"), xp=xp) or (
|
||||||
|
+ isinstance(scalar_type, np.dtype)
|
||||||
|
+ and (
|
||||||
|
+ np.issubdtype(scalar_type, np.character)
|
||||||
|
+ or np.issubdtype(scalar_type, np.void)
|
||||||
|
+ )
|
||||||
|
+ ):
|
||||||
|
# these types cannot represent missing values
|
||||||
|
return full_like(data, dtype=bool, fill_value=False)
|
||||||
|
else:
|
||||||
|
@@ -406,13 +414,22 @@ def _create_nan_agg_method(name, coerce_
|
||||||
|
if invariant_0d and axis == ():
|
||||||
|
return values
|
||||||
|
|
||||||
|
- values = asarray(values)
|
||||||
|
+ xp = get_array_namespace(values)
|
||||||
|
+ values = asarray(values, xp=xp)
|
||||||
|
|
||||||
|
- if coerce_strings and values.dtype.kind in "SU":
|
||||||
|
+ if coerce_strings and dtypes.is_string(values.dtype):
|
||||||
|
values = astype(values, object)
|
||||||
|
|
||||||
|
func = None
|
||||||
|
- if skipna or (skipna is None and values.dtype.kind in "cfO"):
|
||||||
|
+ if skipna or (
|
||||||
|
+ skipna is None
|
||||||
|
+ and (
|
||||||
|
+ dtypes.isdtype(
|
||||||
|
+ values.dtype, ("complex floating", "real floating"), xp=xp
|
||||||
|
+ )
|
||||||
|
+ or dtypes.is_object(values.dtype)
|
||||||
|
+ )
|
||||||
|
+ ):
|
||||||
|
nanname = "nan" + name
|
||||||
|
func = getattr(nanops, nanname)
|
||||||
|
else:
|
||||||
|
@@ -477,8 +494,8 @@ def _datetime_nanmin(array):
|
||||||
|
- numpy nanmin() don't work on datetime64 (all versions at the moment of writing)
|
||||||
|
- dask min() does not work on datetime64 (all versions at the moment of writing)
|
||||||
|
"""
|
||||||
|
- assert array.dtype.kind in "mM"
|
||||||
|
dtype = array.dtype
|
||||||
|
+ assert dtypes.is_datetime_like(dtype)
|
||||||
|
# (NaT).astype(float) does not produce NaN...
|
||||||
|
array = where(pandas_isnull(array), np.nan, array.astype(float))
|
||||||
|
array = min(array, skipna=True)
|
||||||
|
@@ -515,7 +532,7 @@ def datetime_to_numeric(array, offset=No
|
||||||
|
"""
|
||||||
|
# Set offset to minimum if not given
|
||||||
|
if offset is None:
|
||||||
|
- if array.dtype.kind in "Mm":
|
||||||
|
+ if dtypes.is_datetime_like(array.dtype):
|
||||||
|
offset = _datetime_nanmin(array)
|
||||||
|
else:
|
||||||
|
offset = min(array)
|
||||||
|
@@ -527,7 +544,7 @@ def datetime_to_numeric(array, offset=No
|
||||||
|
# This map_blocks call is for backwards compatibility.
|
||||||
|
# dask == 2021.04.1 does not support subtracting object arrays
|
||||||
|
# which is required for cftime
|
||||||
|
- if is_duck_dask_array(array) and np.issubdtype(array.dtype, object):
|
||||||
|
+ if is_duck_dask_array(array) and dtypes.is_object(array.dtype):
|
||||||
|
array = array.map_blocks(lambda a, b: a - b, offset, meta=array._meta)
|
||||||
|
else:
|
||||||
|
array = array - offset
|
||||||
|
@@ -537,11 +554,11 @@ def datetime_to_numeric(array, offset=No
|
||||||
|
array = np.array(array)
|
||||||
|
|
||||||
|
# Convert timedelta objects to float by first converting to microseconds.
|
||||||
|
- if array.dtype.kind in "O":
|
||||||
|
+ if dtypes.is_object(array.dtype):
|
||||||
|
return py_timedelta_to_float(array, datetime_unit or "ns").astype(dtype)
|
||||||
|
|
||||||
|
# Convert np.NaT to np.nan
|
||||||
|
- elif array.dtype.kind in "mM":
|
||||||
|
+ elif dtypes.is_datetime_like(array.dtype):
|
||||||
|
# Convert to specified timedelta units.
|
||||||
|
if datetime_unit:
|
||||||
|
array = array / np.timedelta64(1, datetime_unit)
|
||||||
|
@@ -641,7 +658,7 @@ def mean(array, axis=None, skipna=None,
|
||||||
|
from xarray.core.common import _contains_cftime_datetimes
|
||||||
|
|
||||||
|
array = asarray(array)
|
||||||
|
- if array.dtype.kind in "Mm":
|
||||||
|
+ if dtypes.is_datetime_like(array.dtype):
|
||||||
|
offset = _datetime_nanmin(array)
|
||||||
|
|
||||||
|
# xarray always uses np.datetime64[ns] for np.datetime64 data
|
||||||
|
@@ -689,7 +706,9 @@ def cumsum(array, axis=None, **kwargs):
|
||||||
|
|
||||||
|
def first(values, axis, skipna=None):
|
||||||
|
"""Return the first non-NA elements in this array along the given axis"""
|
||||||
|
- if (skipna or skipna is None) and values.dtype.kind not in "iSU":
|
||||||
|
+ if (skipna or skipna is None) and not (
|
||||||
|
+ dtypes.isdtype(values.dtype, "signed integer") or dtypes.is_string(values.dtype)
|
||||||
|
+ ):
|
||||||
|
# only bother for dtypes that can hold NaN
|
||||||
|
if is_chunked_array(values):
|
||||||
|
return chunked_nanfirst(values, axis)
|
||||||
|
@@ -700,7 +719,9 @@ def first(values, axis, skipna=None):
|
||||||
|
|
||||||
|
def last(values, axis, skipna=None):
|
||||||
|
"""Return the last non-NA elements in this array along the given axis"""
|
||||||
|
- if (skipna or skipna is None) and values.dtype.kind not in "iSU":
|
||||||
|
+ if (skipna or skipna is None) and not (
|
||||||
|
+ dtypes.isdtype(values.dtype, "signed integer") or dtypes.is_string(values.dtype)
|
||||||
|
+ ):
|
||||||
|
# only bother for dtypes that can hold NaN
|
||||||
|
if is_chunked_array(values):
|
||||||
|
return chunked_nanlast(values, axis)
|
||||||
|
Index: xarray-2024.05.0/xarray/core/dtypes.py
|
||||||
|
===================================================================
|
||||||
|
--- xarray-2024.05.0.orig/xarray/core/dtypes.py
|
||||||
|
+++ xarray-2024.05.0/xarray/core/dtypes.py
|
||||||
|
@@ -4,8 +4,9 @@ import functools
|
||||||
|
from typing import Any
|
||||||
|
|
||||||
|
import numpy as np
|
||||||
|
+from pandas.api.types import is_extension_array_dtype
|
||||||
|
|
||||||
|
-from xarray.core import utils
|
||||||
|
+from xarray.core import npcompat, utils
|
||||||
|
|
||||||
|
# Use as a sentinel value to indicate a dtype appropriate NA value.
|
||||||
|
NA = utils.ReprObject("<NA>")
|
||||||
|
@@ -60,22 +61,22 @@ def maybe_promote(dtype: np.dtype) -> tu
|
||||||
|
# N.B. these casting rules should match pandas
|
||||||
|
dtype_: np.typing.DTypeLike
|
||||||
|
fill_value: Any
|
||||||
|
- if np.issubdtype(dtype, np.floating):
|
||||||
|
+ if isdtype(dtype, "real floating"):
|
||||||
|
dtype_ = dtype
|
||||||
|
fill_value = np.nan
|
||||||
|
- elif np.issubdtype(dtype, np.timedelta64):
|
||||||
|
+ elif isinstance(dtype, np.dtype) and np.issubdtype(dtype, np.timedelta64):
|
||||||
|
# See https://github.com/numpy/numpy/issues/10685
|
||||||
|
# np.timedelta64 is a subclass of np.integer
|
||||||
|
# Check np.timedelta64 before np.integer
|
||||||
|
fill_value = np.timedelta64("NaT")
|
||||||
|
dtype_ = dtype
|
||||||
|
- elif np.issubdtype(dtype, np.integer):
|
||||||
|
+ elif isdtype(dtype, "integral"):
|
||||||
|
dtype_ = np.float32 if dtype.itemsize <= 2 else np.float64
|
||||||
|
fill_value = np.nan
|
||||||
|
- elif np.issubdtype(dtype, np.complexfloating):
|
||||||
|
+ elif isdtype(dtype, "complex floating"):
|
||||||
|
dtype_ = dtype
|
||||||
|
fill_value = np.nan + np.nan * 1j
|
||||||
|
- elif np.issubdtype(dtype, np.datetime64):
|
||||||
|
+ elif isinstance(dtype, np.dtype) and np.issubdtype(dtype, np.datetime64):
|
||||||
|
dtype_ = dtype
|
||||||
|
fill_value = np.datetime64("NaT")
|
||||||
|
else:
|
||||||
|
@@ -118,16 +119,16 @@ def get_pos_infinity(dtype, max_for_int=
|
||||||
|
-------
|
||||||
|
fill_value : positive infinity value corresponding to this dtype.
|
||||||
|
"""
|
||||||
|
- if issubclass(dtype.type, np.floating):
|
||||||
|
+ if isdtype(dtype, "real floating"):
|
||||||
|
return np.inf
|
||||||
|
|
||||||
|
- if issubclass(dtype.type, np.integer):
|
||||||
|
+ if isdtype(dtype, "integral"):
|
||||||
|
if max_for_int:
|
||||||
|
return np.iinfo(dtype).max
|
||||||
|
else:
|
||||||
|
return np.inf
|
||||||
|
|
||||||
|
- if issubclass(dtype.type, np.complexfloating):
|
||||||
|
+ if isdtype(dtype, "complex floating"):
|
||||||
|
return np.inf + 1j * np.inf
|
||||||
|
|
||||||
|
return INF
|
||||||
|
@@ -146,24 +147,66 @@ def get_neg_infinity(dtype, min_for_int=
|
||||||
|
-------
|
||||||
|
fill_value : positive infinity value corresponding to this dtype.
|
||||||
|
"""
|
||||||
|
- if issubclass(dtype.type, np.floating):
|
||||||
|
+ if isdtype(dtype, "real floating"):
|
||||||
|
return -np.inf
|
||||||
|
|
||||||
|
- if issubclass(dtype.type, np.integer):
|
||||||
|
+ if isdtype(dtype, "integral"):
|
||||||
|
if min_for_int:
|
||||||
|
return np.iinfo(dtype).min
|
||||||
|
else:
|
||||||
|
return -np.inf
|
||||||
|
|
||||||
|
- if issubclass(dtype.type, np.complexfloating):
|
||||||
|
+ if isdtype(dtype, "complex floating"):
|
||||||
|
return -np.inf - 1j * np.inf
|
||||||
|
|
||||||
|
return NINF
|
||||||
|
|
||||||
|
|
||||||
|
-def is_datetime_like(dtype):
|
||||||
|
+def is_datetime_like(dtype) -> bool:
|
||||||
|
"""Check if a dtype is a subclass of the numpy datetime types"""
|
||||||
|
- return np.issubdtype(dtype, np.datetime64) or np.issubdtype(dtype, np.timedelta64)
|
||||||
|
+ return _is_numpy_subdtype(dtype, (np.datetime64, np.timedelta64))
|
||||||
|
+
|
||||||
|
+
|
||||||
|
+def is_object(dtype) -> bool:
|
||||||
|
+ """Check if a dtype is object"""
|
||||||
|
+ return _is_numpy_subdtype(dtype, object)
|
||||||
|
+
|
||||||
|
+
|
||||||
|
+def is_string(dtype) -> bool:
|
||||||
|
+ """Check if a dtype is a string dtype"""
|
||||||
|
+ return _is_numpy_subdtype(dtype, (np.str_, np.character))
|
||||||
|
+
|
||||||
|
+
|
||||||
|
+def _is_numpy_subdtype(dtype, kind) -> bool:
|
||||||
|
+ if not isinstance(dtype, np.dtype):
|
||||||
|
+ return False
|
||||||
|
+
|
||||||
|
+ kinds = kind if isinstance(kind, tuple) else (kind,)
|
||||||
|
+ return any(np.issubdtype(dtype, kind) for kind in kinds)
|
||||||
|
+
|
||||||
|
+
|
||||||
|
+def isdtype(dtype, kind: str | tuple[str, ...], xp=None) -> bool:
|
||||||
|
+ """Compatibility wrapper for isdtype() from the array API standard.
|
||||||
|
+
|
||||||
|
+ Unlike xp.isdtype(), kind must be a string.
|
||||||
|
+ """
|
||||||
|
+ # TODO(shoyer): remove this wrapper when Xarray requires
|
||||||
|
+ # numpy>=2 and pandas extensions arrays are implemented in
|
||||||
|
+ # Xarray via the array API
|
||||||
|
+ if not isinstance(kind, str) and not (
|
||||||
|
+ isinstance(kind, tuple) and all(isinstance(k, str) for k in kind)
|
||||||
|
+ ):
|
||||||
|
+ raise TypeError(f"kind must be a string or a tuple of strings: {repr(kind)}")
|
||||||
|
+
|
||||||
|
+ if isinstance(dtype, np.dtype):
|
||||||
|
+ return npcompat.isdtype(dtype, kind)
|
||||||
|
+ elif is_extension_array_dtype(dtype):
|
||||||
|
+ # we never want to match pandas extension array dtypes
|
||||||
|
+ return False
|
||||||
|
+ else:
|
||||||
|
+ if xp is None:
|
||||||
|
+ xp = np
|
||||||
|
+ return xp.isdtype(dtype, kind)
|
||||||
|
|
||||||
|
|
||||||
|
def result_type(
|
||||||
|
@@ -184,12 +227,26 @@ def result_type(
|
||||||
|
-------
|
||||||
|
numpy.dtype for the result.
|
||||||
|
"""
|
||||||
|
- types = {np.result_type(t).type for t in arrays_and_dtypes}
|
||||||
|
+ from xarray.core.duck_array_ops import get_array_namespace
|
||||||
|
+
|
||||||
|
+ # TODO(shoyer): consider moving this logic into get_array_namespace()
|
||||||
|
+ # or another helper function.
|
||||||
|
+ namespaces = {get_array_namespace(t) for t in arrays_and_dtypes}
|
||||||
|
+ non_numpy = namespaces - {np}
|
||||||
|
+ if non_numpy:
|
||||||
|
+ [xp] = non_numpy
|
||||||
|
+ else:
|
||||||
|
+ xp = np
|
||||||
|
+
|
||||||
|
+ types = {xp.result_type(t) for t in arrays_and_dtypes}
|
||||||
|
|
||||||
|
- for left, right in PROMOTE_TO_OBJECT:
|
||||||
|
- if any(issubclass(t, left) for t in types) and any(
|
||||||
|
- issubclass(t, right) for t in types
|
||||||
|
- ):
|
||||||
|
- return np.dtype(object)
|
||||||
|
+ if any(isinstance(t, np.dtype) for t in types):
|
||||||
|
+ # only check if there's numpy dtypes – the array API does not
|
||||||
|
+ # define the types we're checking for
|
||||||
|
+ for left, right in PROMOTE_TO_OBJECT:
|
||||||
|
+ if any(np.issubdtype(t, left) for t in types) and any(
|
||||||
|
+ np.issubdtype(t, right) for t in types
|
||||||
|
+ ):
|
||||||
|
+ return xp.dtype(object)
|
||||||
|
|
||||||
|
- return np.result_type(*arrays_and_dtypes)
|
||||||
|
+ return xp.result_type(*arrays_and_dtypes)
|
||||||
|
Index: xarray-2024.05.0/xarray/namedarray/core.py
|
||||||
|
===================================================================
|
||||||
|
--- xarray-2024.05.0.orig/xarray/namedarray/core.py
|
||||||
|
+++ xarray-2024.05.0/xarray/namedarray/core.py
|
||||||
|
@@ -470,10 +470,28 @@ class NamedArray(NamedArrayAggregations,
|
||||||
|
If the underlying data array does not include ``nbytes``, estimates
|
||||||
|
the bytes consumed based on the ``size`` and ``dtype``.
|
||||||
|
"""
|
||||||
|
+ from xarray.namedarray._array_api import _get_data_namespace
|
||||||
|
+
|
||||||
|
if hasattr(self._data, "nbytes"):
|
||||||
|
return self._data.nbytes # type: ignore[no-any-return]
|
||||||
|
+
|
||||||
|
+ if hasattr(self.dtype, "itemsize"):
|
||||||
|
+ itemsize = self.dtype.itemsize
|
||||||
|
+ elif isinstance(self._data, _arrayapi):
|
||||||
|
+ xp = _get_data_namespace(self)
|
||||||
|
+
|
||||||
|
+ if xp.isdtype(self.dtype, "bool"):
|
||||||
|
+ itemsize = 1
|
||||||
|
+ elif xp.isdtype(self.dtype, "integral"):
|
||||||
|
+ itemsize = xp.iinfo(self.dtype).bits // 8
|
||||||
|
+ else:
|
||||||
|
+ itemsize = xp.finfo(self.dtype).bits // 8
|
||||||
|
else:
|
||||||
|
- return self.size * self.dtype.itemsize
|
||||||
|
+ raise TypeError(
|
||||||
|
+ "cannot compute the number of bytes (no array API nor nbytes / itemsize)"
|
||||||
|
+ )
|
||||||
|
+
|
||||||
|
+ return self.size * itemsize
|
||||||
|
|
||||||
|
@property
|
||||||
|
def dims(self) -> _Dims:
|
||||||
|
Index: xarray-2024.05.0/xarray/tests/test_dtypes.py
|
||||||
|
===================================================================
|
||||||
|
--- xarray-2024.05.0.orig/xarray/tests/test_dtypes.py
|
||||||
|
+++ xarray-2024.05.0/xarray/tests/test_dtypes.py
|
||||||
|
@@ -4,6 +4,18 @@ import numpy as np
|
||||||
|
import pytest
|
||||||
|
|
||||||
|
from xarray.core import dtypes
|
||||||
|
+from xarray.tests import requires_array_api_strict
|
||||||
|
+
|
||||||
|
+try:
|
||||||
|
+ import array_api_strict
|
||||||
|
+except ImportError:
|
||||||
|
+
|
||||||
|
+ class DummyArrayAPINamespace:
|
||||||
|
+ bool = None
|
||||||
|
+ int32 = None
|
||||||
|
+ float64 = None
|
||||||
|
+
|
||||||
|
+ array_api_strict = DummyArrayAPINamespace
|
||||||
|
|
||||||
|
|
||||||
|
@pytest.mark.parametrize(
|
||||||
|
@@ -58,7 +70,6 @@ def test_inf(obj) -> None:
|
||||||
|
@pytest.mark.parametrize(
|
||||||
|
"kind, expected",
|
||||||
|
[
|
||||||
|
- ("a", (np.dtype("O"), "nan")), # dtype('S')
|
||||||
|
("b", (np.float32, "nan")), # dtype('int8')
|
||||||
|
("B", (np.float32, "nan")), # dtype('uint8')
|
||||||
|
("c", (np.dtype("O"), "nan")), # dtype('S1')
|
||||||
|
@@ -98,3 +109,54 @@ def test_nat_types_membership() -> None:
|
||||||
|
assert np.datetime64("NaT").dtype in dtypes.NAT_TYPES
|
||||||
|
assert np.timedelta64("NaT").dtype in dtypes.NAT_TYPES
|
||||||
|
assert np.float64 not in dtypes.NAT_TYPES
|
||||||
|
+
|
||||||
|
+
|
||||||
|
+@pytest.mark.parametrize(
|
||||||
|
+ ["dtype", "kinds", "xp", "expected"],
|
||||||
|
+ (
|
||||||
|
+ (np.dtype("int32"), "integral", np, True),
|
||||||
|
+ (np.dtype("float16"), "real floating", np, True),
|
||||||
|
+ (np.dtype("complex128"), "complex floating", np, True),
|
||||||
|
+ (np.dtype("U"), "numeric", np, False),
|
||||||
|
+ pytest.param(
|
||||||
|
+ array_api_strict.int32,
|
||||||
|
+ "integral",
|
||||||
|
+ array_api_strict,
|
||||||
|
+ True,
|
||||||
|
+ marks=requires_array_api_strict,
|
||||||
|
+ id="array_api-int",
|
||||||
|
+ ),
|
||||||
|
+ pytest.param(
|
||||||
|
+ array_api_strict.float64,
|
||||||
|
+ "real floating",
|
||||||
|
+ array_api_strict,
|
||||||
|
+ True,
|
||||||
|
+ marks=requires_array_api_strict,
|
||||||
|
+ id="array_api-float",
|
||||||
|
+ ),
|
||||||
|
+ pytest.param(
|
||||||
|
+ array_api_strict.bool,
|
||||||
|
+ "numeric",
|
||||||
|
+ array_api_strict,
|
||||||
|
+ False,
|
||||||
|
+ marks=requires_array_api_strict,
|
||||||
|
+ id="array_api-bool",
|
||||||
|
+ ),
|
||||||
|
+ ),
|
||||||
|
+)
|
||||||
|
+def test_isdtype(dtype, kinds, xp, expected) -> None:
|
||||||
|
+ actual = dtypes.isdtype(dtype, kinds, xp=xp)
|
||||||
|
+ assert actual == expected
|
||||||
|
+
|
||||||
|
+
|
||||||
|
+@pytest.mark.parametrize(
|
||||||
|
+ ["dtype", "kinds", "xp", "error", "pattern"],
|
||||||
|
+ (
|
||||||
|
+ (np.dtype("int32"), "foo", np, (TypeError, ValueError), "kind"),
|
||||||
|
+ (np.dtype("int32"), np.signedinteger, np, TypeError, "kind"),
|
||||||
|
+ (np.dtype("float16"), 1, np, TypeError, "kind"),
|
||||||
|
+ ),
|
||||||
|
+)
|
||||||
|
+def test_isdtype_error(dtype, kinds, xp, error, pattern):
|
||||||
|
+ with pytest.raises(error, match=pattern):
|
||||||
|
+ dtypes.isdtype(dtype, kinds, xp=xp)
|
||||||
|
Index: xarray-2024.05.0/xarray/core/npcompat.py
|
||||||
|
===================================================================
|
||||||
|
--- xarray-2024.05.0.orig/xarray/core/npcompat.py
|
||||||
|
+++ xarray-2024.05.0/xarray/core/npcompat.py
|
||||||
|
@@ -28,3 +28,33 @@
|
||||||
|
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
|
||||||
|
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
||||||
|
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||||
|
+
|
||||||
|
+try:
|
||||||
|
+ # requires numpy>=2.0
|
||||||
|
+ from numpy import isdtype # type: ignore[attr-defined,unused-ignore]
|
||||||
|
+except ImportError:
|
||||||
|
+ import numpy as np
|
||||||
|
+
|
||||||
|
+ dtype_kinds = {
|
||||||
|
+ "bool": np.bool_,
|
||||||
|
+ "signed integer": np.signedinteger,
|
||||||
|
+ "unsigned integer": np.unsignedinteger,
|
||||||
|
+ "integral": np.integer,
|
||||||
|
+ "real floating": np.floating,
|
||||||
|
+ "complex floating": np.complexfloating,
|
||||||
|
+ "numeric": np.number,
|
||||||
|
+ }
|
||||||
|
+
|
||||||
|
+ def isdtype(dtype, kind):
|
||||||
|
+ kinds = kind if isinstance(kind, tuple) else (kind,)
|
||||||
|
+
|
||||||
|
+ unknown_dtypes = [kind for kind in kinds if kind not in dtype_kinds]
|
||||||
|
+ if unknown_dtypes:
|
||||||
|
+ raise ValueError(f"unknown dtype kinds: {unknown_dtypes}")
|
||||||
|
+
|
||||||
|
+ # verified the dtypes already, no need to check again
|
||||||
|
+ translated_kinds = [dtype_kinds[kind] for kind in kinds]
|
||||||
|
+ if isinstance(dtype, np.generic):
|
||||||
|
+ return any(isinstance(dtype, kind) for kind in translated_kinds)
|
||||||
|
+ else:
|
||||||
|
+ return any(np.issubdtype(dtype, kind) for kind in translated_kinds)
|
||||||
@ -1,130 +0,0 @@
|
|||||||
From 84d23be58bb39be4eb896f5f0dbe0a8f956431fb Mon Sep 17 00:00:00 2001
|
|
||||||
From: Matt Savoie <matthew.savoie@colorado.edu>
|
|
||||||
Date: Wed, 17 Apr 2024 09:57:53 -0600
|
|
||||||
Subject: [PATCH 1/4] DAS-2108: stop pruning datatree_ directory
|
|
||||||
|
|
||||||
Quick fixup of some typing.
|
|
||||||
Removes mypy exclusions for datatree_
|
|
||||||
---
|
|
||||||
MANIFEST.in | 1 -
|
|
||||||
pyproject.toml | 10 +---------
|
|
||||||
xarray/datatree_/datatree/io.py | 10 +++++-----
|
|
||||||
xarray/datatree_/datatree/tests/test_extensions.py | 11 +++++------
|
|
||||||
xarray/datatree_/docs/source/conf.py | 6 +++---
|
|
||||||
5 files changed, 14 insertions(+), 24 deletions(-)
|
|
||||||
delete mode 100644 MANIFEST.in
|
|
||||||
|
|
||||||
Index: xarray-2024.03.0/MANIFEST.in
|
|
||||||
===================================================================
|
|
||||||
--- xarray-2024.03.0.orig/MANIFEST.in
|
|
||||||
+++ xarray-2024.03.0/MANIFEST.in
|
|
||||||
@@ -1 +1,2 @@
|
|
||||||
prune xarray/datatree_*
|
|
||||||
+recursive-include xarray/datatree_/datatree *.py
|
|
||||||
Index: xarray-2024.03.0/pyproject.toml
|
|
||||||
===================================================================
|
|
||||||
--- xarray-2024.03.0.orig/pyproject.toml
|
|
||||||
+++ xarray-2024.03.0/pyproject.toml
|
|
||||||
@@ -96,11 +96,6 @@ warn_redundant_casts = true
|
|
||||||
warn_unused_configs = true
|
|
||||||
warn_unused_ignores = true
|
|
||||||
|
|
||||||
-# Ignore mypy errors for modules imported from datatree_.
|
|
||||||
-[[tool.mypy.overrides]]
|
|
||||||
-module = "xarray.datatree_.*"
|
|
||||||
-ignore_errors = true
|
|
||||||
-
|
|
||||||
# Much of the numerical computing stack doesn't have type annotations yet.
|
|
||||||
[[tool.mypy.overrides]]
|
|
||||||
ignore_missing_imports = true
|
|
||||||
Index: xarray-2024.03.0/xarray/datatree_/datatree/io.py
|
|
||||||
===================================================================
|
|
||||||
--- xarray-2024.03.0.orig/xarray/datatree_/datatree/io.py
|
|
||||||
+++ xarray-2024.03.0/xarray/datatree_/datatree/io.py
|
|
||||||
@@ -3,14 +3,14 @@ from xarray.core.datatree import DataTre
|
|
||||||
|
|
||||||
def _get_nc_dataset_class(engine):
|
|
||||||
if engine == "netcdf4":
|
|
||||||
- from netCDF4 import Dataset # type: ignore
|
|
||||||
+ from netCDF4 import Dataset
|
|
||||||
elif engine == "h5netcdf":
|
|
||||||
- from h5netcdf.legacyapi import Dataset # type: ignore
|
|
||||||
+ from h5netcdf.legacyapi import Dataset
|
|
||||||
elif engine is None:
|
|
||||||
try:
|
|
||||||
from netCDF4 import Dataset
|
|
||||||
except ImportError:
|
|
||||||
- from h5netcdf.legacyapi import Dataset # type: ignore
|
|
||||||
+ from h5netcdf.legacyapi import Dataset
|
|
||||||
else:
|
|
||||||
raise ValueError(f"unsupported engine: {engine}")
|
|
||||||
return Dataset
|
|
||||||
@@ -78,7 +78,7 @@ def _datatree_to_netcdf(
|
|
||||||
|
|
||||||
|
|
||||||
def _create_empty_zarr_group(store, group, mode):
|
|
||||||
- import zarr # type: ignore
|
|
||||||
+ import zarr
|
|
||||||
|
|
||||||
root = zarr.open_group(store, mode=mode)
|
|
||||||
root.create_group(group, overwrite=True)
|
|
||||||
@@ -92,7 +92,7 @@ def _datatree_to_zarr(
|
|
||||||
consolidated: bool = True,
|
|
||||||
**kwargs,
|
|
||||||
):
|
|
||||||
- from zarr.convenience import consolidate_metadata # type: ignore
|
|
||||||
+ from zarr.convenience import consolidate_metadata
|
|
||||||
|
|
||||||
if kwargs.get("group", None) is not None:
|
|
||||||
raise NotImplementedError(
|
|
||||||
Index: xarray-2024.03.0/xarray/datatree_/datatree/tests/test_extensions.py
|
|
||||||
===================================================================
|
|
||||||
--- xarray-2024.03.0.orig/xarray/datatree_/datatree/tests/test_extensions.py
|
|
||||||
+++ xarray-2024.03.0/xarray/datatree_/datatree/tests/test_extensions.py
|
|
||||||
@@ -18,16 +18,15 @@ class TestAccessor:
|
|
||||||
return "bar"
|
|
||||||
|
|
||||||
dt: DataTree = DataTree()
|
|
||||||
- assert dt.demo.foo == "bar" # type: ignore
|
|
||||||
+ assert dt.demo.foo == "bar"
|
|
||||||
|
|
||||||
# accessor is cached
|
|
||||||
- assert dt.demo is dt.demo # type: ignore
|
|
||||||
+ assert dt.demo is dt.demo
|
|
||||||
|
|
||||||
# check descriptor
|
|
||||||
- assert dt.demo.__doc__ == "Demo accessor." # type: ignore
|
|
||||||
- # TODO: typing doesn't seem to work with accessors
|
|
||||||
- assert DataTree.demo.__doc__ == "Demo accessor." # type: ignore
|
|
||||||
- assert isinstance(dt.demo, DemoAccessor) # type: ignore
|
|
||||||
+ assert dt.demo.__doc__ == "Demo accessor."
|
|
||||||
+ assert DataTree.demo.__doc__ == "Demo accessor." # type: ignore
|
|
||||||
+ assert isinstance(dt.demo, DemoAccessor)
|
|
||||||
assert DataTree.demo is DemoAccessor # type: ignore
|
|
||||||
|
|
||||||
with pytest.warns(Warning, match="overriding a preexisting attribute"):
|
|
||||||
Index: xarray-2024.03.0/xarray/datatree_/docs/source/conf.py
|
|
||||||
===================================================================
|
|
||||||
--- xarray-2024.03.0.orig/xarray/datatree_/docs/source/conf.py
|
|
||||||
+++ xarray-2024.03.0/xarray/datatree_/docs/source/conf.py
|
|
||||||
@@ -17,9 +17,9 @@ import inspect
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
|
|
||||||
-import sphinx_autosummary_accessors
|
|
||||||
+import sphinx_autosummary_accessors # type: ignore
|
|
||||||
|
|
||||||
-import datatree
|
|
||||||
+import datatree # type: ignore
|
|
||||||
|
|
||||||
# If extensions (or modules to document with autodoc) are in another directory,
|
|
||||||
# add these directories to sys.path here. If the directory is relative to the
|
|
||||||
@@ -286,7 +286,7 @@ htmlhelp_basename = "datatree_doc"
|
|
||||||
|
|
||||||
# -- Options for LaTeX output --------------------------------------------------
|
|
||||||
|
|
||||||
-latex_elements = {
|
|
||||||
+latex_elements: dict = {
|
|
||||||
# The paper size ('letterpaper' or 'a4paper').
|
|
||||||
# 'papersize': 'letterpaper',
|
|
||||||
# The font size ('10pt', '11pt' or '12pt').
|
|
||||||
73
xarray-pr9305-cftime.patch
Normal file
73
xarray-pr9305-cftime.patch
Normal file
@ -0,0 +1,73 @@
|
|||||||
|
From cc4daebf1a4a41483c6b60fc57d82d8bc30911e5 Mon Sep 17 00:00:00 2001
|
||||||
|
From: Mark Harfouche <mark.harfouche@gmail.com>
|
||||||
|
Date: Sat, 18 May 2024 12:54:03 -0400
|
||||||
|
Subject: [PATCH] Use ME in test_plot instead of M
|
||||||
|
|
||||||
|
```
|
||||||
|
pytest xarray/tests/test_plot.py::TestNcAxisNotInstalled::test_ncaxis_notinstalled_line_plot
|
||||||
|
```
|
||||||
|
|
||||||
|
would return the following error
|
||||||
|
|
||||||
|
```
|
||||||
|
xarray/tests/test_plot.py E [100%]
|
||||||
|
|
||||||
|
======================================= ERRORS =======================================
|
||||||
|
____ ERROR at setup of TestNcAxisNotInstalled.test_ncaxis_notinstalled_line_plot _____
|
||||||
|
|
||||||
|
self = <xarray.tests.test_plot.TestNcAxisNotInstalled object at 0x78ed1992aa10>
|
||||||
|
|
||||||
|
@pytest.fixture(autouse=True)
|
||||||
|
def setUp(self) -> None:
|
||||||
|
"""
|
||||||
|
Create a DataArray with a time-axis that contains cftime.datetime
|
||||||
|
objects.
|
||||||
|
"""
|
||||||
|
month = np.arange(1, 13, 1)
|
||||||
|
data = np.sin(2 * np.pi * month / 12.0)
|
||||||
|
darray = DataArray(data, dims=["time"])
|
||||||
|
> darray.coords["time"] = xr.cftime_range(
|
||||||
|
start="2017", periods=12, freq="1M", calendar="noleap"
|
||||||
|
)
|
||||||
|
|
||||||
|
/home/mark/git/xarray/xarray/tests/test_plot.py:3004:
|
||||||
|
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
|
||||||
|
/home/mark/git/xarray/xarray/coding/cftime_offsets.py:1129: in cftime_range
|
||||||
|
offset = to_offset(freq)
|
||||||
|
/home/mark/git/xarray/xarray/coding/cftime_offsets.py:767: in to_offset
|
||||||
|
_emit_freq_deprecation_warning(freq)
|
||||||
|
/home/mark/git/xarray/xarray/coding/cftime_offsets.py:751: in _emit_freq_deprecation_warning
|
||||||
|
emit_user_level_warning(message, FutureWarning)
|
||||||
|
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
|
||||||
|
|
||||||
|
message = "'M' is deprecated and will be removed in a future version. Please use 'ME' instead of 'M'."
|
||||||
|
category = <class 'FutureWarning'>
|
||||||
|
|
||||||
|
def emit_user_level_warning(message, category=None) -> None:
|
||||||
|
"""Emit a warning at the user level by inspecting the stack trace."""
|
||||||
|
stacklevel = find_stack_level()
|
||||||
|
> return warnings.warn(message, category=category, stacklevel=stacklevel)
|
||||||
|
E FutureWarning: 'M' is deprecated and will be removed in a future version. Please use 'ME' instead of 'M'.
|
||||||
|
|
||||||
|
/home/mark/git/xarray/xarray/core/utils.py:1112: FutureWarning
|
||||||
|
============================== short test summary info ===============================
|
||||||
|
ERROR xarray/tests/test_plot.py::TestNcAxisNotInstalled::test_ncaxis_notinstalled_line_plot - FutureWarning: 'M' is deprecated and will be removed in a future version. Please ...
|
||||||
|
================================== 1 error in 0.64s ==================================
|
||||||
|
```
|
||||||
|
---
|
||||||
|
xarray/tests/test_plot.py | 2 +-
|
||||||
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
||||||
|
|
||||||
|
diff --git a/xarray/tests/test_plot.py b/xarray/tests/test_plot.py
|
||||||
|
index e636be5589f..27f4ded5646 100644
|
||||||
|
--- a/xarray/tests/test_plot.py
|
||||||
|
+++ b/xarray/tests/test_plot.py
|
||||||
|
@@ -3002,7 +3002,7 @@ def setUp(self) -> None:
|
||||||
|
data = np.sin(2 * np.pi * month / 12.0)
|
||||||
|
darray = DataArray(data, dims=["time"])
|
||||||
|
darray.coords["time"] = xr.cftime_range(
|
||||||
|
- start="2017", periods=12, freq="1M", calendar="noleap"
|
||||||
|
+ start="2017", periods=12, freq="1ME", calendar="noleap"
|
||||||
|
)
|
||||||
|
|
||||||
|
self.darray = darray
|
||||||
Loading…
x
Reference in New Issue
Block a user