[Bug]: open_dataset() fails in "Gentle Introduction to xCDAT" notebook due to add_bounds incorrect arg (addressed by #650)

[brian-rose]

What happened?

Following instructions for "Opening a dataset" in the Gentle Introduction to xCDAT. Attempting to open the example file with

ds = xc.open_dataset(filepath, add_bounds=True, decode_times=True, center_times=True)

gives

TypeError: 'bool' object is not iterable

What did you expect to happen? Are there are possible answers you came across?

Expected

the dataset handle should open, with bounds handling, as illustrated in the docs

Possible answers

The full traceback (see below) shows that the error is triggered from running

ds.bounds.add_missing_bounds()

If I remove add_bounds=True, the same code runs without error:

ds = xc.open_dataset(filepath, decode_times=True, center_times=True)

I found the same behavior when trying to use xc.open_dataset on some model output files that I have stored locally.

Is this related to #607?

Minimal Complete Verifiable Example (MVCE)

import xcdat as xc
filepath = "https://esgf-data1.llnl.gov/thredds/dodsC/css03_data/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r10i1p1f1/Amon/tas/gn/v20200605/tas_Amon_ACCESS-ESM1-5_historical_r10i1p1f1_gn_185001-201412.nc"
ds = xc.open_dataset(filepath, add_bounds=True, decode_times=True, center_times=True)

Relevant log output

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[1], line 3
      1 import xcdat as xc
      2 filepath = "https://esgf-data1.llnl.gov/thredds/dodsC/css03_data/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r10i1p1f1/Amon/tas/gn/v20200605/tas_Amon_ACCESS-ESM1-5_historical_r10i1p1f1_gn_185001-201412.nc"
----> 3 ds = xc.open_dataset(filepath, add_bounds=True, decode_times=True, center_times=True)

File ~/miniconda3/envs/test-xcdat/lib/python3.12/site-packages/xcdat/dataset.py:122, in open_dataset(path, data_var, add_bounds, decode_times, center_times, lon_orient, **kwargs)
    119     except KeyError as err:
    120         logger.warning(err)
--> 122 ds = _postprocess_dataset(ds, data_var, center_times, add_bounds, lon_orient)
    124 return ds

File ~/miniconda3/envs/test-xcdat/lib/python3.12/site-packages/xcdat/dataset.py:524, in _postprocess_dataset(dataset, data_var, center_times, add_bounds, lon_orient)
    521     ds = center_times_func(dataset)
    523 if add_bounds is not None:
--> 524     ds = ds.bounds.add_missing_bounds(axes=add_bounds)
    526 if lon_orient is not None:
    527     ds = swap_lon_axis(ds, to=lon_orient, sort_ascending=True)

File ~/miniconda3/envs/test-xcdat/lib/python3.12/site-packages/xcdat/bounds.py:166, in BoundsAccessor.add_missing_bounds(self, axes)
    129 """Adds missing coordinate bounds for supported axes in the Dataset.
    130 
    131 This function loops through the Dataset's axes and attempts to adds
   (...)
    162 xr.Dataset
    163 """
    164 ds = self._dataset.copy()
--> 166 for axis in axes:
    167     try:
    168         coords = get_dim_coords(ds, axis)

TypeError: 'bool' object is not iterable

Anything else we need to know?

This is related to my review of the JOSS paper openjournals/joss-reviews#6426

Environment

xCDAT version

0.7.0

Output from xr.show_versions()

INSTALLED VERSIONS
------------------
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: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.14.3
libnetcdf: 4.9.2

xarray: 2024.5.0
pandas: 2.2.2
numpy: 1.26.4
scipy: 1.13.1
netCDF4: 1.6.5
pydap: None
h5netcdf: None
h5py: None
zarr: None
cftime: 1.6.3
nc_time_axis: 1.4.1
iris: None
bottleneck: None
dask: 2024.5.2
distributed: 2024.5.2
matplotlib: 3.8.4
cartopy: 0.23.0
seaborn: None
numbagg: None
fsspec: 2024.6.0
cupy: None
pint: None
sparse: 0.15.4
flox: None
numpy_groupies: None
setuptools: 70.0.0
pip: 24.0
conda: None
pytest: None
mypy: None
IPython: 8.25.0
sphinx: None

Output of mamba env list

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
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        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.15.3) supported by @QuantStack

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█████████████████████████████████████████████████████████████

# packages in environment at /Users/br546577/miniconda3/envs/test-xcdat:
#
# Name                    Version                   Build  Channel
anyio                     4.4.0              pyhd8ed1ab_0    conda-forge
appnope                   0.1.4              pyhd8ed1ab_0    conda-forge
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aws-c-auth                0.7.22               h27bc0eb_5    conda-forge
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aws-c-common              0.9.19               h99b78c6_0    conda-forge
aws-c-compression         0.2.18               h5db4892_6    conda-forge
aws-c-event-stream        0.4.2               h4de9e5c_13    conda-forge
aws-c-http                0.8.2                h2c662d3_2    conda-forge
aws-c-io                  0.14.9               h8709d7d_2    conda-forge
aws-c-mqtt                0.10.4               h5fc5ab5_6    conda-forge
aws-c-s3                  0.5.10               h48f01f6_3    conda-forge
aws-c-sdkutils            0.1.16               h5db4892_2    conda-forge
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icu                       73.2                 hc8870d7_0    conda-forge
idna                      3.7                pyhd8ed1ab_0    conda-forge
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libsodium                 1.0.18               h27ca646_1    conda-forge
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llvm-openmp               18.1.6               hde57baf_0    conda-forge
llvmlite                  0.42.0          py312h17030e7_1    conda-forge
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matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.8           py312h157fec4_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert                 7.16.4               hd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.16.4               hd8ed1ab_0    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
nc-time-axis              1.4.1              pyhd8ed1ab_0    conda-forge
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nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
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pthread-stubs             0.4               h27ca646_1001    conda-forge
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pyarrow                   16.1.0          py312h37858a2_1    conda-forge
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pyarrow-hotfix            0.6                pyhd8ed1ab_0    conda-forge
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pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
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pyproj                    3.6.1           py312h71aa0db_6    conda-forge
pyshp                     2.3.1              pyhd8ed1ab_0    conda-forge
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python                    3.12.3          h4a7b5fc_0_cpython    conda-forge
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python_abi                3.12                    4_cp312    conda-forge
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setuptools                70.0.0             pyhd8ed1ab_0    conda-forge
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sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sparse                    0.15.4             pyhd8ed1ab_0    conda-forge
sqlite                    3.45.3               hf2abe2d_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
tblib                     3.0.0              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh31c8845_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.1             pyhd8ed1ab_0    conda-forge
tornado                   6.4.1           py312h7e5086c_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.1               hd8ed1ab_0    conda-forge
typing_extensions         4.12.1             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.6.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.11             pyhd8ed1ab_0    conda-forge
xarray                    2024.5.0           pyhd8ed1ab_0    conda-forge
xcdat                     0.7.0              pyhd8ed1ab_0    conda-forge
xesmf                     0.8.5              pyhd8ed1ab_0    conda-forge
xgcm                      0.8.1              pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hb547adb_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xyzservices               2024.6.0           pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zeromq                    4.3.5                hcc0f68c_4    conda-forge
zict                      3.0.0              pyhd8ed1ab_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                hfb2fe0b_1    conda-forge
zstd                      1.5.6                hb46c0d2_0    conda-forge

[pochedls]

@brian-rose – thanks for reporting this. We are currently going through all of our docs to catch issues like this; it looks like this was caught and the PR is being finalized.

We previously accepted add_bounds as a Boolean, which would add bounds to all axes. This was deprecated in favor of having the user specify the axes which bounds should be added to (if missing). We included deprecation warnings before the change, but obviously missed this in the documentation. We will fix this soon.

This line will be updated from add_bounds=True to:

ds = xc.open_dataset(filepath, add_bounds=["X", "Y"], decode_times=True, center_times=True)

(or ["X", "Y", "T"])

[tomvothecoder]

@brian-rose Thanks for reporting this! I just merged PR #650 which addresses this issue. The "latest" version on Read The Docs will reflect this change soon: https://xcdat.readthedocs.io/en/latest/examples/introduction-to-xcdat.html.