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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
1827010471 I_kwDOAMm_X85s5fen 8029 ' ' at end of variable name causes to_netcdf() to crash 28raining 18679628 closed 0     6 2023-07-28T19:48:53Z 2023-08-14T16:15:40Z 2023-08-14T16:15:40Z NONE      

What happened?

If variable name ends in a ' ' (space) then to_netcdf crashes.

In my opinion - At least the error message could tell which variable name has the issue - If space at the end is not allowed, then could you rstrip everything - It works with scipy xarr.to_netcdf(newName, engine="scipy")

This is related to https://github.com/pydata/xarray/issues/7943

Our tool converts csv files to XARRAY. So these kind of errors need to self-heal, otherwise we have to feedback to the user and get them to change the csv file. Which would be frustrating for everyone

What did you expect to happen?

No response

Minimal Complete Verifiable Example

```Python with open('endSpace.csv','w') as f: f.write('''PASS ,temperature PASS, 10 FAIL, 20''')

import pandas as pd df = pd.read_csv('endSpace.csv') index = ['temperature'] df = df.set_index(index) xarr = df.to_xarray() xarr.to_netcdf("new.nc") ```

MVCE confirmation

  • [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • [X] Complete example — the example is self-contained, including all data and the text of any traceback.
  • [X] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • [X] New issue — a search of GitHub Issues suggests this is not a duplicate.

Relevant log output

Python Traceback (most recent call last): File "/Users/will/Documents/GitHub/czdashboard/old/coordNameBug.py", line 11, in <module> xarr.to_netcdf("new.nc") File "/opt/homebrew/lib/python3.11/site-packages/xarray/core/dataset.py", line 1911, in to_netcdf return to_netcdf( # type: ignore # mypy cannot resolve the overloads:( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/lib/python3.11/site-packages/xarray/backends/api.py", line 1217, in to_netcdf dump_to_store( File "/opt/homebrew/lib/python3.11/site-packages/xarray/backends/api.py", line 1264, in dump_to_store store.store(variables, attrs, check_encoding, writer, unlimited_dims=unlimited_dims) File "/opt/homebrew/lib/python3.11/site-packages/xarray/backends/common.py", line 271, in store self.set_variables( File "/opt/homebrew/lib/python3.11/site-packages/xarray/backends/common.py", line 309, in set_variables target, source = self.prepare_variable( ^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/lib/python3.11/site-packages/xarray/backends/netCDF4_.py", line 488, in prepare_variable nc4_var = self.ds.createVariable( ^^^^^^^^^^^^^^^^^^^^^^^ File "src/netCDF4/_netCDF4.pyx", line 2945, in netCDF4._netCDF4.Dataset.createVariable File "src/netCDF4/_netCDF4.pyx", line 4164, in netCDF4._netCDF4.Variable.__init__ File "src/netCDF4/_netCDF4.pyx", line 2014, in netCDF4._netCDF4._ensure_nc_success RuntimeError: NetCDF: Name contains illegal characters

Anything else we need to know?

No response

Environment

commit : 2e218d10984e9919f0296931d92ea851c6a6faf5 python : 3.11.2.final.0 python-bits : 64 OS : Darwin OS-release : 22.5.0 Version : Darwin Kernel Version 22.5.0: Thu Jun 8 22:21:34 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T8112 machine : arm64 processor : arm byteorder : little LC_ALL : None LANG : en_US.UTF-8 LOCALE : en_US.UTF-8 pandas : 1.5.3 numpy : 1.24.2 pytz : 2023.3 dateutil : 2.8.2 setuptools : 65.6.3 pip : 23.1.1 Cython : None pytest : None hypothesis : None sphinx : None blosc : None feather : None xlsxwriter : None lxml.etree : None html5lib : None pymysql : None psycopg2 : None jinja2 : 3.1.2 IPython : None pandas_datareader: None bs4 : None bottleneck : None brotli : None fastparquet : None fsspec : 2023.3.0 gcsfs : None matplotlib : None numba : None numexpr : None odfpy : None openpyxl : None pandas_gbq : None pyarrow : None pyreadstat : None pyxlsb : None s3fs : None scipy : 1.10.1 snappy : None sqlalchemy : None tables : None tabulate : None xarray : 2023.2.0 xlrd : None xlwt : None zstandard : None tzdata : None 
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   completed xarray 13221727 issue
1775325545 I_kwDOAMm_X85p0VFp 7943 '/' in variable name causes to_netcdf() to crash 28raining 18679628 closed 0     8 2023-06-26T18:17:18Z 2023-07-06T15:11:51Z 2023-07-06T15:11:51Z NONE      

What happened?

If variable name includes a '/' then to_netcdf crashes

What did you expect to happen?

No response

Minimal Complete Verifiable Example

```Python import pandas as pd df = pd.read_csv('slashCSV.csv') index = ['temperature'] df = df.set_index(index) xarr = df.to_xarray() xarr.to_netcdf("new.nc")

  • slashCSV.csv contents: PASS/FAIL,temperature PASS, 10 FAIL, 20 ```

MVCE confirmation

  • [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • [X] Complete example — the example is self-contained, including all data and the text of any traceback.
  • [X] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • [X] New issue — a search of GitHub Issues suggests this is not a duplicate.

Relevant log output

Python File "/opt/homebrew/lib/python3.11/site-packages/xarray/backends/netCDF4_.py", line 56, in __init__ array = self.get_array() ^^^^^^^^^^^^^^^^ File "/opt/homebrew/lib/python3.11/site-packages/xarray/backends/netCDF4_.py", line 83, in get_array variable = ds.variables[self.variable_name] ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ KeyError: 'PASS/FAIL'

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.11.2 (main, Mar 24 2023, 00:16:47) [Clang 14.0.0 (clang-1400.0.29.202)] python-bits: 64 OS: Darwin OS-release: 22.5.0 machine: arm64 processor: arm byteorder: little LC_ALL: None 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: 1.24.2 scipy: 1.10.1 netCDF4: 1.6.3 pydap: None h5netcdf: 1.1.0 h5py: 3.8.0 Nio: None zarr: 2.14.2 cftime: 1.6.2 nc_time_axis: None PseudoNetCDF: None rasterio: 1.3.6 cfgrib: 0.9.10.3 iris: None bottleneck: None dask: None distributed: None matplotlib: None cartopy: None seaborn: None numbagg: None fsspec: 2023.3.0 cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 65.6.3 pip: 23.1.1 conda: None pytest: None mypy: None IPython: None sphinx: None 
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   completed xarray 13221727 issue
1649994877 I_kwDOAMm_X85iWOx9 7705 Using xarray in Docker on a mac fails with "No such file or directory: 'gdal-config'" 28raining 18679628 closed 0     6 2023-03-31T20:35:22Z 2023-05-04T20:07:27Z 2023-04-03T15:52:04Z NONE      

What is your issue?

Hi,

This is my docker file "Dockerfile": FROM python:3.11.2-slim RUN /usr/local/bin/python -m pip install --upgrade pip RUN pip install xarray[io]

Which is built with this command: docker build -t "name:Dockerfile" .

My docker version is: Docker version 20.10.23, build 7155243

And I'm running macOS Ventura 13.3

Error message: ```

6 11.79 Downloading rasterio-1.3.6.tar.gz (408 kB)

6 11.83 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 408.5/408.5 kB 12.4 MB/s eta 0:00:00

6 11.86 Installing build dependencies: started

6 14.05 Installing build dependencies: finished with status 'done'

6 14.05 Getting requirements to build wheel: started

6 14.17 Getting requirements to build wheel: finished with status 'error'

6 14.17 error: subprocess-exited-with-error

6 14.17

6 14.17 × Getting requirements to build wheel did not run successfully.

6 14.17 │ exit code: 1

6 14.17 ╰─> [2 lines of output]

6 14.17 WARNING:root:Failed to get options via gdal-config: [Errno 2] No such file or directory: 'gdal-config'

6 14.17 ERROR: A GDAL API version must be specified. Provide a path to gdal-config using a GDAL_CONFIG environment variable or use a GDAL_VERSION environment variable.

6 14.17 [end of output]

```

 
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   completed xarray 13221727 issue

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