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id | node_id | number | title | user | state | locked | assignee | milestone | comments | created_at | updated_at ▲ | closed_at | author_association | active_lock_reason | draft | pull_request | body | reactions | performed_via_github_app | state_reason | repo | type |
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2118308210 | I_kwDOAMm_X85-QtFy | 8707 | Weird interaction between aggregation and multiprocessing on DaskArrays | saschahofmann 24508496 | closed | 0 | 10 | 2024-02-05T11:35:28Z | 2024-04-29T16:20:45Z | 2024-04-29T16:20:44Z | CONTRIBUTOR | What happened?When I try to run a modified version of the example from the dropna documentation (see below), it creates a never terminating process. To reproduce it I added a rolling operation before dropping nans and then run 4 processes using the standard library multiprocessing What did you expect to happen?There is nothing obvious to me why this wouldn't just work unless there is a weird interaction between the Dask threads and the different processes. Using Xarray+Dask+Multiprocessing seems to work for me on other functions, it seems to be this particular combination that is problematic. Minimal Complete Verifiable Example```Python import xarray as xr import numpy as np from multiprocessing import Pool datasets = [xr.Dataset( { "temperature": ( ["time", "location"], [[23.4, 24.1], [np.nan if i>1 else 23.4, 22.1 if i<2 else np.nan], [21.8 if i<3 else np.nan, 24.2], [20.5, 25.3]], ) }, coords={"time": [1, 2, 3, 4], "location": ["A", "B"]}, ).chunk(time=2) for i in range(4)] def process(dataset): return dataset.rolling(dim={'time':2}).sum().dropna(dim="time", how="all").compute() This works as expecteddropped = [] for dataset in datasets: dropped.append(process(dataset)) This seems to never finishwith Pool(4) as p: dropped = p.map(process, datasets) ``` MVCE confirmation
Relevant log outputNo response Anything else we need to know?I am still running on 2023.08.0 see below for more details about the environment Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.11.6 (main, Jan 25 2024, 20:42:03) [GCC 7.5.0]
python-bits: 64
OS: Linux
OS-release: 5.4.0-124-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.9.3-development
xarray: 2023.8.0
pandas: 2.1.4
numpy: 1.26.3
scipy: 1.12.0
netCDF4: 1.6.5
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: 2.16.1
cftime: 1.6.3
nc_time_axis: 1.4.1
PseudoNetCDF: None
iris: None
bottleneck: 1.3.7
dask: 2024.1.1
distributed: 2024.1.1
matplotlib: 3.8.2
cartopy: 0.22.0
seaborn: None
numbagg: None
fsspec: 2023.12.2
cupy: None
pint: 0.23
sparse: None
flox: 0.9.0
numpy_groupies: 0.10.2
setuptools: 69.0.3
pip: 23.2.1
conda: None
pytest: 8.0.0
mypy: None
IPython: 8.18.1
sphinx: None
|
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completed | xarray 13221727 | issue | ||||||
2220487961 | PR_kwDOAMm_X85rb6ea | 8903 | Update docstring for compute and persist | saschahofmann 24508496 | closed | 0 | 2 | 2024-04-02T13:10:02Z | 2024-04-03T07:45:10Z | 2024-04-02T23:52:32Z | CONTRIBUTOR | 0 | pydata/xarray/pulls/8903 |
|
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xarray 13221727 | pull | |||||
2220228856 | I_kwDOAMm_X86EVgD4 | 8901 | Is .persist in place or like .compute? | saschahofmann 24508496 | closed | 0 | 3 | 2024-04-02T11:09:59Z | 2024-04-02T23:52:33Z | 2024-04-02T23:52:33Z | CONTRIBUTOR | What is your issue?I am playing around with using In either case, I would make a PR to clarify in the docs whether persists leaves the original data untouched or not. |
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completed | xarray 13221727 | issue | ||||||
2205239889 | PR_kwDOAMm_X85qoWZT | 8873 | Add dt.date to plottable types | saschahofmann 24508496 | closed | 0 | 6 | 2024-03-25T09:07:33Z | 2024-03-29T14:35:44Z | 2024-03-29T14:35:41Z | CONTRIBUTOR | 0 | pydata/xarray/pulls/8873 | Simply adds Matplotlib handles Do I need to add a test for this? Any pointers on where I would put it that?
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xarray 13221727 | pull | |||||
2202163545 | I_kwDOAMm_X86DQllZ | 8866 | Cannot plot datetime.date dimension | saschahofmann 24508496 | closed | 0 | 9 | 2024-03-22T10:18:04Z | 2024-03-29T14:35:42Z | 2024-03-29T14:35:42Z | CONTRIBUTOR | What happened?I noticed that xarray doesnt support plotting when the x-axis is a I am pretty sure that matplotlib supports date on the x-axis so maybe adding it to an acceptable type in plot/utils.py L675 in I am happy to look into this if this is a wanted feature. What did you expect to happen?No response Minimal Complete Verifiable Example```Python import xarray as xr import numpy as np import datetime start = datetime.datetime(2024, 1,1) time = [start + datetime.timedelta(hours=x) for x in range(720)] data = xr.DataArray(np.random.randn(len(time)), coords=dict(time=('time', time))) data.groupby('time.date').mean().plot() ``` MVCE confirmation
Relevant log output
Anything else we need to know?No response Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.10.13 (main, Aug 24 2023, 12:59:26) [Clang 15.0.0 (clang-1500.1.0.2.5)]
python-bits: 64
OS: Darwin
OS-release: 22.1.0
machine: arm64
processor: arm
byteorder: little
LC_ALL: None
LANG: None
LOCALE: (None, 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.9.3-development
xarray: 2023.12.0
pandas: 2.1.4
numpy: 1.26.3
scipy: 1.12.0
netCDF4: 1.6.5
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: 2.16.1
cftime: 1.6.3
nc_time_axis: 1.4.1
iris: None
bottleneck: 1.3.7
dask: 2024.1.1
distributed: None
matplotlib: 3.8.2
cartopy: None
seaborn: None
numbagg: None
fsspec: 2023.12.2
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 69.1.0
pip: 24.0
conda: None
pytest: None
mypy: None
IPython: 8.21.0
sphinx: None
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completed | xarray 13221727 | issue | ||||||
1607155972 | I_kwDOAMm_X85fy0EE | 7576 | Rezarring an opened dataset with object dtype fails due to added filter | saschahofmann 24508496 | closed | 0 | 2 | 2023-03-02T16:50:56Z | 2023-03-20T15:41:32Z | 2023-03-20T15:41:31Z | CONTRIBUTOR | What happened?I am trying to save an
I can also safely save to netcdf (which makes sense since this encoding is probably ignored then). What did you expect to happen?I should be able to open and resave a file to zarr. Minimal Complete Verifiable Example```Python import xarray as xr import numpy as np da= xr.DataArray(np.array(['126469-423', '130042-0-10046', '120259-10343'], dtype='object'), dims=['asset'], name='asset') da.to_dataset().to_zarr('~/Downloads/test.zarr', mode='w') Fails with the error belowopened = xr.open_zarr('~/Downloads/test.zarr') opened.to_zarr('~/Downloads/test2.zarr', mode='w') Saves successfullyopened.asset.encoding.pop('filters') opened.to_zarr('~Downloads/test2.zarr', mode='w') ``` MVCE confirmation
Relevant log output```Python TypeError Traceback (most recent call last) <ipython-input-16-b1f2f1d2b5a0> in <module> 6 opened = xr.open_zarr('~/Downloads/test.zarr') 7 ----> 8 opened.to_zarr('~/Downloads/test2.zarr', mode='w') ~/micromamba/envs/xr/lib/python3.8/site-packages/xarray/core/dataset.py in to_zarr(self, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options, zarr_version) 2097 from xarray.backends.api import to_zarr 2098 -> 2099 return to_zarr( # type: ignore 2100 self, 2101 store=store, ~/micromamba/envs/xr/lib/python3.8/site-packages/xarray/backends/api.py in to_zarr(dataset, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options, zarr_version) 1668 writer = ArrayWriter() 1669 # TODO: figure out how to properly handle unlimited_dims -> 1670 dump_to_store(dataset, zstore, writer, encoding=encoding) 1671 writes = writer.sync(compute=compute) 1672 ~/micromamba/envs/xr/lib/python3.8/site-packages/xarray/backends/api.py in dump_to_store(dataset, store, writer, encoder, encoding, unlimited_dims) 1277 variables, attrs = encoder(variables, attrs) 1278 -> 1279 store.store(variables, attrs, check_encoding, writer, unlimited_dims=unlimited_dims) ... 2112 # check object encoding numcodecs/vlen.pyx in numcodecs.vlen.VLenUTF8.encode() TypeError: expected unicode string, found 3 ``` Anything else we need to know?No response Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.8.5 (default, Sep 4 2020, 07:30:14)
[GCC 7.3.0]
python-bits: 64
OS: Linux
OS-release: 5.4.0-124-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.10.6
libnetcdf: 4.7.4
xarray: 2023.1.0
pandas: 1.5.3
numpy: 1.22.4
scipy: 1.4.1
netCDF4: 1.5.4
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: 2.11.0
cftime: 1.4.1
nc_time_axis: 1.2.0
PseudoNetCDF: None
rasterio: None
cfgrib: 0.9.8.5
iris: None
bottleneck: 1.3.2
dask: 2022.01.1
distributed: 2022.01.1
matplotlib: 3.3.2
cartopy: 0.18.0
seaborn: None
numbagg: None
fsspec: 0.8.4
cupy: None
pint: 0.16.1
sparse: None
flox: None
numpy_groupies: None
setuptools: 50.3.0.post20201006
pip: 20.2.3
conda: None
pytest: 7.0.1
mypy: None
IPython: 7.18.1
sphinx: None
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completed | xarray 13221727 | issue |
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