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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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2024104632 | I_kwDOAMm_X854pWK4 | 8515 | Inconsistant behaviour of groupby_bins mean when using flox and numbagg | daanscheltens 21100296 | closed | 0 | 5 | 2023-12-04T15:17:51Z | 2023-12-05T08:21:44Z | 2023-12-04T18:57:30Z | NONE | What happened?When I group an xarray.DataArray in a single group and calculate the mean, then I expect the mean of this group to be the same as the mean of the input data. When I have flox and numbagg installed next to xarray, I get inconsistant behavoir. The behaviour is consistent again when setting the option "use_flox" to False. What did you expect to happen?I expected xarray to give the mean of the values in the group. I expected this mean to be the same with flox as without flox. More specifically, I expected it to be (almost) equal to the numpy.mean. Minimal Complete Verifiable Example```Python in a clean python.org environment:pip install xarray, numbagg, floximport numpy as np import xarray as xr def grouped_mean(number): # Generate a set of random values np.random.seed(0) values = np.random.rand(number) # Use numpy to calculated the expected mean expected = np.mean(values) # Create an xarray dataset with coordinates data = xr.DataArray(values, [("dim_0", np.arange(number, dtype=float))]) # Group the coordinates to that all values fall in a single bin grouped = data.groupby_bins("dim_0", [-1.0, number + 1.0])
for number in [127, 128, 255, 256, 1000]: grouped_mean(number) ``` MVCE confirmation
Relevant log output
Anything else we need to know?This behaviour is only there when installing numbagg and flox next to xarray. (pip install xarray flox numbagg) The above mentioned output is from a github action, using linux and windows latest with python 3.11 Environment
Run python -c "import xarray as xr;print(xr.show_versions())"
/opt/hostedtoolcache/Python/3.[11](https://github.com/daanscheltens/test_xarray/actions/runs/7088608658/job/19291471251#step:10:12).6/x64/lib/python3.11/site-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
warnings.warn("Setuptools is replacing distutils.")
INSTALLED VERSIONS
------------------
commit: None
python: 3.11.6 (main, Oct 3 2023, 04:42:57) [GCC 11.4.0]
python-bits: 64
OS: Linux
OS-release: 6.2.0-10[16](https://github.com/daanscheltens/test_xarray/actions/runs/7088608658/job/19291471251#step:10:17)-azure
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: C.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: None
libnetcdf: None
xarray: [20](https://github.com/daanscheltens/test_xarray/actions/runs/7088608658/job/19291471251#step:10:21)[23](https://github.com/daanscheltens/test_xarray/actions/runs/7088608658/job/19291471251#step:10:24).11.0
pandas: 2.1.3
numpy: 1.[26](https://github.com/daanscheltens/test_xarray/actions/runs/7088608658/job/19291471251#step:10:27).2
scipy: 1.11.4
netCDF4: None
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: None
cftime: None
nc_time_axis: None
iris: None
bottleneck: None
dask: None
distributed: None
matplotlib: None
cartopy: None
seaborn: None
numbagg: 0.6.4
fsspec: None
cupy: None
pint: None
sparse: None
flox: 0.8.5
numpy_groupies: 0.10.2
setuptools: 65.5.0
pip: 23.3.1
conda: None
pytest: None
mypy: None
IPython: None
sphinx: None
None
|
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completed | xarray 13221727 | issue | ||||||
1399324758 | I_kwDOAMm_X85TaABW | 7136 | import xarray causes fatal python crash on windows when h5netcdf and netcdf4 are installed | daanscheltens 21100296 | closed | 0 | 3 | 2022-10-06T10:38:59Z | 2023-01-30T14:41:52Z | 2023-01-30T14:41:52Z | NONE | What happened?On Windows with python (3.9 and 3.10) the command What did you expect to happen?I expected that xarray would import normally, without a fatal python error. Minimal Complete Verifiable Example```Python On windows:pip install xarray pip install h5netcdf pip install netcdf4 This results in a crashpython -c "import xarray" The crash does not occur when I first import h5netcdf and then import xarray, so the next line does not result in a crash:python -c "import h5netcdf;import xarray" The crash does not occur on linux.The crash does not occur when I have only h5netcdf or netcdf4 installed.``` MVCE confirmation
Relevant log output```Python command: python -c "import xarray" C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\h5py__init__.py:36: UserWarning: h5py is running against HDF5 1.12.1 when it was built against 1.12.2, this may cause problems _warn(("h5py is running against HDF5 {0} when it was built against {1}, " Warning! HDF5 library version mismatched error The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.12.2, library is 1.12.1 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information:
Compiling Options:
Linking Options:
Statically Linked Executables: OFF LDFLAGS: /machine:x64 H5_LDFLAGS: AM_LDFLAGS: Extra libraries: D:/bld/hdf5_split_1646412547396/_h_env/Library/lib/libcurl.lib;D:/bld/hdf5_split_1646412547396/_h_env/Library/lib/libssl.lib;D:/bld/hdf5_split_1646412547396/_h_env/Library/lib/libcrypto.lib Archiver: C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Tools/MSVC/14.16.27023/bin/HostX64/x64/lib.exe Ranlib: : Languages:
Features:
Parallel Filtered Dataset Writes: Large Parallel I/O: High-level library: ON Build HDF5 Tests: ON Build HDF5 Tools: ON Threadsafety: ON (recursive RW locks: ) Default API mapping: v112 With deprecated public symbols: ON I/O filters (external): DEFLATE MPE: Direct VFD: Mirror VFD: (Read-Only) S3 VFD: 1 (Read-Only) HDFS VFD: dmalloc: Packages w/ extra debug output: API Tracing: OFF Using memory checker: OFF Memory allocation sanity checks: OFF Function Stack Tracing: OFF Use file locking: best-effort Strict File Format Checks: OFF Optimization Instrumentation: Bye... Error: Process completed with exit code 1. ``` Anything else we need to know?This bug is reproduced by the github action runner: https://github.com/daanscheltens/test-netcdf4/actions/runs/3196339371/jobs/5218135577 This action is part of a dedicated empty repository that just contains this action workflow: https://github.com/daanscheltens/test-netcdf4/blob/main/.github/workflows/action.yml Environmentpython -c "import h5netcdf; import xarray as xr;xr.show_versions()"
INSTALLED VERSIONS
------------------
commit: None
python: 3.9.13 (tags/v3.9.13:6de2ca5, May 17 2022, 16:36:42) [MSC v.1929 64 bit (AMD64)]
python-bits: 64
OS: Windows
OS-release: 10
machine: AMD64
processor: Intel64 Family 6 Model 106 Stepping 6, GenuineIntel
byteorder: little
LC_ALL: None
LANG: None
LOCALE: ('English_United States', '1252')
libhdf5: 1.12.2
libnetcdf: None
xarray: 2022.9.0
pandas: 1.5.0
numpy: 1.23.3
scipy: None
netCDF4: None
pydap: None
h5netcdf: 1.0.2
h5py: 3.7.0
Nio: None
zarr: None
cftime: 1.6.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: None
distributed: None
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
fsspec: None
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 5[8](https://github.com/daanscheltens/test-netcdf4/actions/runs/3196339371/jobs/5218135408#step:15:9).1.0
pip: [22](https://github.com/daanscheltens/test-netcdf4/actions/runs/3196339371/jobs/5218135408#step:15:23).2.2
conda: None
pytest: None
IPython: None
sphinx: None
|
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completed | xarray 13221727 | issue |
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