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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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1617395129 | I_kwDOAMm_X85gZ325 | 7601 | groupby_bins groups not correctly applied with built-in methods | michaelaye 69774 | closed | 0 | 3 | 2023-03-09T14:44:15Z | 2023-03-29T16:28:30Z | 2023-03-29T16:28:30Z | NONE | What happened?SetupI want to calculate image statistics per chunk in one dimension. Let's assume a very small image for demonstration purposes:
To force the even chunking of the image I need to call it with these parameters:
IssueBut now, calculating the mean value of each group, I get different results when doing it by hand using the groups or doing it using the groups inherent method Indeed, I verified, that these results are what one gets, using the first version of applying the bins:
The same is true when I use the elliptical operator to receive the mean over the remaining dimensions (note, the 2nd cell here is using the ApplicationI believe that What did you expect to happen?That the inherent stats methods of the I also have verified that the same problem exists with Minimal Complete Verifiable Example```Python import xarray as xr import numpy as np a = xr.DataArray(np.arange(12).reshape(6,2), dims=('x', 'y')) x_bins = (0, 2, 4, 6) default_groups = a.groupby_bins('x', x_bins) my_groups = a.groupby_bins('x', x_bins, include_lowest=True, right=False) print("Weird grouping using default call:") for iv, g in default_groups: print("Interval:",iv) print(g.data) print() print("Evenly chunked using print("Calculating mean on my own using loop over groups:") for iv, g in my_groups: print(g.mean('x').data) print("Calculting same using my_groups.mean()") print("No dim given:") print(my_groups.mean().data.T) print("using mean('x'):") print(my_groups.mean('x').data.T) print("These results come from the default groups!:") for iv, g in default_groups: print(g.mean('x').data) print("STD has the same issue") ``` MVCE confirmation
Relevant log outputNo response Anything else we need to know?No response Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:20:04) [GCC 11.3.0]
python-bits: 64
OS: Linux
OS-release: 6.0.12-76060006-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: en_US.UTF-8
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.9.1
xarray: 2023.2.0
pandas: 1.5.3
numpy: 1.23.5
scipy: 1.10.1
netCDF4: 1.6.3
pydap: None
h5netcdf: None
h5py: 3.8.0
Nio: None
zarr: None
cftime: 1.6.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: 1.3.6
cfgrib: None
iris: None
bottleneck: 1.3.7
dask: 2023.3.0
distributed: 2023.3.0
matplotlib: 3.7.1
cartopy: 0.21.1
seaborn: 0.12.2
numbagg: None
fsspec: 2023.3.0
cupy: None
pint: None
sparse: None
flox: 0.6.8
numpy_groupies: 0.9.20
setuptools: 67.5.1
pip: 23.0.1
conda: installed
pytest: 7.1.3
mypy: None
IPython: 8.7.0
sphinx: None
|
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completed | xarray 13221727 | issue | ||||||
662505658 | MDU6SXNzdWU2NjI1MDU2NTg= | 4240 | jupyter repr caching deleted netcdf file | michaelaye 69774 | closed | 0 | 9 | 2020-07-21T02:50:04Z | 2022-10-18T16:40:41Z | 2022-10-18T16:40:41Z | NONE | What happened: Testing xarray data storage in a jupyter notebook with varying data sizes and storing to a netcdf, i noticed that open_dataset/array (both show this behaviour) continue to return data from the first testing run, ignoring the fact that each run deletes the previously created netcdf file.
This only happens once the This was hard to track down as it depends on the precise sequence in jupyter. What you expected to happen: when i use Minimal Complete Verifiable Example: ```python import xarray as xr from pathlib import Path import numpy as np def test_repr(nx): ds = xr.DataArray(np.random.rand(nx)) path = Path("saved_on_disk.nc") if path.exists(): path.unlink() ds.to_netcdf(path) return path ``` When executed in a cell with print for display, all is fine:
but as soon as one cell used the jupyter repr:
all future file reads, even after executing the test function again and even using Anything else we need to know?: Here's a notebook showing the issue: https://gist.github.com/05c2542ed33662cdcb6024815cc0c72c Environment: Output of <tt>xr.show_versions()</tt>INSTALLED VERSIONS ------------------ commit: None python: 3.7.6 | packaged by conda-forge | (default, Jun 1 2020, 18:57:50) [GCC 7.5.0] python-bits: 64 OS: Linux OS-release: 5.4.0-40-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: 0.16.0 pandas: 1.0.5 numpy: 1.19.0 scipy: 1.5.1 netCDF4: 1.5.3 pydap: None h5netcdf: None h5py: 2.10.0 Nio: None zarr: None cftime: 1.2.1 nc_time_axis: None PseudoNetCDF: None rasterio: 1.1.5 cfgrib: None iris: None bottleneck: None dask: 2.21.0 distributed: 2.21.0 matplotlib: 3.3.0 cartopy: 0.18.0 seaborn: 0.10.1 numbagg: None pint: None setuptools: 49.2.0.post20200712 pip: 20.1.1 conda: installed pytest: 6.0.0rc1 IPython: 7.16.1 sphinx: 3.1.2 |
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completed | xarray 13221727 | issue | ||||||
657792526 | MDExOlB1bGxSZXF1ZXN0NDQ5ODUxMTk4 | 4230 | provide set_option `collapse_html` to control HTML repr collapsed state | michaelaye 69774 | closed | 0 | 15 | 2020-07-16T02:29:07Z | 2021-05-13T17:02:55Z | 2021-05-13T17:02:54Z | NONE | 1 | pydata/xarray/pulls/4230 |
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xarray 13221727 | pull | |||||
657769716 | MDU6SXNzdWU2NTc3Njk3MTY= | 4229 | FR: Provide option for collapsing the HTML display in notebooks | michaelaye 69774 | closed | 0 | 1 | 2020-07-16T01:27:15Z | 2021-04-27T01:37:54Z | 2021-04-27T01:37:54Z | NONE | Issue descriptionThe overly long output of the text repr of xarray always bugged so I was very happy that the recently implemented html repr collapsed the data part, and equally sad to see that 0.16.0 reverted that, IMHO, correct design implementation back, presumably to align it with the text repr. Suggested solutionAs the opinions will vary on what a good repr should do, similar to existing xarray.set_options I would like to have an option that let's me control if the data part (and maybe other parts?) appear in a collapsed fashion for the html repr. Additional questions
Any guidance on * which files need to change * potential pitfalls would be welcome. I'm happy to work on this, as I seem to be the only one not liking the current implementation. |
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completed | xarray 13221727 | issue | ||||||
650231649 | MDU6SXNzdWU2NTAyMzE2NDk= | 4194 | AttributeError accessing data_array.variable | michaelaye 69774 | closed | 0 | 3 | 2020-07-02T22:16:58Z | 2020-07-02T22:34:01Z | 2020-07-02T22:29:48Z | NONE | What happened: accessing
What you expected to happen: According to https://xarray.pydata.org/en/stable/terminology.html all DataArrays should have "an underlying variable that can be accessed via Minimal Complete Verifiable Example: Using the example code from the docs:
Environment: Python 3.7 on Kubuntu 20.04 using Brave browser in Jupyterlab, up-to-date conda env. Output of <tt>xr.show_versions()</tt>INSTALLED VERSIONS ------------------ commit: None python: 3.7.6 | packaged by conda-forge | (default, Jun 1 2020, 18:57:50) [GCC 7.5.0] python-bits: 64 OS: Linux OS-release: 5.4.0-40-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: 0.15.1 pandas: 1.0.5 numpy: 1.18.5 scipy: 1.5.0 netCDF4: 1.5.3 pydap: None h5netcdf: None h5py: 2.10.0 Nio: None zarr: None cftime: 1.1.3 nc_time_axis: None PseudoNetCDF: None rasterio: 1.1.5 cfgrib: None iris: None bottleneck: None dask: 2.19.0 distributed: 2.19.0 matplotlib: 3.2.2 cartopy: 0.18.0 seaborn: 0.10.1 numbagg: None setuptools: 47.3.1.post20200616 pip: 20.1.1 conda: installed pytest: 5.4.3 IPython: 7.16.1 sphinx: 3.1.1 |
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completed | xarray 13221727 | issue |
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