search

projectmesa / mesa-geo

GIS Extension for Mesa Agent-Based Modeling
Apache License 2.0
159 stars 54 forks source link

docs: RTD build failing due to `jupyter_client.kernelspec.NoSuchKernel` #225

Closed wang-boyu closed 2 months ago

wang-boyu commented 3 months ago

Describe the bug

ReadtheDocs build is failing due to error jupyter_client.kernelspec.NoSuchKernel: No such kernel named mesa_geo

Full Error ```bash Running Sphinx v8.0.2 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist Converting `source_suffix = ['.rst', '.md']` to `source_suffix = {'.rst': 'restructuredtext', '.md': 'restructuredtext'}`. loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) myst-nb v1.1.1: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', execution_mode='cache', execution_cache_path='', execution_excludepatterns=(), execution_timeout=60, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/checkouts/main/_readthedocs/.jupyter_cache building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 17 source files that are out of date updating environment: [new config] 17 added, 0 changed, 0 removed reading sources... [ 6%] README /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 12%] apis/api_main /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 18%] apis/geo_base reading sources... [ 24%] apis/geoagent reading sources... [ 29%] apis/geospace reading sources... [ 35%] apis/raster_layers reading sources... [ 41%] apis/tile_layers reading sources... [ 47%] apis/visualization /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/solara/validate_hooks.py:122: UserWarning: /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/mesa/experimental/jupyter_viz.py:163: JupyterViz: `use_state` found within a nested function created on line 155 To suppress this check, replace the line with: grid_layout, set_grid_layout = solara.use_state(grid_layout_initial) # noqa: SH104 Make sure you understand the consequences of this, by reading about the rules of hooks at: https://solara.dev/documentation/advanced/understanding/rules-of-hooks warnings.warn(str(e)) reading sources... [ 53%] examples/geo_schelling /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 59%] examples/geo_schelling_points /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 65%] examples/geo_sir /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 71%] examples/overview /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 76%] examples/population /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 82%] examples/rainfall /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 88%] examples/urban_growth /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [ 94%] index /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): reading sources... [100%] tutorials/intro_tutorial /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. if path.endswith(suffix): /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/checkouts/main/docs/tutorials/intro_tutorial.ipynb: Executing notebook using local CWD [mystnb] WARNING: autodoc: failed to import module 'modules.__init__' from module 'visualization'; the following exception was raised: No module named 'visualization.modules' [autodoc.import_object] WARNING: autodoc: failed to import module 'modules.MapVisualization' from module 'visualization'; the following exception was raised: No module named 'visualization.modules' [autodoc.import_object] Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/sphinx/cmd/build.py", line 337, in build_main app.build(args.force_all, args.filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/sphinx/application.py", line 378, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/sphinx/builders/__init__.py", line 296, in build_update self.build(to_build, File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/sphinx/builders/__init__.py", line 317, in build updated_docnames = set(self.read()) ^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/sphinx/builders/__init__.py", line 424, in read self._read_serial(docnames) File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/sphinx/builders/__init__.py", line 476, in _read_serial self.read_doc(docname) File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/sphinx/builders/__init__.py", line 535, in read_doc publisher.publish() File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/docutils/core.py", line 234, in publish self.document = self.reader.read(self.source, self.parser, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/sphinx/io.py", line 106, in read self.parse() File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/docutils/readers/__init__.py", line 76, in parse self.parser.parse(self.input, document) File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/sphinx_.py", line 152, in parse with create_client( File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/execute/base.py", line 79, in __enter__ self.start_client() File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/myst_nb/core/execute/cache.py", line 72, in start_client result = single_nb_execution( ^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution executenb( File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/nbclient/client.py", line 1314, in execute return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped return loop.run_until_complete(inner) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.12.3/lib/python3.12/asyncio/base_events.py", line 687, in run_until_complete return future.result() ^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/nbclient/client.py", line 693, in async_execute async with self.async_setup_kernel(**kwargs): File "/home/docs/.asdf/installs/python/3.12.3/lib/python3.12/contextlib.py", line 210, in __aenter__ return await anext(self.gen) ^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/nbclient/client.py", line 648, in async_setup_kernel await self.async_start_new_kernel(**kwargs) File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/nbclient/client.py", line 550, in async_start_new_kernel await ensure_async(self.km.start_kernel(extra_arguments=self.extra_arguments, **kwargs)) File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 198, in ensure_async result = await obj ^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_client/manager.py", line 96, in wrapper raise e File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_client/manager.py", line 87, in wrapper out = await method(self, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_client/manager.py", line 435, in _async_start_kernel kernel_cmd, kw = await self._async_pre_start_kernel(**kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_client/manager.py", line 397, in _async_pre_start_kernel self.kernel_spec, ^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_client/manager.py", line 195, in kernel_spec self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_client/kernelspec.py", line 285, in get_kernel_spec raise NoSuchKernel(kernel_name) jupyter_client.kernelspec.NoSuchKernel: No such kernel named mesa_geo Exception occurred: File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo/envs/main/lib/python3.12/site-packages/jupyter_client/kernelspec.py", line 285, in get_kernel_spec raise NoSuchKernel(kernel_name) jupyter_client.kernelspec.NoSuchKernel: No such kernel named mesa_geo The full traceback has been saved in /tmp/sphinx-err-ycc8zhmq.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. A bug report can be filed in the tracker at . Thanks! ```

Expected behavior

ReadtheDocs should build successfully.

To Reproduce

In the visual environment, install docs dependency:

pip install -e ".[dev]"

Then in the docs folder, run:

python -m sphinx -T -b html -d _build/doctrees -D language=en . html

Additional context

This is likely caused by https://github.com/projectmesa/mesa-geo/blob/5b05dcd29dd1c3d8f9ed893abfb816f0dd53b591/docs/tutorials/intro_tutorial.ipynb#L1112-L1117

I'm not sure whether removing these will have any side effects.

wang-boyu commented 2 months ago

Fixed by https://github.com/projectmesa/mesa-geo/pull/229. Closing.