Issue with DataFetcher

[tjryankeogh]

I've just installed argopy and working through the examples on the readthedocs website.

MCVE Code Sample

from argopy import DataFetcher

# Example 1 from readthedocs
ds = DataFetcher().region([-75, -45, 20, 30, 0, 10, '2011-01', '2011-06']).load().data

# Example 2 from readthedocs
f = DataFetcher()
f = f.float(6902746)
f.load().data

# Example 3 from GitHub home page
ArgoSet = DataFetcher().region([-85,-45,10.,20.,0,10.])
ds = ArgoSet.to_xarray()

Expected Output

According to the examples this should return an xarray dataset with all the variables available.

Problem Description

The following error messages are returned.

FutureWarning: The return type of Dataset.dims will be changed to return a set of dimension names in future, in order to be more consistent with DataArray.dims. To access a mapping from dimension names to lengths, please use Dataset.sizes.
self._dims = list(xarray_obj.dims.keys())

AttributeError: 'ScipyArrayWrapper' object has no attribute 'oindex'

I am then unable to proceed with any of the other examples of how to manipulate and work with the data.

Versions

SYSTEM

commit: None
python: 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:35:20) [Clang 16.0.6 ]
python-bits: 64
OS: Darwin
OS-release: 23.5.0
machine: arm64
processor: arm
byteorder: little
LC_ALL: None
LANG: None
LOCALE: None.UTF-8
libhdf5: 1.14.3
libnetcdf: 4.9.2

INSTALLED VERSIONS: CORE

aiohttp : 3.9.3
argopy : 0.1.15
erddapy : 2.2.0
fsspec : 2023.10.0
netCDF4 : 1.6.5
packaging : 24.0
requests : 2.31.0
scipy : 1.13.0
toolz : 0.12.1
xarray : 2024.3.0

INSTALLED VERSIONS: EXT.UTIL

gsw : 3.6.17
tqdm : 4.66.2
zarr : 2.18.2

INSTALLED VERSIONS: EXT.PERF

dask : 2024.4.1
distributed : 2024.4.1
h5netcdf : 1.3.0
pyarrow : 15.0.2

INSTALLED VERSIONS: EXT.PLOT

IPython : 8.22.2
cartopy : 0.23.0
ipykernel : 6.29.3
ipywidgets : 8.1.3
matplotlib : 3.8.4
pyproj : 3.6.1
seaborn : 0.13.2

INSTALLED VERSIONS: DEV

aiofiles : -
black : -
bottleneck : 1.3.8
cfgrib : -
cftime : 1.6.3
conda : -
flake8 : -
nc_time_axis: -
numpy : 1.26.4
pandas : 2.2.2
pip : 24.0
pytest : -
pytest_cov : -
pytest_env : -
pytest_localftpserver: -
setuptools : 69.5.1
sphinx : -

INSTALLED VERSIONS: PIP

pytest-reportlog: -

[gaelforget]

same issue, also on arm64

[gmaze]

Hi @tjryankeogh, @gaelforget
thanks for reporting this !

the issue is known and will be fix in the next release
in the mean time, a quick fix is to work with xarray < 2024.3

[gmaze]

hi @tjryankeogh
We just released a new argopy version (v0.1.16) that should fix this issue by pinning xarray to versions lower than 2024.3
The problem is coming from: pydata/xarray#8909
We shall release another version to unpinned xarray when this will be fixed

New argopy version 0.1.16 is available from pypi and in a matter of hours or days on conda as well.

[gaelforget]

hi @tjryankeogh We just released a new argopy version (v0.1.16) that should fix this issue by pinning xarray to versions lower than 2024.3 The problem is coming from: pydata/xarray#8909 We shall release another version to unpinned xarray when this will be fixed

New argopy version 0.1.16 is available from pypi and in a matter of hours or days on conda as well.

With 0.1.16 , I no longer get AttributeError: 'ScipyArrayWrapper' object has no attribute 'oindex'

but now I get another error :

ValueError: Unable to avoid copy while creating an array as requested.
If using `np.array(obj, copy=False)` replace it with `np.asarray(obj)` to allow a copy when needed (no behavior change in NumPy 1.x).
For more details, see https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.

[gmaze]

looks like you're on numpy > 2, is it ?
you should not
argopy works with all the environment definitions:
https://github.com/euroargodev/argopy/tree/master/ci/requirements

[gaelforget]

looks like you're on numpy > 2, is it ? you should not argopy works with all the environment definitions: https://github.com/euroargodev/argopy/tree/master/ci/requirements

Thanks @gmaze!

It seems that I am using scipy 1.14.1 though :

(myenv) (base) √ ArgoData.jl % pip list
Package            Version
------------------ -----------
aiohappyeyeballs   2.4.0
aiohttp            3.10.5
aiosignal          1.3.1
anyio              4.4.0
argopy             0.1.16
async-timeout      4.0.3
attrs              24.2.0
certifi            2024.7.4
cftime             1.6.4
charset-normalizer 3.3.2
decorator          5.1.1
erddapy            2.2.0
exceptiongroup     1.2.2
frozenlist         1.4.1
fsspec             2024.6.1
h11                0.14.0
httpcore           1.0.5
httpx              0.27.2
idna               3.8
multidict          6.0.5
netCDF4            1.7.1.post2
numpy              2.1.0
packaging          24.1
pandas             2.2.2
pip                24.2
python-dateutil    2.9.0.post0
pytz               2024.1
requests           2.32.3
scipy              1.14.1
setuptools         65.5.0
six                1.16.0
sniffio            1.3.1
toolz              0.12.1
typing_extensions  4.12.2
tzdata             2024.1
urllib3            2.2.2
xarray             2024.2.0
yarl               1.9.4

[gmaze]

but your numpy is 2.1.0
until xarray get along, can't move up to 2

[gaelforget]

but your numpy is 2.1.0 until xarray get along, can't move up to 2

Right!! Sorry for getting confused between scipy v numpy earlier. Works now after pip install "numpy<2".

Thanks again!

[gmaze]

@tjryankeogh did you manage to fix your install issue ?

[tjryankeogh]

@gmaze Yes I did thank you. I've managed to get it working by making xarray < 2024.3. Thank you

[gmaze]

awesome then !