Example 03 execution issues #3
Description
-> % uv pip list
Using Python 3.13.5 environment at: ~/src/MPoL/.venv
Package Version
------------------------------------ ---------------------
absl-py 2.3.1
accessible-pygments 0.0.5
alabaster 1.0.0
anyio 4.9.0
appdirs 1.4.4
argon2-cffi 25.1.0
argon2-cffi-bindings 21.2.0
argparse-dataclass 2.0.0
arrow 1.3.0
arviz 0.22.0
asciitree 0.3.3
asdf 4.2.0
asdf-standard 1.3.0
asdf-transform-schemas 0.6.0
astropy 7.1.0
astropy-iers-data 0.2025.7.14.0.40.29
asttokens 3.0.0
async-lru 2.0.5
attrs 25.3.0
babel 2.17.0
beautifulsoup4 4.13.4
bleach 6.2.0
bokeh 3.7.3
certifi 2025.7.14
cffi 1.17.1
cftime 1.6.4.post1
charset-normalizer 3.4.2
click 8.2.1
cloudpickle 3.1.1
comm 0.2.2
conda-inject 1.3.2
configargparse 1.7.1
connection-pool 0.0.3
contourpy 1.3.2
coverage 7.9.2
cycler 0.12.1
dask 2025.5.1
debugpy 1.8.14
decorator 5.2.1
defusedxml 0.7.1
deprecated 1.2.18
distributed 2025.5.1
dm-tree 0.1.9
docutils 0.21.2
dpath 2.2.0
executing 2.2.0
fast-histogram 0.14
fasteners 0.19
fastjsonschema 2.21.1
filelock 3.18.0
fonttools 4.58.5
fqdn 1.5.1
frank 1.2.3
fsspec 2025.5.1
gitdb 4.0.12
gitpython 3.1.45
greenlet 3.2.3
grpcio 1.73.1
h11 0.16.0
h5netcdf 1.6.3
h5py 3.14.0
httpcore 1.0.9
httpx 0.28.1
humanfriendly 10.0
idna 3.10
imagesize 1.4.1
immutables 0.21
importlib-metadata 8.7.0
iniconfig 2.1.0
ipykernel 6.29.5
ipython 9.4.0
ipython-pygments-lexers 1.1.1
ipywidgets 8.1.7
isoduration 20.11.0
jedi 0.19.2
jinja2 3.1.6
jmespath 1.0.1
json5 0.12.0
jsonpointer 3.0.0
jsonschema 4.24.0
jsonschema-specifications 2025.4.1
jupyter 1.1.1
jupyter-cache 1.0.1
jupyter-client 8.6.3
jupyter-console 6.6.3
jupyter-core 5.8.1
jupyter-events 0.12.0
jupyter-lsp 2.2.5
jupyter-server 2.16.0
jupyter-server-terminals 0.5.3
jupyterlab 4.4.4
jupyterlab-pygments 0.3.0
jupyterlab-server 2.27.3
jupyterlab-widgets 3.0.15
jupytext 1.17.2
kiwisolver 1.4.8
llvmlite 0.44.0
locket 1.0.0
markdown 3.8.2
markdown-it-py 3.0.0
markupsafe 3.0.2
matplotlib 3.10.3
matplotlib-inline 0.1.7
mdit-py-plugins 0.4.2
mdurl 0.1.2
mistune 3.1.3
mpmath 1.3.0
mpol 0.3.0a1.dev4+gf1facdb
msgpack 1.1.1
mypy 1.16.1
mypy-extensions 1.1.0
myst-nb 1.3.0
myst-parser 4.0.1
narwhals 1.47.0
nbclient 0.10.2
nbconvert 7.16.6
nbformat 5.10.4
nbsphinx 0.9.7
nest-asyncio 1.6.0
netcdf4 1.7.2
networkx 3.5
notebook 7.4.4
notebook-shim 0.2.4
numba 0.61.2
numcodecs 0.15.1
numpy 2.2.6
nvidia-cublas-cu12 12.6.4.1
nvidia-cuda-cupti-cu12 12.6.80
nvidia-cuda-nvrtc-cu12 12.6.77
nvidia-cuda-runtime-cu12 12.6.77
nvidia-cudnn-cu12 9.5.1.17
nvidia-cufft-cu12 11.3.0.4
nvidia-cufile-cu12 1.11.1.6
nvidia-curand-cu12 10.3.7.77
nvidia-cusolver-cu12 11.7.1.2
nvidia-cusparse-cu12 12.5.4.2
nvidia-cusparselt-cu12 0.6.3
nvidia-nccl-cu12 2.26.2
nvidia-nvjitlink-cu12 12.6.85
nvidia-nvtx-cu12 12.6.77
opt-einsum 3.4.0
overrides 7.7.0
packaging 25.0
pandas 2.3.1
pandocfilters 1.5.1
parso 0.8.4
partd 1.4.2
pathspec 0.12.1
pexpect 4.9.0
pillow 11.3.0
platformdirs 4.3.8
pluggy 1.6.0
prometheus-client 0.22.1
prompt-toolkit 3.0.51
protobuf 6.31.1
psutil 7.0.0
ptyprocess 0.7.0
pulp 3.2.2
pure-eval 0.2.3
pycparser 2.22
pydata-sphinx-theme 0.15.4
pyerfa 2.0.1.5
pygments 2.19.2
pyparsing 3.2.3
pyro-api 0.1.2
pyro-ppl 1.9.1
pytest 8.4.1
pytest-cov 6.2.1
python-dateutil 2.9.0.post0
python-json-logger 3.3.0
pytz 2025.2
pyyaml 6.0.2
pyzmq 27.0.0
referencing 0.36.2
requests 2.32.4
reretry 0.11.8
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rpds-py 0.26.0
ruff 0.12.3
scipy 1.16.0
semantic-version 2.10.0
send2trash 1.8.3
setuptools 80.9.0
six 1.17.0
smart-open 7.3.0.post1
smmap 5.0.2
snakemake 9.9.0
snakemake-interface-common 1.21.0
snakemake-interface-executor-plugins 9.3.9
snakemake-interface-logger-plugins 1.2.4
snakemake-interface-report-plugins 1.2.0
snakemake-interface-storage-plugins 4.2.2
sniffio 1.3.1
snowballstemmer 3.0.1
sortedcontainers 2.4.0
soupsieve 2.7
sphinx 8.1.3
sphinx-book-theme 1.1.4
sphinx-copybutton 0.5.2
sphinxcontrib-applehelp 2.0.0
sphinxcontrib-devhelp 2.0.0
sphinxcontrib-htmlhelp 2.1.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-mermaid 1.0.0
sphinxcontrib-qthelp 2.0.0
sphinxcontrib-serializinghtml 2.0.0
sqlalchemy 2.0.41
stack-data 0.6.3
sympy 1.14.0
tabulate 0.9.0
tblib 3.1.0
tensorboard 2.19.0
tensorboard-data-server 0.7.2
terminado 0.18.1
throttler 1.2.2
tinycss2 1.4.0
toolz 1.0.0
torch 2.7.1
torchaudio 2.7.1
torchkbnufft 1.5.2
torchvision 0.22.1
tornado 6.5.1
tqdm 4.67.1
traitlets 5.14.3
triton 3.3.1
types-python-dateutil 2.9.0.20250708
typing-extensions 4.14.1
tzdata 2025.2
ujson 5.10.0
uri-template 1.3.0
urllib3 2.5.0
visread 0.0.5
wcwidth 0.2.13
webcolors 24.11.1
webencodings 0.5.1
websocket-client 1.8.0
werkzeug 3.1.3
widgetsnbextension 4.0.14
wrapt 1.17.2
xarray 2025.7.1
xarray-einstats 0.9.1
xyzservices 2025.4.0
yte 1.9.0
zarr 2.18.7
zict 3.0.0
zipp 3.23.0I am working through the examples for my review but attempting to run example 3 errors quickly with an reference to a missing notebook_setup script trying to be run (see full error).
-> % jupytext --to ipynb --execute pyro.md
[jupytext] Reading pyro.md in format md
[jupytext] Executing notebook with kernel python3
Traceback (most recent call last):
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/jupyter_core/utils/__init__.py", line 154, in wrapped
asyncio.get_running_loop()
~~~~~~~~~~~~~~~~~~~~~~~~^^
RuntimeError: no running event loop
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/matthew/src/MPoL/.venv/bin/jupytext", line 10, in <module>
sys.exit(jupytext())
~~~~~~~~^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/jupytext/cli.py", line 497, in jupytext
exit_code += jupytext_single_file(nb_file, args, log)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/jupytext/cli.py", line 741, in jupytext_single_file
exec_proc.preprocess(notebook, resources=resources)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/nbconvert/preprocessors/execute.py", line 103, in preprocess
self.preprocess_cell(cell, resources, index)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/nbconvert/preprocessors/execute.py", line 124, in preprocess_cell
cell = self.execute_cell(cell, index, store_history=True)
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/jupyter_core/utils/__init__.py", line 158, in wrapped
return loop.run_until_complete(inner)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^
File "/usr/lib/python3.13/asyncio/base_events.py", line 725, in run_until_complete
return future.result()
~~~~~~~~~~~~~^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell
await self._check_raise_for_error(cell, cell_index, exec_reply)
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
%matplotlib inline
%run notebook_setup
------------------
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
File ~/src/MPoL/.venv/lib/python3.13/site-packages/IPython/core/magics/execution.py:728, in ExecutionMagics.run(self, parameter_s, runner, file_finder)
727 fpath = arg_lst[0]
--> 728 filename = file_finder(fpath)
729 except IndexError as e:
File ~/src/MPoL/.venv/lib/python3.13/site-packages/IPython/utils/path.py:90, in get_py_filename(name)
89 return py_name
---> 90 raise IOError("File `%r` not found." % name)
OSError: File `'notebook_setup'` not found.
The above exception was the direct cause of the following exception:
Exception Traceback (most recent call last)
Cell In[1], line 2
1 get_ipython().run_line_magic('matplotlib', 'inline')
----> 2 get_ipython().run_line_magic('run', 'notebook_setup')
File ~/src/MPoL/.venv/lib/python3.13/site-packages/IPython/core/interactiveshell.py:2504, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
2502 kwargs['local_ns'] = self.get_local_scope(stack_depth)
2503 with self.builtin_trap:
-> 2504 result = fn(*args, **kwargs)
2506 # The code below prevents the output from being displayed
2507 # when using magics with decorator @output_can_be_silenced
2508 # when the last Python token in the expression is a ';'.
2509 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
File ~/src/MPoL/.venv/lib/python3.13/site-packages/IPython/core/magics/execution.py:739, in ExecutionMagics.run(self, parameter_s, runner, file_finder)
737 if os.name == 'nt' and re.match(r"^'.*'$",fpath):
738 warn('For Windows, use double quotes to wrap a filename: %run "mypath\\myfile.py"')
--> 739 raise Exception(msg) from e
740 except TypeError:
741 if fpath in sys.meta_path:
Exception: File `'notebook_setup'` not found.I see that notebook_setup.py exists in the large-tutorials directory. Pointing the pyro.md file there via %run ../large-tutorials/notebook_setup though also produces an issue when making the dirty image.
-> % jupytext --to ipynb --execute pyro.md
[jupytext] Reading pyro.md in format md
[jupytext] Executing notebook with kernel python3
Traceback (most recent call last):
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/jupyter_core/utils/__init__.py", line 154, in wrapped
asyncio.get_running_loop()
~~~~~~~~~~~~~~~~~~~~~~~~^^
RuntimeError: no running event loop
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/matthew/src/MPoL/.venv/bin/jupytext", line 10, in <module>
sys.exit(jupytext())
~~~~~~~~^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/jupytext/cli.py", line 497, in jupytext
exit_code += jupytext_single_file(nb_file, args, log)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/jupytext/cli.py", line 741, in jupytext_single_file
exec_proc.preprocess(notebook, resources=resources)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/nbconvert/preprocessors/execute.py", line 103, in preprocess
self.preprocess_cell(cell, resources, index)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/nbconvert/preprocessors/execute.py", line 124, in preprocess_cell
cell = self.execute_cell(cell, index, store_history=True)
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/jupyter_core/utils/__init__.py", line 158, in wrapped
return loop.run_until_complete(inner)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^
File "/usr/lib/python3.13/asyncio/base_events.py", line 725, in run_until_complete
return future.result()
~~~~~~~~~~~~~^^
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell
await self._check_raise_for_error(cell, cell_index, exec_reply)
File "/home/matthew/src/MPoL/.venv/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
img, beam = make_dirty_image(np.real(data), np.imag(data))
# set plot dimensions
xx = 8 # in
cax_width = 0.2 # in
cax_sep = 0.1 # in
mmargin = 1.2
lmargin = 0.7
rmargin = 0.7
tmargin = 0.3
bmargin = 0.5
npanels = 2
# the size of image axes + cax_sep + cax_width
block_width = (xx - lmargin - rmargin - mmargin * (npanels - 1) )/npanels
ax_width = block_width - cax_width - cax_sep
ax_height = ax_width
yy = bmargin + ax_height + tmargin
fig = plt.figure(figsize=(xx, yy))
ax = []
cax = []
for i in range(npanels):
ax.append(fig.add_axes([(lmargin + i * (block_width + mmargin))/xx, bmargin/yy, ax_width/xx, ax_height/yy]))
cax.append(fig.add_axes([(lmargin + i * (block_width + mmargin) + ax_width + cax_sep)/xx, bmargin/yy, cax_width/xx, ax_height/yy]))
# single-channel image cube
chan = 0
im_beam = ax[0].imshow(beam[chan], **kw)
cbar = plt.colorbar(im_beam, cax=cax[0])
ax[0].set_title("beam")
# zoom in a bit
r = 0.3
ax[0].set_xlim(r, -r)
ax[0].set_ylim(-r, r)
im = ax[1].imshow(img[chan], **kw)
ax[1].set_title("dirty image")
cbar = plt.colorbar(im, cax=cax[1])
cbar.set_label(r"Jy/$\mathrm{arcsec}^2$")
for a in ax:
a.set_xlabel(r"$\Delta \alpha \cos \delta$ [${}^{\prime\prime}$]")
a.set_ylabel(r"$\Delta \delta$ [${}^{\prime\prime}$]")
------------------
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[7], line 1
----> 1 img, beam = make_dirty_image(np.real(data), np.imag(data))
3 # set plot dimensions
4 xx = 8 # in
Cell In[6], line 35, in make_dirty_image(data_real, data_imag, robust)
14 """
15 Make a plot of the dirty beam and dirty image (in units of Jy/arcsec^2).
16
(...) 23 beam, image numpy arrays
24 """
26 imager = gridding.DirtyImager(
27 coords=coords,
28 uu=uu,
(...) 32 data_im=data_imag,
33 )
---> 35 return imager.get_dirty_image(weighting="briggs", robust=robust, unit="Jy/arcsec^2")
File ~/src/MPoL/.venv/lib/python3.13/site-packages/mpol/gridding.py:1172, in DirtyImager.get_dirty_image(self, weighting, robust, taper_function, unit, check_visibility_scatter, max_scatter, **beam_kwargs)
1167 # for units of Jy/arcsec^2, we could just leave out the C constant *if* we were
1168 # doing uniform weighting. The relationships get more complex for robust or
1169 # natural weighting, however, so it's safer to calculate the number of
1170 # arcseconds^2 per beam
1171 if unit == "Jy/arcsec^2":
-> 1172 beam_area_per_chan = self.get_dirty_beam_area(**beam_kwargs) # [arcsec^2]
1174 # convert image
1175 # (Jy/1 arcsec^2) = (Jy/ 1 beam) * (1 beam/ n arcsec^2)
1176 # beam_area_per_chan is the n of arcsec^2 per 1 beam
1178 img /= beam_area_per_chan[:, np.newaxis, np.newaxis]
File ~/src/MPoL/.venv/lib/python3.13/site-packages/mpol/gridding.py:1067, in DirtyImager.get_dirty_beam_area(self, ntheta, single_channel_estimate)
1042 def get_dirty_beam_area(
1043 self, ntheta: int = 24, single_channel_estimate: bool = True
1044 ) -> npt.NDArray[np.floating[Any]]:
1045 r"""
1046 Compute the effective area of the dirty beam for each channel. Assumes that the
1047 beam has already been generated by running
(...) 1065 :math:`[\mathrm{arcsec}^{2}]`
1066 """
-> 1067 nulled = self._null_dirty_beam(
1068 ntheta=ntheta, single_channel_estimate=single_channel_estimate
1069 )
1070 area: npt.NDArray[np.floating[Any]] = self.coords.cell_size**2 * np.sum(
1071 nulled, axis=(1, 2)
1072 ) # arcsec^2
1073 return area
File ~/src/MPoL/.venv/lib/python3.13/site-packages/mpol/gridding.py:1027, in DirtyImager._null_dirty_beam(self, ntheta, single_channel_estimate)
1024 ind_neg_and_az = ind_neg & ind_azimuth
1026 # find the smallest r within this slice
-> 1027 min_r = np.min(rr[ind_neg_and_az])
1029 # null all pixels within this slice with radii r or greater
1030 ind_r = rr >= min_r
File ~/src/MPoL/.venv/lib/python3.13/site-packages/numpy/_core/fromnumeric.py:3302, in min(a, axis, out, keepdims, initial, where)
3190 @array_function_dispatch(_min_dispatcher)
3191 def min(a, axis=None, out=None, keepdims=np._NoValue, initial=np._NoValue,
3192 where=np._NoValue):
3193 """
3194 Return the minimum of an array or minimum along an axis.
3195
(...) 3300 6
3301 """
-> 3302 return _wrapreduction(a, np.minimum, 'min', axis, None, out,
3303 keepdims=keepdims, initial=initial, where=where)
File ~/src/MPoL/.venv/lib/python3.13/site-packages/numpy/_core/fromnumeric.py:86, in _wrapreduction(obj, ufunc, method, axis, dtype, out, **kwargs)
83 else:
84 return reduction(axis=axis, out=out, **passkwargs)
---> 86 return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation minimum which has no identityAdditionally, all the mermaid inclusions appear to be broken in the mardown file.