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- Xarray does not support full range of netcdf-python compression options · 6 ✖
id | html_url | issue_url | node_id | user | created_at | updated_at ▲ | author_association | body | reactions | performed_via_github_app | issue |
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1519536791 | https://github.com/pydata/xarray/issues/7388#issuecomment-1519536791 | https://api.github.com/repos/pydata/xarray/issues/7388 | IC_kwDOAMm_X85akkqX | markelg 6883049 | 2023-04-24T07:32:26Z | 2023-04-24T07:32:26Z | CONTRIBUTOR | Good question. Right now ci/requirements/environment.yml is resolving libnetcdf 4.9.1, so fixing 4.9.2 would not work. I am not sure why or how to change this, as few package versions are pinned. |
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Xarray does not support full range of netcdf-python compression options 1503046820 | |
1517820737 | https://github.com/pydata/xarray/issues/7388#issuecomment-1517820737 | https://api.github.com/repos/pydata/xarray/issues/7388 | IC_kwDOAMm_X85aeBtB | markelg 6883049 | 2023-04-21T13:15:03Z | 2023-04-21T13:15:03Z | CONTRIBUTOR | I think it is about these two issues only, so backporting the fixes it should work. |
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Xarray does not support full range of netcdf-python compression options 1503046820 | |
1511596653 | https://github.com/pydata/xarray/issues/7388#issuecomment-1511596653 | https://api.github.com/repos/pydata/xarray/issues/7388 | IC_kwDOAMm_X85aGSJt | markelg 6883049 | 2023-04-17T15:28:21Z | 2023-04-17T15:29:43Z | CONTRIBUTOR | Thanks. It looks like the errors are related to this bug https://github.com/Unidata/netcdf-c/issues/2674 The fix has been merged so I hope they include it in the next netcdf-c release. For the moment I prefer not to merge this as netcdf 4.9.2 and dask do not seem to play well together. |
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Xarray does not support full range of netcdf-python compression options 1503046820 | |
1503827455 | https://github.com/pydata/xarray/issues/7388#issuecomment-1503827455 | https://api.github.com/repos/pydata/xarray/issues/7388 | IC_kwDOAMm_X85ZopX_ | markelg 6883049 | 2023-04-11T17:38:51Z | 2023-04-11T17:38:51Z | CONTRIBUTOR | Hi. I updated the branch and created a fresh python environment with the idea of writing another, final test for this. However before doing it I run the test suite, and got some bad HDF5 errors in test_backends.py::test_open_mfdataset_manyfiles[netcdf4-20-True-None-5]
I am not sure what is going on. It seems that the currently resolved netcdf4-hdf5 versions do not like the default parameters we are supplying. My environment is ``` Name Version Build Channel_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge affine 2.4.0 pyhd8ed1ab_0 conda-forge aiobotocore 2.5.0 pyhd8ed1ab_0 conda-forge aiohttp 3.8.4 py310h1fa729e_0 conda-forge aioitertools 0.11.0 pyhd8ed1ab_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge antlr-python-runtime 4.7.2 py310hff52083_1003 conda-forge asciitree 0.3.3 py_2 conda-forge async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge attrs 22.2.0 pyh71513ae_0 conda-forge backports.zoneinfo 0.2.1 py310hff52083_7 conda-forge beautifulsoup4 4.12.2 pyha770c72_0 conda-forge blosc 1.21.3 hafa529b_0 conda-forge boost-cpp 1.78.0 h5adbc97_2 conda-forge boto3 1.26.76 pyhd8ed1ab_0 conda-forge botocore 1.29.76 pyhd8ed1ab_0 conda-forge bottleneck 1.3.7 py310h0a54255_0 conda-forge brotli 1.0.9 h166bdaf_8 conda-forge brotli-bin 1.0.9 h166bdaf_8 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 ha61ee94_1014 conda-forge cartopy 0.21.1 py310hcb7e713_0 conda-forge cdat_info 8.2.1 pyhd8ed1ab_2 conda-forge cdms2 3.1.5 py310hb9168da_16 conda-forge cdtime 3.1.4 py310h87e304a_8 conda-forge certifi 2022.12.7 pyhd8ed1ab_0 conda-forge cf-units 3.1.1 py310hde88566_2 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge cfgrib 0.9.10.3 pyhd8ed1ab_0 conda-forge cfgv 3.3.1 pyhd8ed1ab_0 conda-forge cfitsio 4.2.0 hd9d235c_0 conda-forge cftime 1.6.2 py310hde88566_1 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge click 8.1.3 unix_pyhd8ed1ab_2 conda-forge click-plugins 1.1.1 py_0 conda-forge cligj 0.7.2 pyhd8ed1ab_1 conda-forge cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge contourpy 1.0.7 py310hdf3cbec_0 conda-forge coverage 7.2.3 py310h1fa729e_0 conda-forge cryptography 40.0.1 py310h34c0648_0 conda-forge curl 7.88.1 hdc1c0ab_1 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cytoolz 0.12.0 py310h5764c6d_1 conda-forge dask-core 2023.3.2 pyhd8ed1ab_0 conda-forge distarray 2.12.2 pyh050c7b8_4 conda-forge distlib 0.3.6 pyhd8ed1ab_0 conda-forge distributed 2023.3.2.1 pyhd8ed1ab_0 conda-forge docopt 0.6.2 py_1 conda-forge eccodes 2.29.0 h54fcba4_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge esmf 8.4.1 nompi_he2e5181_0 conda-forge esmpy 8.4.1 pyhc1e730c_0 conda-forge exceptiongroup 1.1.1 pyhd8ed1ab_0 conda-forge execnet 1.9.0 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge fasteners 0.17.3 pyhd8ed1ab_0 conda-forge filelock 3.11.0 pyhd8ed1ab_0 conda-forge findlibs 0.0.2 pyhd8ed1ab_0 conda-forge flox 0.6.10 pyhd8ed1ab_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.39.3 py310h1fa729e_0 conda-forge freeglut 3.2.2 h9c3ff4c_1 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge freexl 1.0.6 h166bdaf_1 conda-forge frozenlist 1.3.3 py310h5764c6d_0 conda-forge fsspec 2023.4.0 pyh1a96a4e_0 conda-forge future 0.18.3 pyhd8ed1ab_0 conda-forge g2clib 1.6.3 hbecde78_1 conda-forge geos 3.11.1 h27087fc_0 conda-forge geotiff 1.7.1 h7a142b4_6 conda-forge gettext 0.21.1 h27087fc_0 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge h5netcdf 1.1.0 pyhd8ed1ab_1 conda-forge h5py 3.8.0 nompi_py310h0311031_100 conda-forge hdf4 4.2.15 h9772cbc_5 conda-forge hdf5 1.12.2 nompi_h4df4325_101 conda-forge heapdict 1.0.1 py_0 conda-forge hypothesis 6.71.0 pyha770c72_0 conda-forge icu 70.1 h27087fc_0 conda-forge identify 2.5.22 pyhd8ed1ab_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-metadata 6.3.0 pyha770c72_0 conda-forge importlib_metadata 6.3.0 hd8ed1ab_0 conda-forge importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge iris 3.4.1 pyhd8ed1ab_0 conda-forge jasper 2.0.33 h0ff4b12_1 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge jpeg 9e h0b41bf4_3 conda-forge json-c 0.16 hc379101_0 conda-forge jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge jupyter_core 5.3.0 py310hff52083_0 conda-forge kealib 1.5.0 ha7026e8_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py310hbf28c38_1 conda-forge krb5 1.20.1 h81ceb04_0 conda-forge lazy-object-proxy 1.9.0 py310h1fa729e_0 conda-forge lcms2 2.15 hfd0df8a_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_8 conda-forge libbrotlidec 1.0.9 h166bdaf_8 conda-forge libbrotlienc 1.0.9 h166bdaf_8 conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcdms 3.1.2 h9366c0b_120 conda-forge libcf 1.0.3 py310h71500c5_116 conda-forge libcurl 7.88.1 hdc1c0ab_1 conda-forge libdeflate 1.17 h0b41bf4_0 conda-forge libdrs 3.1.2 h01ed8d5_119 conda-forge libdrs_f 3.1.2 h059c5b8_115 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgdal 3.6.2 h6c674c2_9 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libglib 2.74.1 h606061b_1 conda-forge libglu 9.0.0 he1b5a44_1001 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libkml 1.3.0 h37653c0_1015 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libllvm11 11.1.0 he0ac6c6_5 conda-forge libnetcdf 4.9.1 nompi_h34a3ff0_101 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libpng 1.6.39 h753d276_0 conda-forge libpq 15.2 hb675445_0 conda-forge librttopo 1.1.0 ha49c73b_12 conda-forge libspatialite 5.0.1 h221c8f1_23 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 hf14f497_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libtiff 4.5.0 h6adf6a1_2 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.0 h0b41bf4_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.10.3 hca2bb57_4 conda-forge libxslt 1.1.37 h873f0b0_0 conda-forge libzip 1.9.2 hc929e4a_1 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge llvmlite 0.39.1 py310h58363a5_1 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge lxml 4.9.2 py310hbdc0903_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge markupsafe 2.1.2 py310h1fa729e_0 conda-forge matplotlib-base 3.7.1 py310he60537e_0 conda-forge msgpack-python 1.0.5 py310hdf3cbec_0 conda-forge multidict 6.0.4 py310h1fa729e_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge nbformat 5.8.0 pyhd8ed1ab_0 conda-forge nc-time-axis 1.4.1 pyhd8ed1ab_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge netcdf-fortran 4.6.0 nompi_heb5813c_103 conda-forge netcdf4 1.6.3 nompi_py310h0feb132_100 conda-forge nodeenv 1.7.0 pyhd8ed1ab_0 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.89 he45b914_0 conda-forge numba 0.56.4 py310h0e39c9b_1 conda-forge numbagg 0.2.2 pyhd8ed1ab_1 conda-forge numcodecs 0.11.0 py310heca2aa9_1 conda-forge numexpr 2.8.4 py310h690d005_100 conda-forge numpy 1.23.5 py310h53a5b5f_0 conda-forge numpy_groupies 0.9.20 pyhd8ed1ab_0 conda-forge openblas 0.3.21 pthreads_h320a7e8_3 conda-forge openjpeg 2.5.0 hfec8fc6_2 conda-forge openssl 3.1.0 h0b41bf4_0 conda-forge packaging 23.0 pyhd8ed1ab_0 conda-forge pandas 1.5.3 py310h9b08913_1 conda-forge partd 1.3.0 pyhd8ed1ab_0 conda-forge patsy 0.5.3 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge pillow 9.4.0 py310h023d228_1 conda-forge pint 0.20.1 pyhd8ed1ab_0 conda-forge pip 23.0.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge platformdirs 3.2.0 pyhd8ed1ab_0 conda-forge pluggy 1.0.0 pyhd8ed1ab_5 conda-forge pooch 1.7.0 pyha770c72_3 conda-forge poppler 23.03.0 h091648b_0 conda-forge poppler-data 0.4.12 hd8ed1ab_0 conda-forge postgresql 15.2 h3248436_0 conda-forge pre-commit 3.2.2 pyha770c72_0 conda-forge proj 9.1.1 h8ffa02c_2 conda-forge pseudonetcdf 3.2.2 pyhd8ed1ab_0 conda-forge psutil 5.9.4 py310h5764c6d_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pydap 3.4.0 pyhd8ed1ab_0 conda-forge pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyproj 3.5.0 py310h15e2413_0 conda-forge pyrsistent 0.19.3 py310h1fa729e_0 conda-forge pyshp 2.3.1 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.3.0 pyhd8ed1ab_0 conda-forge pytest-cov 4.0.0 pyhd8ed1ab_0 conda-forge pytest-env 0.8.1 pyhd8ed1ab_0 conda-forge pytest-xdist 3.2.1 pyhd8ed1ab_0 conda-forge python 3.10.10 he550d4f_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-eccodes 1.5.1 py310h0a54255_0 conda-forge python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge python-xxhash 3.2.0 py310h1fa729e_0 conda-forge python_abi 3.10 3_cp310 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py310h5764c6d_5 conda-forge rasterio 1.3.6 py310h3e853a9_0 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.28.2 pyhd8ed1ab_1 conda-forge s3transfer 0.6.0 pyhd8ed1ab_0 conda-forge scipy 1.10.1 py310h8deb116_0 conda-forge seaborn 0.12.2 hd8ed1ab_0 conda-forge seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge setuptools 67.6.1 pyhd8ed1ab_0 conda-forge shapely 2.0.1 py310h8b84c32_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge snuggs 1.4.7 py_0 conda-forge sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge sparse 0.14.0 pyhd8ed1ab_0 conda-forge sqlite 3.40.0 h4ff8645_0 conda-forge statsmodels 0.13.5 py310hde88566_2 conda-forge tblib 1.7.0 pyhd8ed1ab_0 conda-forge tiledb 2.13.2 hd532e3d_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tornado 6.2 py310h5764c6d_1 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.5.0 hd8ed1ab_0 conda-forge typing_extensions 4.5.0 pyha770c72_0 conda-forge tzcode 2023c h0b41bf4_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge udunits2 2.2.28 hc3e0081_0 conda-forge ukkonen 1.0.1 py310hbf28c38_3 conda-forge unicodedata2 15.0.0 py310h5764c6d_0 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge virtualenv 20.21.0 pyhd8ed1ab_0 conda-forge webob 1.8.7 pyhd8ed1ab_0 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge wrapt 1.15.0 py310h1fa729e_0 conda-forge xarray 2023.3.0 pyhd8ed1ab_0 conda-forge xerces-c 3.2.4 h55805fa_1 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xxhash 0.8.1 h0b41bf4_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yarl 1.8.2 py310h5764c6d_0 conda-forge zarr 2.14.2 pyhd8ed1ab_0 conda-forge zict 2.2.0 pyhd8ed1ab_0 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge ``` |
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Xarray does not support full range of netcdf-python compression options 1503046820 | |
1441513675 | https://github.com/pydata/xarray/issues/7388#issuecomment-1441513675 | https://api.github.com/repos/pydata/xarray/issues/7388 | IC_kwDOAMm_X85V68DL | markelg 6883049 | 2023-02-23T10:23:21Z | 2023-02-23T10:23:21Z | CONTRIBUTOR | With the PR the test above works, and also bzip2. I can't get it to apply blosc filters for some reason, it works but it does not really apply them. This is the full snippet I am using: ``` import xarray as xr import numpy as np shape = (10, 20) chunksizes = (1, 10) encoding = { 'compression': 'bzip2', 'shuffle': True, 'complevel': 8, 'fletcher32': False, 'contiguous': False, 'chunksizes': chunksizes } da = xr.DataArray( data=np.random.rand(*shape), dims=['y', 'x'], name="foo", attrs={"bar": "baz"} ) da.encoding = encoding ds = da.to_dataset() fname = "test.nc" ds.to_netcdf(fname, engine="netcdf4", mode="w") with xr.open_dataset(fname, engine="netcdf4") as ds1: print(ds1.foo.encoding) ``` Also, I was not able to make the conda environment in ci/environment.yml to resolve libnetcdf 4.9.1. I had to build an environment on my own. I also added the hdf5 filters
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Xarray does not support full range of netcdf-python compression options 1503046820 | |
1383643668 | https://github.com/pydata/xarray/issues/7388#issuecomment-1383643668 | https://api.github.com/repos/pydata/xarray/issues/7388 | IC_kwDOAMm_X85SeLoU | markelg 6883049 | 2023-01-16T08:15:41Z | 2023-01-16T08:15:41Z | CONTRIBUTOR | I'll have a look. Sorry about that, I guess we assumed that encoding was passed with "**kwargs". I did not try it with netcdf-c 4.9.x since is it not yet available in conda-forge and I did not find the time to compile it. |
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Xarray does not support full range of netcdf-python compression options 1503046820 |
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