[JOSS] Error running matchpoint.ipynb
Closed this issue · 5 comments
malmans2 commented
Describe the bug
I'm getting a plotting issue when I try this: https://nctoolkit.readthedocs.io/en/latest/matchpoint.html
I tried both the latest and the stable version of nctoolkit, and I'm using Jupyter Lab.
To Reproduce
import nctoolkit as nc
ds = nc.open_thredds('https://data.nodc.noaa.gov/thredds/dodsC/ncei/woa/nitrate/all/1.00/woa18_all_n01_01.nc', checks = False)
ds.crop(lon = [-40, 20], lat = [40, 70], nco = True)
ds.subset(variables = "n_an")
ds.run()
ds.plot()Checking if nctoolkit is available
Warning: xarray could not decode times!
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/IPython/core/formatters.py:974, in MimeBundleFormatter.__call__(self, obj, include, exclude)
971 method = get_real_method(obj, self.print_method)
973 if method is not None:
--> 974 return method(include=include, exclude=exclude)
975 return None
976 else:
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/core/dimension.py:1290, in Dimensioned._repr_mimebundle_(self, include, exclude)
1283 def _repr_mimebundle_(self, include=None, exclude=None):
1284 """
1285 Resolves the class hierarchy for the class rendering the
1286 object using any display hooks registered on Store.display
1287 hooks. The output of all registered display_hooks is then
1288 combined and returned.
1289 """
-> 1290 return Store.render(self)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/core/options.py:1425, in Store.render(cls, obj)
1423 data, metadata = {}, {}
1424 for hook in hooks:
-> 1425 ret = hook(obj)
1426 if ret is None:
1427 continue
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/ipython/display_hooks.py:280, in pprint_display(obj)
278 if not ip.display_formatter.formatters['text/plain'].pprint:
279 return None
--> 280 return display(obj, raw_output=True)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/ipython/display_hooks.py:248, in display(obj, raw_output, **kwargs)
246 elif isinstance(obj, (CompositeOverlay, ViewableElement)):
247 with option_state(obj):
--> 248 output = element_display(obj)
249 elif isinstance(obj, (Layout, NdLayout, AdjointLayout)):
250 with option_state(obj):
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/ipython/display_hooks.py:142, in display_hook.<locals>.wrapped(element)
140 try:
141 max_frames = OutputSettings.options['max_frames']
--> 142 mimebundle = fn(element, max_frames=max_frames)
143 if mimebundle is None:
144 return {}, {}
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/ipython/display_hooks.py:188, in element_display(element, max_frames)
185 if type(element) not in Store.registry[backend]:
186 return None
--> 188 return render(element)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/ipython/display_hooks.py:69, in render(obj, **kwargs)
66 if renderer.fig == 'pdf':
67 renderer = renderer.instance(fig='png')
---> 69 return renderer.components(obj, **kwargs)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/plotting/renderer.py:399, in Renderer.components(self, obj, fmt, comm, **kwargs)
396 embed = (not (dynamic or streams or self.widget_mode == 'live') or config.embed)
398 if embed or config.comms == 'default':
--> 399 return self._render_panel(plot, embed, comm)
400 return self._render_ipywidget(plot)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/plotting/renderer.py:406, in Renderer._render_panel(self, plot, embed, comm)
404 doc = Document()
405 with config.set(embed=embed):
--> 406 model = plot.layout._render_model(doc, comm)
407 if embed:
408 return render_model(model, comm)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/panel/viewable.py:736, in Viewable._render_model(self, doc, comm)
734 if comm is None:
735 comm = state._comm_manager.get_server_comm()
--> 736 model = self.get_root(doc, comm)
738 if self._design and self._design.theme.bokeh_theme:
739 doc.theme = self._design.theme.bokeh_theme
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/panel/layout/base.py:289, in Panel.get_root(self, doc, comm, preprocess)
285 def get_root(
286 self, doc: Optional[Document] = None, comm: Optional[Comm] = None,
287 preprocess: bool = True
288 ) -> Model:
--> 289 root = super().get_root(doc, comm, preprocess)
290 # ALERT: Find a better way to handle this
291 if hasattr(root, 'styles') and 'overflow-x' in root.styles:
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/panel/viewable.py:658, in Renderable.get_root(self, doc, comm, preprocess)
656 wrapper = self._design._wrapper(self)
657 if wrapper is self:
--> 658 root = self._get_model(doc, comm=comm)
659 if preprocess:
660 self._preprocess(root)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/panel/layout/base.py:173, in Panel._get_model(self, doc, root, parent, comm)
171 root = root or model
172 self._models[root.ref['id']] = (model, parent)
--> 173 objects, _ = self._get_objects(model, [], doc, root, comm)
174 props = self._get_properties(doc)
175 props[self._property_mapping['objects']] = objects
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/panel/layout/base.py:155, in Panel._get_objects(self, model, old_objects, doc, root, comm)
153 else:
154 try:
--> 155 child = pane._get_model(doc, root, model, comm)
156 except RerenderError as e:
157 if e.layout is not None and e.layout is not self:
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/panel/pane/holoviews.py:411, in HoloViews._get_model(self, doc, root, parent, comm)
409 plot = self.object
410 else:
--> 411 plot = self._render(doc, comm, root)
413 plot.pane = self
414 backend = plot.renderer.backend
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/panel/pane/holoviews.py:506, in HoloViews._render(self, doc, comm, root)
503 if comm:
504 kwargs['comm'] = comm
--> 506 return renderer.get_plot(self.object, **kwargs)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/plotting/bokeh/renderer.py:70, in BokehRenderer.get_plot(self_or_cls, obj, doc, renderer, **kwargs)
63 @bothmethod
64 def get_plot(self_or_cls, obj, doc=None, renderer=None, **kwargs):
65 """
66 Given a HoloViews Viewable return a corresponding plot instance.
67 Allows supplying a document attach the plot to, useful when
68 combining the bokeh model with another plot.
69 """
---> 70 plot = super().get_plot(obj, doc, renderer, **kwargs)
71 if plot.document is None:
72 plot.document = Document() if self_or_cls.notebook_context else curdoc()
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/plotting/renderer.py:241, in Renderer.get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
238 defaults = [kd.default for kd in plot.dimensions]
239 init_key = tuple(v if d is None else d for v, d in
240 zip(plot.keys[0], defaults))
--> 241 plot.update(init_key)
242 else:
243 plot = obj
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/plotting/plot.py:936, in DimensionedPlot.update(self, key)
934 def update(self, key):
935 if len(self) == 1 and ((key == 0) or (key == self.keys[0])) and not self.drawn:
--> 936 return self.initialize_plot()
937 item = self.__getitem__(key)
938 self.traverse(lambda x: setattr(x, '_updated', True))
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/plotting/bokeh/element.py:1527, in ElementPlot.initialize_plot(self, ranges, plot, plots, source)
1525 if self.autorange:
1526 self._setup_autorange()
-> 1527 self._init_glyphs(plot, element, ranges, source)
1528 if not self.overlaid:
1529 self._update_plot(key, plot, style_element)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/plotting/bokeh/element.py:1469, in ElementPlot._init_glyphs(self, plot, element, ranges, source)
1467 else:
1468 style = self.style[self.cyclic_index]
-> 1469 data, mapping, style = self.get_data(element, ranges, style)
1470 current_id = element._plot_id
1472 with abbreviated_exception():
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/plotting/bokeh/raster.py:114, in RasterPlot.get_data(self, element, ranges, style)
112 if i > 2 and 'hover' not in self.handles:
113 break
--> 114 img = element.dimension_values(i, flat=False)
115 if img.dtype.kind == 'b':
116 img = img.astype(np.int8)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/core/data/__init__.py:199, in PipelineMeta.pipelined.<locals>.pipelined_fn(*args, **kwargs)
196 inst._in_method = True
198 try:
--> 199 result = method_fn(*args, **kwargs)
200 if PipelineMeta.disable:
201 return result
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/core/data/__init__.py:1093, in Dataset.dimension_values(self, dimension, expanded, flat)
1077 """Return the values along the requested dimension.
1078
1079 Args:
(...)
1090 NumPy array of values along the requested dimension
1091 """
1092 dim = self.get_dimension(dimension, strict=True)
-> 1093 values = self.interface.values(self, dim, expanded, flat)
1094 if dim.nodata is not None:
1095 # Ensure nodata applies to boolean data in py2
1096 values = np.where(values==dim.nodata, np.NaN, values)
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/core/data/xarray.py:421, in XArrayInterface.values(cls, dataset, dim, expanded, flat, compute, keep_index)
419 data = cupy.asnumpy(data)
420 if not keep_index:
--> 421 data = cls.canonicalize(dataset, data, data_coords=data_coords,
422 virtual_coords=virtual_coords)
423 return data.T.flatten() if flat and not keep_index else data
424 elif expanded:
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/holoviews/core/data/grid.py:329, in GridInterface.canonicalize(cls, dataset, data, data_coords, virtual_coords)
327 data = data.flatten()
328 else:
--> 329 data = np.squeeze(data, axis=tuple(dropped))
331 if not any(cls.irregular(dataset, d) for d in dataset.kdims):
332 inds = [dims.index(kd.name) for kd in dataset.kdims]
File ~/mambaforge/envs/nctoolkit/lib/python3.11/site-packages/numpy/core/fromnumeric.py:1558, in squeeze(a, axis)
1556 return squeeze()
1557 else:
-> 1558 return squeeze(axis=axis)
ValueError: cannot select an axis to squeeze out which has size not equal to oneExpected behavior
Reproduce documentation plot.
Desktop (please complete the following information):
- OS: macOS
- Browser Chrome
Additional context
Add any other context about the problem here.
conda list
# packages in environment at /Users/mattia/mambaforge/envs/nctoolkit:
#
# Name Version Build Channel
anyio 3.7.0 pyhd8ed1ab_1 conda-forge
appnope 0.1.3 pyhd8ed1ab_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h5547dcb_3 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.2 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
babel 2.12.1 pyhd8ed1ab_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.4 heccf04b_0 conda-forge
bokeh 3.1.1 pyhd8ed1ab_0 conda-forge
brotli 1.0.9 hb7f2c08_8 conda-forge
brotli-bin 1.0.9 hb7f2c08_8 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
c-ares 1.19.1 h0dc2134_0 conda-forge
ca-certificates 2023.5.7 h8857fd0_0 conda-forge
cairo 1.16.0 h09dd18c_1016 conda-forge
cartopy 0.21.1 py311hb21c73c_1 conda-forge
cdo 2.2.0 h9d92bdb_4 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py311ha86e640_3 conda-forge
cftime 1.6.2 py311hd5badaa_1 conda-forge
charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
colorcet 3.0.1 pyhd8ed1ab_0 conda-forge
comm 0.1.3 pyhd8ed1ab_0 conda-forge
contourpy 1.1.0 py311h5fe6e05_0 conda-forge
curl 8.1.2 hbee3ae8_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
debugpy 1.6.7 py311h814d153_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dill 0.3.6 pyhd8ed1ab_1 conda-forge
eccodes 2.30.2 hecd1f2b_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
esmf 8.4.2 mpi_mpich_h39d0f2c_100 conda-forge
exceptiongroup 1.1.1 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hf0c8a7f_1 conda-forge
fftw 3.3.10 nompi_h4fa670e_108 conda-forge
findlibs 0.0.5 pyhd8ed1ab_0 conda-forge
flit-core 3.9.0 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 h5bb23bf_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.40.0 py311h2725bcf_0 conda-forge
freetype 2.12.1 h3f81eb7_1 conda-forge
fribidi 1.0.10 hbcb3906_0 conda-forge
geos 3.11.2 hf0c8a7f_0 conda-forge
gettext 0.21.1 h8a4c099_0 conda-forge
graphite2 1.3.13 h2e338ed_1001 conda-forge
gsl 2.7 h93259b0_0 conda-forge
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hdf4 4.2.15 h9804679_6 conda-forge
hdf5 1.14.0 mpi_mpich_h18663c6_3 conda-forge
holoviews 1.16.2 pyhd8ed1ab_0 conda-forge
hvplot 0.8.4 pyhd8ed1ab_1 conda-forge
icu 72.1 h7336db1_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.7.0 pyha770c72_0 conda-forge
importlib_metadata 6.7.0 hd8ed1ab_0 conda-forge
importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.23.1 pyh736e0ef_0 conda-forge
ipython 8.14.0 pyhd1c38e8_0 conda-forge
jasper 4.0.0 h794afb9_1 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.3.1 py311h6eed73b_0 conda-forge
jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge
jupyter_server 2.6.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.2 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.23.0 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.4 py311hd2070f0_1 conda-forge
krb5 1.20.1 h049b76e_0 conda-forge
lcms2 2.15 h2dcdeff_1 conda-forge
lerc 4.0.0 hb486fe8_0 conda-forge
libaec 1.0.6 hf0c8a7f_1 conda-forge
libblas 3.9.0 17_osx64_openblas conda-forge
libbrotlicommon 1.0.9 hb7f2c08_8 conda-forge
libbrotlidec 1.0.9 hb7f2c08_8 conda-forge
libbrotlienc 1.0.9 hb7f2c08_8 conda-forge
libcblas 3.9.0 17_osx64_openblas conda-forge
libcurl 8.1.2 hbee3ae8_0 conda-forge
libcxx 16.0.6 hd57cbcb_0 conda-forge
libdeflate 1.18 hac1461d_0 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
libexpat 2.5.0 hf0c8a7f_1 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libgfortran 5.0.0 11_3_0_h97931a8_31 conda-forge
libgfortran5 12.2.0 he409387_31 conda-forge
libglib 2.76.3 hc62aa5d_0 conda-forge
libiconv 1.17 hac89ed1_0 conda-forge
libjpeg-turbo 2.1.5.1 hb7f2c08_0 conda-forge
liblapack 3.9.0 17_osx64_openblas conda-forge
libnetcdf 4.9.2 mpi_mpich_h4b56550_5 conda-forge
libnghttp2 1.52.0 he2ab024_0 conda-forge
libopenblas 0.3.23 openmp_h429af6e_0 conda-forge
libpng 1.6.39 ha978bb4_0 conda-forge
libsodium 1.0.18 hbcb3906_1 conda-forge
libsqlite 3.42.0 h58db7d2_0 conda-forge
libssh2 1.11.0 hd019ec5_0 conda-forge
libtiff 4.5.1 hf955e92_0 conda-forge
libuuid 2.38.1 hb7f2c08_0 conda-forge
libwebp-base 1.3.0 hb7f2c08_0 conda-forge
libxcb 1.15 hb7f2c08_0 conda-forge
libxml2 2.11.4 hd95e348_0 conda-forge
libzip 1.9.2 h6db710c_1 conda-forge
libzlib 1.2.13 h8a1eda9_5 conda-forge
linkify-it-py 2.0.0 pyhd8ed1ab_0 conda-forge
llvm-openmp 16.0.6 hff08bdf_0 conda-forge
lz4-c 1.9.4 hf0c8a7f_0 conda-forge
magics 4.13.0 hb1c45c1_5 conda-forge
magics-python 1.5.8 pyhd8ed1ab_1 conda-forge
markdown 3.4.3 pyhd8ed1ab_0 conda-forge
markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.3 py311h2725bcf_0 conda-forge
matplotlib-base 3.7.1 py311h2bf763f_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdit-py-plugins 0.4.0 pyhd8ed1ab_0 conda-forge
mdurl 0.1.0 pyhd8ed1ab_0 conda-forge
metpy 1.5.0 pyhd8ed1ab_0 conda-forge
mistune 3.0.0 pyhd8ed1ab_0 conda-forge
mpi 1.0 mpich conda-forge
mpich 4.1.1 hd33e60e_100 conda-forge
multiprocess 0.70.14 py311h5547dcb_3 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.6.0 pyhd8ed1ab_0 conda-forge
nbformat 5.9.0 pyhd8ed1ab_0 conda-forge
nco 5.1.6 h0317220_0 conda-forge
ncplot 0.3.4 py311h9bdd199_0 conda-forge
nctoolkit 0.9.4 dev_0 <develop>
ncurses 6.4 hf0c8a7f_0 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.1 mpi_mpich_h2786e36_0 conda-forge
netcdf4 1.6.4 nompi_py311h6222480_100 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
numpy 1.25.0 py311hc44ba51_0 conda-forge
openjpeg 2.5.0 h13ac156_2 conda-forge
openssl 3.1.1 h8a1eda9_1 conda-forge
overrides 7.3.1 pyhd8ed1ab_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
pandas 2.0.2 py311hab14417_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panel 1.1.0 pyhd8ed1ab_2 conda-forge
pango 1.50.14 hbce5e75_1 conda-forge
parallelio 2.5.10 mpi_mpich_hda3997c_102 conda-forge
param 1.13.0 pyh1a96a4e_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pcre2 10.40 h1c4e4bc_0 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.5.0 py311h7cb0e2d_1 conda-forge
pint 0.22 pyhd8ed1ab_1 conda-forge
pip 23.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 hbcb3906_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
platformdirs 3.6.0 pyhd8ed1ab_0 conda-forge
pooch 1.7.0 pyha770c72_3 conda-forge
proj 9.2.1 hc8d59c9_0 conda-forge
prometheus_client 0.17.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.38 pyha770c72_0 conda-forge
prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge
psutil 5.9.5 py311h5547dcb_0 conda-forge
pthread-stubs 0.4 hc929b4f_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pygments 2.15.1 pyhd8ed1ab_0 conda-forge
pyobjc-core 9.2 py311hf110eff_0 conda-forge
pyobjc-framework-cocoa 9.2 py311hf110eff_0 conda-forge
pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge
pyproj 3.6.0 py311h854a015_1 conda-forge
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pyshp 2.3.1 pyhd8ed1ab_0 conda-forge
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python 3.11.4 h30d4d87_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.11 3_cp311 conda-forge
pytz 2023.3 pyhd8ed1ab_0 conda-forge
pyviz_comms 2.3.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py311h5547dcb_5 conda-forge
pyzmq 25.1.0 py311h5dacc12_0 conda-forge
readline 8.2 h9e318b2_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
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robertjwilson commented
Hi @malmans2. I am able to reproduce this. I've pinned it down to an upgrade to numpy 3 days ago breaking something within hvplot. Downgrading numpy to 1.24.3 seems to fix the problem.
I'll put together a reproducible example and raise an issue over at hvplot. It seems to only apply to cases with multiple depths, and the numpy change appears to be changing the behaviour of xarray which is causing the problem in hvplot.
malmans2 commented
Did you end up opening an issue? If yes, I would add the reference here.
robertjwilson commented
I thought I had closed this off. My bad. This should now work fine.
Updates to panel broke ncplot in web browsers in May, and my "fixes" meant files like this weren't plotting. But it should be fine in ncplot v0.3.5.
malmans2 commented
This is now working, so I'm closing the issue.
A couple of things I noticed tho:
- There's a few xarray's deprecation warnings:
Warning: xarray could not decode times!
Calling int on a single element Series is deprecated and will raise a TypeError in the future. Use int(ser.iloc[0]) instead
Calling int on a single element Series is deprecated and will raise a TypeError in the future. Use int(ser.iloc[0]) instead
nc.open_data("~/Downloads/tas_day_GFDL-CM4_historical_r1i1p1f1_gr1_18500101-18691231.nc", checks = False)did not work, I had to provide the absolute path. I suggest to add support for it.
robertjwilson commented
Thanks. I've just raised an issue. This only impacts macOS, and I've been meaning to fix it for a while. #92
I'll double check the deprecation warnings. Last time I looked there was nothing within nctoolkit itself throwing the warnings, it was purely hvplot. So little that could be done in nctoolkit itself.