build_docs action is failing

[sjsrey]

Missing kernelspec.

Is this related to a recent ci change?

@jGaboardi ?

[jGaboardi]

a1a3642#r173844594

[jGaboardi]

That's my first guess, anyhow. Hopefully simply adding the deps will do the trick.

[knaaptime]

it looks like its a problem running the notebooks with nbsphinx. But i dont think we were always running the notebook in this repo; i thought just the rendered books were committed

[sjsrey]

So the idea is to run the notebooks locally and check them in but not run them on the CI?

[jGaboardi]

Something seems to be really screwy. Trying to build the docs locally and getting errors. Not successful.

[knaaptime]

So the idea is to run the notebooks locally and check them in but not run them on the CI?

i no longer remember which repos have the notebooks actually execute with nbsphinx as part of a docs run, but yes. I thought we were just committing the notebooks here after they'd been run locally

[martinfleis]

I believe no repos execute notebooks but ideally all should.

Check geopandas, we execute everything there. I can check myself tomorrow if needed.

[jGaboardi]

Here's the error I'm seeing locally:

~/github_repos/pysal/pointpats/docs/generated/pointpats.Knox.rst:: ERROR: Anonymous hyperlink mismatch: 2 references but 0 targets.
See "backrefs" attribute for IDs. [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.Knox:59: ERROR: Unknown target name: "ns". [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.Knox:59: ERROR: Unknown target name: "nt". [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.Knox:59: ERROR: Unknown target name: "ns". [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.Knox:59: ERROR: Unknown target name: "nt". [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.KnoxLocal:109: WARNING: Title underline too short.

Examples
------- [docutils]
~/github_repos/pysal/pointpats/docs/generated/pointpats.KnoxLocal.rst:: ERROR: Anonymous hyperlink mismatch: 2 references but 0 targets.
See "backrefs" attribute for IDs. [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.KnoxLocal:68: ERROR: Unknown target name: "ns". [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.KnoxLocal:68: ERROR: Unknown target name: "nt". [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.KnoxLocal:68: ERROR: Unknown target name: "ns". [docutils]
~/github_repos/pysal/pointpats/pointpats/spacetime.py:docstring of pointpats.spacetime.KnoxLocal:68: ERROR: Unknown target name: "nt". [docutils]

Notebook error!

Versions
========

* Platform:         darwin; (macOS-26.2-arm64-arm-64bit-Mach-O)
* Python version:   3.13.9 (CPython)
* Sphinx version:   8.2.3
* Docutils version: 0.21.2
* Jinja2 version:   3.1.6
* Pygments version: 2.19.2

Last Messages
=============

    installation


    reading sources... [ 85%]
    references


    reading sources... [ 87%]
    user-guide/Quadrat_statistics

Loaded Extensions
=================

* sphinx.ext.mathjax (8.2.3)
* alabaster (1.0.0)
* sphinxcontrib.applehelp (2.0.0)
* sphinxcontrib.devhelp (2.0.0)
* sphinxcontrib.htmlhelp (2.1.0)
* sphinxcontrib.serializinghtml (1.1.10)
* sphinxcontrib.qthelp (2.0.0)
* sphinx.ext.autodoc.preserve_defaults (8.2.3)
* sphinx.ext.autodoc.type_comment (8.2.3)
* sphinx.ext.autodoc.typehints (8.2.3)
* sphinx.ext.autodoc (8.2.3)
* sphinx.ext.autosummary (8.2.3)
* sphinx.ext.viewcode (8.2.3)
* sphinxcontrib.bibtex (2.6.5)
* sphinx.ext.doctest (8.2.3)
* sphinx.ext.intersphinx (8.2.3)
* numpydoc (1.10.0)
* matplotlib.sphinxext.plot_directive (3.10.8)
* nbsphinx (0.9.8)

Traceback
=========

      File "~/miniforge3/envs/py313_pointpats-latest/lib/python3.13/site-packages/nbsphinx/__init__.py", line 660, in parse
        raise NotebookError('\n'.join(lines))
    nbsphinx.NotebookError: CellExecutionError in user-guide/Quadrat_statistics.ipynb:
    ------------------
    csr_process = csr(pp_juv.window, pp_juv.n, 999, asPP=True)
    ------------------
    
    
    ---------------------------------------------------------------------------
    TypeError                                 Traceback (most recent call last)
    Cell In[16], line 1
    ----> 1 csr_process = csr(pp_juv.window, pp_juv.n, 999, asPP=True)
    
    File ~/github_repos/pysal/pointpats/pointpats/process.py:252, in PoissonPointProcess.__init__(self, window, n, samples, conditioning, asPP)
        250 def __init__(self, window, n, samples, conditioning=False, asPP=False):
        251     self.conditioning = conditioning
    --> 252     super(PoissonPointProcess, self).__init__(window, n, samples, asPP)
    
    File ~/github_repos/pysal/pointpats/pointpats/process.py:112, in PointProcess.__init__(self, window, n, samples, asPP, **args)
        110 self.setup()
        111 for sample in range(samples):
    --> 112     self.realizations[sample] = self.draw(self.parameters[sample])
        113 if asPP:
        114     for sample in self.realizations:
    
    File ~/github_repos/pysal/pointpats/pointpats/process.py:145, in PointProcess.draw(self, parameter)
        143 while c < n:
        144     pnts = self.realize(n)
    --> 145     pnts = [ps.cg.shapes.Point((x, y)) for x, y in pnts]
        146     pins = self.window.filter_contained(pnts)
        147     sample.extend(pins)
    
    File ~/miniforge3/envs/py313_pointpats-latest/lib/python3.13/site-packages/libpysal/cg/shapes.py:100, in Point.__init__(self, loc)
         98 def __init__(self, loc):
         99     warnings.warn(dep_msg, FutureWarning, stacklevel=2)
    --> 100     self.__loc = tuple(map(float, loc))
    
    TypeError: only 0-dimensional arrays can be converted to Python scalars
    
    You can ignore this error by setting the following in conf.py:
    
        nbsphinx_allow_errors = True

[jGaboardi]

But also throwing a ton of warnings when running make html. Docstrings themselves need some love.

[sjsrey]

I'm able to build the docs locally?

[sjsrey]

Yes, I'm working my way through the warnings :->

[jGaboardi]

I'm able to build the docs locally?

Is this a typo or question?

[sjsrey]

I can build them locally (with the warnings)