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holoviz-dev / nbsite

Build a tested, sphinx-based website from notebooks
https://nbsite.pyviz.org
BSD 3-Clause "New" or "Revised" License
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Error when importing pyodide for sphinx documentation build #288

Open timonmerk opened 11 months ago

timonmerk commented 11 months ago

I am following this tutorial (https://panel.holoviz.org/how_to/wasm/sphinx.html), but unfortunately did not manage to build the documentation which show's the panel in sphix due to an import error based on pyodide in nbsite. I included in a rst file the following pyodide block:

.. pyodide::
   import panel
   settings = {"key1" : 5, "key2" : 45}
   settings_panel = panel.pane.JSON(settings, name="JSON")
   settings_panel

and also included the nbsite_pyodide_conf configuration in the sphinx conf.py:

from panel.io.convert import BOKEH_VERSION, MINIMUM_VERSIONS, PY_VERSION
from panel.io.convert import BOKEH_VERSION, MINIMUM_VERSIONS, PY_VERSION
from panel.io.resources import CDN_DIST

def base_version(version: str) -> str:
    """Extract the final release and if available pre-release (alpha, beta,
    release candidate) segments of a PEP440 version, defined with three
    components (major.minor.micro).

    Useful to avoid nbsite/sphinx to display the documentation HTML title
    with a not so informative and rather ugly long version (e.g.
    ``0.13.0a19.post4+g0695e214``). Use it in ``conf.py``::

        version = release = base_version(package.__version__)

    Return the version passed as input if no match is found with the pattern.
    """
    # look at the start for e.g. 0.13.0, 0.13.0rc1, 0.13.0a19, 0.13.0b10
    pattern = r"([\d]+\.[\d]+\.[\d]+(?:a|rc|b)?[\d]*)"
    match = re.match(pattern, version)
    if match:
        return match.group()
    else:
        return version

version = release = base_version(panel.__version__)

if panel.__version__ != version and (PANEL_ROOT / 'dist' / 'wheels').is_dir():
    py_version = panel.__version__.replace("-dirty", "")
    panel_req = f'./wheels/panel-{py_version}-py3-none-any.whl'
    bokeh_req = f'./wheels/bokeh-{BOKEH_VERSION}-py3-none-any.whl'
else:
    panel_req = f'{CDN_DIST}wheels/panel-{PY_VERSION}-py3-none-any.whl'
    bokeh_req = f'{CDN_DIST}wheels/bokeh-{BOKEH_VERSION}-py3-none-any.whl'

def get_requirements():
    with open('pyodide_dependencies.json') as deps:
        dependencies = json.load(deps)
    requirements = {}
    for src, deps in dependencies.items():
        if deps is None:
            continue
        src = src.replace('.ipynb', '').replace('.md', '')
        for name, min_version in MINIMUM_VERSIONS.items():
            if any(name in req for req in deps):
                deps = [f'{name}>={min_version}' if name in req else req for req in deps]
        requirements[src] = deps
    return requirements

nbsite_pyodide_conf = {
    'PYODIDE_URL': 'https://cdn.jsdelivr.net/pyodide/v0.23.1/full/pyodide.js',
    'requirements': [bokeh_req, panel_req, 'pyodide-http'],
    'requires': get_requirements()
}

When trying to run the documentation with make html I get however this error:

Exception occurred: File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\nbsite\pyodide__init__.py", line 257, in run current_source = self.state_machine.get_source() TypeError: StateMachine.get_source() missing 1 required positional argument: 'line_offset'

I checked the official site of pyodide but could not see that the same line is being called.

For compleness here the full traceback from sphinx:

# Sphinx version: 5.3.0
# Python version: 3.10.12 (CPython)
# Docutils version: 0.18.1 release
# Jinja2 version: 3.1.2
# Last messages:
#   reading sources... [ 66%] nm_projection
#   reading sources... [ 70%] nm_rereference
#   reading sources... [ 73%] nm_resample
#   reading sources... [ 76%] nm_run_analysis
#   reading sources... [ 80%] nm_settings
#   reading sources... [ 83%] nm_sharpwaves
#   reading sources... [ 86%] outline_analysis
#   reading sources... [ 90%] outline_featureestimation
#   reading sources... [ 93%] outline_parametrization
#   reading sources... [ 96%] param
# Loaded extensions:
#   sphinx.ext.mathjax (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\mathjax.py
#   sphinxcontrib.applehelp (1.0.4) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinxcontrib\applehelp\__init__.py
#   sphinxcontrib.devhelp (1.0.2) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinxcontrib\devhelp\__init__.py
#   sphinxcontrib.htmlhelp (2.0.1) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinxcontrib\htmlhelp\__init__.py
#   sphinxcontrib.serializinghtml (1.1.5) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinxcontrib\serializinghtml\__init__.py
#   sphinxcontrib.qthelp (1.0.3) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinxcontrib\qthelp\__init__.py
#   alabaster (0.7.13) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\alabaster\__init__.py
#   sphinx.ext.autodoc.preserve_defaults (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\autodoc\preserve_defaults.py
#   sphinx.ext.autodoc.type_comment (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\autodoc\type_comment.py
#   sphinx.ext.autodoc.typehints (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\autodoc\typehints.py
#   sphinx.ext.autodoc (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\autodoc\__init__.py
#   sphinx.ext.autosummary (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\autosummary\__init__.py
#   sphinx.ext.doctest (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\doctest.py
#   sphinx.ext.intersphinx (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\intersphinx.py
#   sphinx.ext.viewcode (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\viewcode.py
#   numpydoc (1.5.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\numpydoc\__init__.py
#   sphinx.ext.napoleon (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\napoleon\__init__.py
#   sphinx.ext.autosectionlabel (5.3.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\ext\autosectionlabel.py
#   sphinx_gallery.gen_gallery (0.13.0) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx_gallery\gen_gallery.py
#   nbsphinx (0.9.2) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\nbsphinx\__init__.py
#   recommonmark (0.7.1) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\recommonmark\__init__.py
#   nbsite.pyodide (0.5) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\nbsite\pyodide\__init__.py
#   pydata_sphinx_theme (unknown version) from C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\pydata_sphinx_theme\__init__.py
Traceback (most recent call last):
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\cmd\build.py", line 281, in build_main
    app.build(args.force_all, args.filenames)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\application.py", line 347, in build
    self.builder.build_update()
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\builders\__init__.py", line 310, in build_update
    self.build(to_build,
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\builders\__init__.py", line 326, in build
    updated_docnames = set(self.read())
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\builders\__init__.py", line 433, in read
    self._read_serial(docnames)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\builders\__init__.py", line 454, in _read_serial
    self.read_doc(docname)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\builders\__init__.py", line 510, in read_doc
    publisher.publish()
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\core.py", line 217, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\io.py", line 104, in read
    self.parse()
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\readers\__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\sphinx\parsers.py", line 78, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 170, in run
    results = StateMachineWS.run(self, input_lines, input_offset,
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\statemachine.py", line 240, in run
    context, next_state, result = self.check_line(
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\statemachine.py", line 452, in check_line
    return method(match, context, next_state)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 2779, in underline
    self.section(title, source, style, lineno - 1, messages)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 327, in section
    self.new_subsection(title, lineno, messages)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 393, in new_subsection
    newabsoffset = self.nested_parse(
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 281, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 196, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\statemachine.py", line 240, in run
    context, next_state, result = self.check_line(
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\statemachine.py", line 452, in check_line
    return method(match, context, next_state)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 2352, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 2364, in explicit_construct
    return method(self, expmatch)
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 2101, in directive
    return self.run_directive(
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\docutils\parsers\rst\states.py", line 2151, in run_directive
    result = directive_instance.run()
  File "C:\Users\ICN_admin\Anaconda3\envs\pynm-test\lib\site-packages\nbsite\pyodide\__init__.py", line 257, in run
    current_source = self.state_machine.get_source()
TypeError: StateMachine.get_source() missing 1 required positional argument: 'line_offset'