Instructions to create a development environment for M1/M2/osx-arm64

[kafitzgerald]

What is your issue?

The current instructions to create a development environment for MacOS don't work for an M1/M2 Mac.

The conda environment solve fails on cdsm2 presumably because it's not available for osx-arm64.

I tried looking for related discussion and/or issues with recommendations, but didn't see any.

[kafitzgerald]

After removing cdsm2 from the environment yml file, installing, and running the test suite I'm seeing a bunch of failures related to pandas imports:
ImportError: Pandas requires version '2022.03.0' or newer of 'xarray' (version '0.1.dev4835+g31c6e62.d20231106' currently installed)

Happy to add more detail here and/or log a separate issue if that would be helpful.

[jhamman]

@kafitzgerald - thanks for filing this issue. We should update the contributing docs here to make this an easier process.

For your second problem, can you share what xr.show_versions() returns? It seems like the test suite is picking up an old version of xarray?

[kafitzgerald]

No problem (see below). I think it's just the editable install it's seeing?

versions

>>> xr.show_versions() /Users/katelynw/miniconda3/envs/xarray-tests/lib/python3.10/site-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils. warnings.warn("Setuptools is replacing distutils.")

INSTALLED VERSIONS

commit: None
python: 3.10.13 | packaged by conda-forge | (main, Oct 26 2023, 18:09:17) [Clang 16.0.6 ]
python-bits: 64
OS: Darwin
OS-release: 21.6.0
machine: arm64
processor: arm
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.14.2
libnetcdf: 4.9.2

xarray: 0.1.dev4835+g31c6e62.d20231106
pandas: 2.1.2
numpy: 1.24.4
scipy: 1.11.3
netCDF4: 1.6.5
pydap: installed
h5netcdf: 1.2.0
h5py: 3.10.0
Nio: None
zarr: 2.16.1
cftime: 1.6.3
nc_time_axis: 1.4.1
PseudoNetCDF: 3.2.2
iris: 3.7.0
bottleneck: 1.3.7
dask: 2023.10.1
distributed: 2023.10.1
matplotlib: 3.8.1
cartopy: 0.22.0
seaborn: 0.13.0
numbagg: 0.6.0
fsspec: 2023.10.0
cupy: None
pint: 0.20.1
sparse: 0.14.0
flox: 0.8.1
numpy_groupies: 0.10.2
setuptools: 68.2.2
pip: 23.3.1
conda: None
pytest: 7.4.3
mypy: None
IPython: None
sphinx: None

[max-sixty]

That is surprising — we try and fallback to a much higher version if setuptools_scm resolve the version...

I don't have the g31c6e62 commit on my end locally — could we try switching to the main branch?

Not to get too deep into git, but are the tags updated?

[kafitzgerald]

🤦🏻‍♀️ I hadn't fetched the tags. My bad (nothing wrong with the contrib docs here). All is looking good now on that front.

Interestingly I did see what looks to be a duplicate of #7879 consistently when not using the optional -n argument.

log for the segfault on test_open_mfdataset_manyfiles

pytest xarray     
========================================================= test session starts =========================================================
platform darwin -- Python 3.10.13, pytest-7.4.3, pluggy-1.3.0
rootdir: /Users/katelynw/xarray
configfile: pyproject.toml
plugins: timeout-2.2.0, cov-4.1.0, hypothesis-6.88.3, xdist-3.3.1, env-1.1.1
collected 17513 items / 1 skipped                                                                                                     

xarray/tests/test_accessor_dt.py .............................................................................................. [  0%]
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xarray/tests/test_accessor_str.py ............................................................................................. [  2%]
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xarray/tests/test_array_api.py ...........                                                                                      [  2%]
xarray/tests/test_backends.py ..................................x................................................s............. [  3%]
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x...................................................................................................................sssssssssss [  6%]
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sssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [  7%]
sssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [  8%]
sssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [  9%]
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.......................s.XXXXXXXXXXXXXXXXXXXXXXXXFatal Python error: Segmentation fault

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  File "/Users/katelynw/xarray/xarray/backends/store.py", line 43 in open_dataset
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zsh: segmentation fault  pytest xarray

[max-sixty]

🤦🏻‍♀️ I hadn't fetched the tags. My bad (nothing wrong with the contrib docs here). All is looking good now on that front.

No stress!

Out of interest, was this an old clone? Or did a new clone hit this issue? We should fix on our end if a new clone could have this issue...

Interestingly I did see what looks to be a duplicate of #7879 consistently when not using the optional -n argument.

Interesting, thanks. These are plausibly bugs in netCDF. Xarray is pure-python, so we can't segfault ourselves, though we can call libraries incorrectly. It's somewhat of an intractable problem to push these upstream though...

In the meantime, if you don't need to run netcdf tests, uninstalling it will work!

[keewis]

just for reference, we're in the process of removing cdms2 support entirely from xarray (it is deprecated since the first release after May this year): cdms2 itself is in maintenance-only mode and will be archived end of this year. For the removal to happen in xarray, we just need to decide on a date / target version.

As for the segfaults: these are caused by netcdf4 dropping the global library lock in recent versions, which exposed our own locks not working properly for netcdf4 (but only for a threading scheduler). Concurrency issues like this are really tricky to debug, though, which I think is the reason why nobody got around to fixing these yet.

[kafitzgerald]

Out of interest, was this an old clone? Or did a new clone hit this issue? We should fix on our end if a new clone could have this issue...

It was a new clone of my new fork, but I hadn't added or fetched the upstream repo yet per the instructions and therefore didn't have the tags.

And thanks for the info on cdms2 and netcdf4!