Code cells not rendered under 0.4.0

Question

Code cells not rendered under 0.4.0

CommonClimate opened this issue 2 years ago · 11 comments

Hi,
I'm trying to switch the Pyleoclim to use jupyter-sphinx instead of IPython directives to execute our code and produce figures for the docs. Having installed jupyter-sphinx 0.4.0, I've modified our conf.py file so the extensions now list jupyter_sphinx as per your updated instructions, and the doc build (with Sphinx 5.3.0) fails with the following error message:

Exception occurred:
File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/jupyter_sphinx/ast.py", line 46, in load_content
raise OSError(f"File {filename} not found or reading it failed")
OSError: File /Users/julieneg/Documents/GitHub/Pyleoclim_util/doc_build/core/python not found or reading it failed
The full traceback has been saved in /var/folders/bf/_x19bm694857h_hrw44j0p7w0000gn/T/sphinx-err-bpckb7ne.log, if you want to report the issue to the developers.

If I revert to jupyter_sphinx.execute in conf.py, the doc does build, but the HTML is blank where there should be jupyter cells (code and figures).(I'd share the HTML output, but GitHub doesn't allow that). I've set SPHINXOPTS=-v but I get no error message, so it's hard to diagnose the problem. Any tips on how to troubleshoot?

Answer 1 · 2022-12-18T15:35:10.000Z

For a start, do you observe the same problem when building e.g. jupyter-sphinx docs in your environment?

Answer 2 · 2022-12-19T04:22:11.000Z

Thank you for the prompt action @akhmerov . Indeed, this is for a local build using Python 3.10.8. Here are the contents of my environment.yml file.

A MWE is this:

.. jupyter-execute:: 
            
            data = pd.read_csv('https://raw.githubusercontent.com/LinkedEarth/Pyleoclim_util/Development/example_data/soi_data.csv',skiprows=0,header=1)
            ts = pyleo.Series(time=data.iloc[:,1], value=data.iloc[:,2], time_name='Year C.E', value_name='SOI', label='SOI')
            ssa = ts.ssa()
            
            fig, ax = ssa.modeplot()
            pyleo.closefig(fig)

(where pd is the standard pandas alias, and pyleo resolves to "pyleoclim", our package, cited above. However, I'm pretty sure any Matplotlib command would reproduce the problem)

Let me know if you need any other information.

packages

name: pyleo310
channels:

conda-forge
defaults
dependencies:
_ipython_minor_entry_point=8.7.0=hb6b4a82_0
alabaster=0.7.12=py_0
anyio=3.6.2=pyhd8ed1ab_0
appnope=0.1.3=pyhd8ed1ab_0
argon2-cffi=21.3.0=pyhd8ed1ab_0
argon2-cffi-bindings=21.2.0=py310h90acd4f_3
asttokens=2.2.1=pyhd8ed1ab_0
attrs=22.1.0=pyh71513ae_1
babel=2.11.0=pyhd8ed1ab_0
backcall=0.2.0=pyh9f0ad1d_0
backports=1.0=pyhd8ed1ab_3
backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
beautifulsoup4=4.11.1=pyha770c72_0
bleach=5.0.1=pyhd8ed1ab_0
brotli=1.0.9=hb7f2c08_8
brotli-bin=1.0.9=hb7f2c08_8
brotlipy=0.7.0=py310h90acd4f_1005
bzip2=1.0.8=h0d85af4_4
c-ares=1.18.1=h0d85af4_0
ca-certificates=2022.12.7=h033912b_0
cartopy=0.21.1=py310h578c2b2_0
certifi=2022.12.7=pyhd8ed1ab_0
cffi=1.15.1=py310ha78151a_3
charset-normalizer=2.1.1=pyhd8ed1ab_0
colorama=0.4.6=pyhd8ed1ab_0
comm=0.1.2=pyhd8ed1ab_0
contourpy=1.0.6=py310ha23aa8a_0
cryptography=38.0.4=py310hdd0c95c_0
cycler=0.11.0=pyhd8ed1ab_0
debugpy=1.6.4=py310h7a76584_0
decorator=5.1.1=pyhd8ed1ab_0
defusedxml=0.7.1=pyhd8ed1ab_0
entrypoints=0.4=pyhd8ed1ab_0
executing=1.2.0=pyhd8ed1ab_0
flit-core=3.8.0=pyhd8ed1ab_0
fonttools=4.38.0=py310h90acd4f_1
freetype=2.12.1=h3f81eb7_1
geos=3.11.1=hf0c8a7f_0
gettext=0.21.1=h8a4c099_0
glib=2.74.1=hbc0c0cd_1
glib-tools=2.74.1=hbc0c0cd_1
gst-plugins-base=1.21.2=h37e1711_0
gstreamer=1.21.2=h1d18e73_0
icu=70.1=h96cf925_0
idna=3.4=pyhd8ed1ab_0
imagesize=1.4.1=pyhd8ed1ab_0
importlib-metadata=5.1.0=pyha770c72_0
importlib_resources=5.10.1=pyhd8ed1ab_0
ipykernel=6.19.2=pyh736e0ef_0
ipython=8.7.0=pyhd1c38e8_0
ipython_genutils=0.2.0=py_1
ipywidgets=8.0.3=pyhd8ed1ab_0
jedi=0.18.2=pyhd8ed1ab_0
jinja2=3.1.2=pyhd8ed1ab_1
jpeg=9e=hac89ed1_2
jsonschema=4.17.3=pyhd8ed1ab_0
jupyter=1.0.0=py310h2ec42d9_8
jupyter_client=7.4.8=pyhd8ed1ab_0
jupyter_console=6.4.4=pyhd8ed1ab_0
jupyter_core=5.1.0=py310h2ec42d9_0
jupyter_events=0.5.0=pyhd8ed1ab_0
jupyter_server=2.0.1=pyhd8ed1ab_0
jupyter_server_terminals=0.4.2=pyhd8ed1ab_0
jupyter_sphinx=0.4.0=py310h2ec42d9_1
jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
jupyterlab_widgets=3.0.4=pyhd8ed1ab_0
kiwisolver=1.4.4=py310ha23aa8a_1
krb5=1.19.3=hb98e516_0
lcms2=2.14=h90f4b2a_0
lerc=4.0.0=hb486fe8_0
libblas=3.9.0=16_osx64_openblas
libbrotlicommon=1.0.9=hb7f2c08_8
libbrotlidec=1.0.9=hb7f2c08_8
libbrotlienc=1.0.9=hb7f2c08_8
libcblas=3.9.0=16_osx64_openblas
libclang=15.0.6=default_h20dc2f0_0
libclang13=15.0.6=default_hc4b5f92_0
libcurl=7.86.0=h581aaea_1
libcxx=14.0.6=hccf4f1f_0
libdeflate=1.14=hb7f2c08_0
libedit=3.1.20191231=h0678c8f_2
libev=4.33=haf1e3a3_1
libffi=3.4.2=h0d85af4_5
libgfortran=5.0.0=11_3_0_h97931a8_27
libgfortran5=11.3.0=h082f757_27
libglib=2.74.1=h4c723e1_1
libiconv=1.17=hac89ed1_0
liblapack=3.9.0=16_osx64_openblas
libllvm15=15.0.6=h7001e86_0
libnghttp2=1.47.0=h5aae05b_1
libogg=1.3.4=h35c211d_1
libopenblas=0.3.21=openmp_h429af6e_3
libopus=1.3.1=hc929b4f_1
libpng=1.6.39=ha978bb4_0
libpq=15.1=hb1ae2b1_1
libsodium=1.0.18=hbcb3906_1
libsqlite=3.40.0=ha978bb4_0
libssh2=1.10.0=h47af595_3
libtiff=4.4.0=hdb44e8a_4
libvorbis=1.3.7=h046ec9c_0
libwebp-base=1.2.4=h775f41a_0
libxcb=1.13=h0d85af4_1004
libxml2=2.10.3=hb9e07b5_0
libzlib=1.2.13=hfd90126_4
llvm-openmp=15.0.6=h61d9ccf_0
markupsafe=2.1.1=py310h90acd4f_2
matplotlib-base=3.6.2=py310he725631_0
matplotlib-inline=0.1.6=pyhd8ed1ab_0
mistune=2.0.4=pyhd8ed1ab_0
munkres=1.1.4=pyh9f0ad1d_0
mysql-common=8.0.31=hc4b2c72_0
mysql-libs=8.0.31=h8658499_0
nbclassic=0.4.8=pyhd8ed1ab_0
nbclient=0.7.2=pyhd8ed1ab_0
nbconvert=7.2.6=pyhd8ed1ab_0
nbconvert-core=7.2.6=pyhd8ed1ab_0
nbconvert-pandoc=7.2.6=pyhd8ed1ab_0
nbformat=5.7.0=pyhd8ed1ab_0
nbsphinx=0.8.10=pyhd8ed1ab_0
ncurses=6.3=h96cf925_1
nest-asyncio=1.5.6=pyhd8ed1ab_0
notebook=6.5.2=pyha770c72_1
notebook-shim=0.2.2=pyhd8ed1ab_0
nspr=4.35=hea0b92c_0
nss=3.78=ha8197d3_0
numpy=1.23.5=py310h1b7c290_0
numpydoc=1.5.0=pyhd8ed1ab_0
openjpeg=2.5.0=h5d0d7b0_1
openssl=3.0.7=hfd90126_1
packaging=22.0=pyhd8ed1ab_0
pandoc=2.19.2=h694c41f_1
pandocfilters=1.5.0=pyhd8ed1ab_0
parso=0.8.3=pyhd8ed1ab_0
pcre2=10.40=h1c4e4bc_0
pexpect=4.8.0=pyh1a96a4e_2
pickleshare=0.7.5=py_1003
pillow=9.2.0=py310hffcf78b_3
pip=22.3.1=pyhd8ed1ab_0
pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
platformdirs=2.6.0=pyhd8ed1ab_0
proj=9.1.0=hcbd9701_0
prometheus_client=0.15.0=pyhd8ed1ab_0
prompt-toolkit=3.0.36=pyha770c72_0
prompt_toolkit=3.0.36=hd8ed1ab_0
psutil=5.9.4=py310h90acd4f_0
pthread-stubs=0.4=hc929b4f_1001
ptyprocess=0.7.0=pyhd3deb0d_0
pure_eval=0.2.2=pyhd8ed1ab_0
pycparser=2.21=pyhd8ed1ab_0
pygments=2.13.0=pyhd8ed1ab_0
pyopenssl=22.1.0=pyhd8ed1ab_0
pyparsing=3.0.9=pyhd8ed1ab_0
pyproj=3.4.1=py310h8c678d5_0
pyqt=5.15.7=py310hdd03f62_2
pyqt5-sip=12.11.0=py310h415000c_2
pyrsistent=0.19.2=py310h90acd4f_0
pyshp=2.3.1=pyhd8ed1ab_0
pysocks=1.7.1=pyha2e5f31_6
python=3.10.8=he7542f4_0_cpython
python-dateutil=2.8.2=pyhd8ed1ab_0
python-fastjsonschema=2.16.2=pyhd8ed1ab_0
python-json-logger=2.0.1=pyh9f0ad1d_0
python.app=1.4=py310h90acd4f_1
python_abi=3.10=3_cp310
pytz=2022.6=pyhd8ed1ab_0
pyyaml=6.0=py310h90acd4f_5
pyzmq=24.0.1=py310hf615a82_1
qt-main=5.15.6=h0916ed4_4
qtconsole=5.4.0=pyhd8ed1ab_0
qtconsole-base=5.4.0=pyha770c72_0
qtpy=2.3.0=pyhd8ed1ab_0
readline=8.1.2=h3899abd_0
requests=2.28.1=pyhd8ed1ab_1
scipy=1.9.3=py310h240c617_2
send2trash=1.8.0=pyhd8ed1ab_0
setuptools=65.5.1=pyhd8ed1ab_0
shapely=2.0.0=py310h4e43f2a_0
sip=6.7.5=py310h7a76584_0
six=1.16.0=pyh6c4a22f_0
sniffio=1.3.0=pyhd8ed1ab_0
snowballstemmer=2.2.0=pyhd8ed1ab_0
soupsieve=2.3.2.post1=pyhd8ed1ab_0
sphinx=5.3.0=pyhd8ed1ab_0
sphinxcontrib-applehelp=1.0.2=py_0
sphinxcontrib-devhelp=1.0.2=py_0
sphinxcontrib-htmlhelp=2.0.0=pyhd8ed1ab_0
sphinxcontrib-jsmath=1.0.1=py_0
sphinxcontrib-qthelp=1.0.3=py_0
sphinxcontrib-serializinghtml=1.1.5=pyhd8ed1ab_2
sqlite=3.40.0=h9ae0607_0
stack_data=0.6.2=pyhd8ed1ab_0
terminado=0.17.1=pyhd1c38e8_0
tinycss2=1.2.1=pyhd8ed1ab_0
tk=8.6.12=h5dbffcc_0
toml=0.10.2=pyhd8ed1ab_0
tornado=6.2=py310h90acd4f_1
traitlets=5.7.1=pyhd8ed1ab_0
typing_extensions=4.4.0=pyha770c72_0
tzdata=2022g=h191b570_0
unicodedata2=15.0.0=py310h90acd4f_0
urllib3=1.26.13=pyhd8ed1ab_0
wcwidth=0.2.5=pyh9f0ad1d_2
webencodings=0.5.1=py_1
websocket-client=1.4.2=pyhd8ed1ab_0
wheel=0.38.4=pyhd8ed1ab_0
widgetsnbextension=4.0.4=pyhd8ed1ab_0
xorg-libxau=1.0.9=h35c211d_0
xorg-libxdmcp=1.1.3=h35c211d_0
xz=5.2.6=h775f41a_0
yaml=0.2.5=h0d85af4_2
zeromq=4.3.4=he49afe7_1
zipp=3.11.0=pyhd8ed1ab_0
zstd=1.5.2=hfa58983_4
pip:
- bagit==1.8.1
- cython==0.29.32
- demjson3==3.0.6
- dill==0.3.6
- docutils==0.17.1
- joblib==1.2.0
- lipd==0.2.8.8
- llvmlite==0.39.1
- multiprocess==0.70.14
- networkx==2.8.8
- nibabel==4.0.2
- nitime==0.9
- numba==0.56.4
- pandas==1.5.2
- pathos==0.3.0
- patsy==0.5.3
- ply==3.11
- pox==0.3.2
- ppft==1.7.6.6
- pyhht==0.1.0
- readthedocs-sphinx-search==0.1.2
- scikit-learn==1.2.0
- seaborn==0.12.1
- sphinx-rtd-theme==1.1.1
- statsmodels==0.13.5
- tabulate==0.9.0
- tftb==0.1.4
- threadpoolctl==3.1.0
- tqdm==4.64.1
- unidecode==1.3.6
- wget==3.2
- xlrd==2.0.1

Answer 3 · 2022-12-19T11:56:48.000Z

I've tried building the jupyter-sphinx docs with the latest sphinx, and I cannot reproduce the issue, so it should be working at least in the simplest setting. Could this be something about the theme you are using or so?

Unfortunately your MWE is neither minimal nor working, please see an example guideline. I don't have the bandwidth to install the pyleoclim development environment. To figure out what goes wrong I would also need a minimal conf.py and an index.rst that reproduces the failure. Please also exclude the packages that aren't relevant for the error from the environment.

Answer 4 · 2022-12-19T19:43:05.000Z

Fair enough. The issue with making a truly minimal working example is that our documentation is very large, so whittling it down to what you want is a challenge.

Instead, I cloned your repo to experiment locally, editing jupyter-sphinx's conf.py so that it is very similar to pyleoclim's (same sphinx extensions, same html theme, etc). So far everything runs as it should for your doc, but not mine. That rules out basic bugs, but it doesn't tell me why mine fails.

The main difference I can spot is that in pyleoclim, the code cells to render/execute are embedded in docstrings, which are parsed by sphinx.ext.autodoc. As far as I can see, that is not the case for your documentation, so it is my leading hypothesis for the source of the bug. A telling sign is that building your doc generates a "jupyter" directory that contains a .py file, a .ipynb file and a png file for the inline figure generated; that folder and similar files never get created when I build my doc with .. jupyter-execute:: in my source code's docstrings (and the jupyter-execute directive in conf.py, naturally).

Your doc says that " jupyter-execute may also be used in docstrings within your Python code, and will be executed
when they are included with Sphinx autodoc." Have you tested that using Sphinx 5.3.0 and jupyter-sphinx 0.4.0?

I tried an example where I added this section to your index.rst file

SsaRes (pyleoclim.SsaRes)
"""""""""""""""""""""""""

.. autoclass:: pyleoclim.core.ssares.SsaRes
   :members:

then ran Sphinx (using make clean html). I got the following error message, which may be related to something more basic, but that's where I got stuck:

# Sphinx version: 5.3.0
# Python version: 3.10.8 (CPython)
# Docutils version: 0.19 
# Jinja2 version: 3.1.2
# Last messages:
#   Running Sphinx v5.3.0
# Loaded extensions:
#   sphinx.ext.mathjax (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/mathjax.py
#   sphinxcontrib.applehelp (1.0.2) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinxcontrib/applehelp/__init__.py
#   sphinxcontrib.devhelp (1.0.2) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinxcontrib/devhelp/__init__.py
#   sphinxcontrib.htmlhelp (2.0.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinxcontrib/htmlhelp/__init__.py
#   sphinxcontrib.serializinghtml (1.1.5) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinxcontrib/serializinghtml/__init__.py
#   sphinxcontrib.qthelp (1.0.3) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinxcontrib/qthelp/__init__.py
#   alabaster (0.7.12) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/alabaster/__init__.py
#   sphinx.ext.autodoc.preserve_defaults (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/autodoc/preserve_defaults.py
#   sphinx.ext.autodoc.type_comment (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/autodoc/type_comment.py
#   sphinx.ext.autodoc.typehints (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/autodoc/typehints.py
#   sphinx.ext.autodoc (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py
#   sphinx.ext.doctest (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/doctest.py
#   sphinx.ext.viewcode (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/viewcode.py
#   sphinx.ext.coverage (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/coverage.py
#   sphinx.ext.autosummary (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/autosummary/__init__.py
#   sphinx.ext.intersphinx (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/intersphinx.py
#   sphinx.ext.napoleon (5.3.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/napoleon/__init__.py
#   jupyter_sphinx (0.4.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/jupyter_sphinx/__init__.py
#   matplotlib.sphinxext.plot_directive (3.6.2) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/matplotlib/sphinxext/plot_directive.py
#   IPython.sphinxext.ipython_console_highlighting (unknown version) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/IPython/sphinxext/ipython_console_highlighting.py
#   IPython.sphinxext.ipython_directive (unknown version) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/IPython/sphinxext/ipython_directive.py
#   numpydoc (1.5.0) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/numpydoc/__init__.py
#   sphinx_search.extension (0.1.2) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx_search/extension.py
#   sphinx_rtd_theme (unknown version) from /Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx_rtd_theme/__init__.py
Traceback (most recent call last):
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/jupyter_sphinx/ast.py", line 43, in load_content
    with Path(filename).open() as f:
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/pathlib.py", line 1119, in open
    return self._accessor.open(self, mode, buffering, encoding, errors,
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julieneg/Documents/GitHub/jupyter-sphinx/doc/source/python'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/cmd/build.py", line 281, in build_main
    app.build(args.force_all, args.filenames)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/application.py", line 347, in build
    self.builder.build_update()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 310, in build_update
    self.build(to_build,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 326, in build
    updated_docnames = set(self.read())
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 433, in read
    self._read_serial(docnames)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 454, in _read_serial
    self.read_doc(docname)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 510, in read_doc
    publisher.publish()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/core.py", line 224, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/io.py", line 104, in read
    self.parse()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/readers/__init__.py", line 76, in parse
    self.parser.parse(self.input, document)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/parsers.py", line 78, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 169, in run
    results = StateMachineWS.run(self, input_lines, input_offset,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2785, in underline
    self.section(title, source, style, lineno - 1, messages)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 325, in section
    self.new_subsection(title, lineno, messages)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 391, in new_subsection
    newabsoffset = self.nested_parse(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 279, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2785, in underline
    self.section(title, source, style, lineno - 1, messages)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 325, in section
    self.new_subsection(title, lineno, messages)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 391, in new_subsection
    newabsoffset = self.nested_parse(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 279, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2355, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2367, in explicit_construct
    return method(self, expmatch)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2104, in directive
    return self.run_directive(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2154, in run_directive
    result = directive_instance.run()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/autodoc/directive.py", line 159, in run
    result = parse_generated_content(self.state, params.result, documenter)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/ext/autodoc/directive.py", line 106, in parse_generated_content
    state.nested_parse(content, 0, node)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 279, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2355, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2367, in explicit_construct
    return method(self, expmatch)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2104, in directive
    return self.run_directive(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2154, in run_directive
    result = directive_instance.run()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/domains/__init__.py", line 281, in run
    return super().run()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/directives/__init__.py", line 263, in run
    nested_parse_with_titles(self.state, self.content, contentnode)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/util/nodes.py", line 340, in nested_parse_with_titles
    return state.nested_parse(content, 0, node, match_titles=1)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 279, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2357, in explicit_markup
    self.explicit_list(blank_finish)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2382, in explicit_list
    newline_offset, blank_finish = self.nested_list_parse(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 316, in nested_list_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2660, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2367, in explicit_construct
    return method(self, expmatch)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2104, in directive
    return self.run_directive(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2154, in run_directive
    result = directive_instance.run()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/domains/__init__.py", line 281, in run
    return super().run()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/directives/__init__.py", line 263, in run
    nested_parse_with_titles(self.state, self.content, contentnode)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/sphinx/util/nodes.py", line 340, in nested_parse_with_titles
    return state.nested_parse(content, 0, node, match_titles=1)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 279, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2355, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2367, in explicit_construct
    return method(self, expmatch)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2104, in directive
    return self.run_directive(
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2154, in run_directive
    result = directive_instance.run()
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/jupyter_sphinx/ast.py", line 136, in run
    content = load_content(self, location, logger)
  File "/Users/julieneg/opt/miniconda3/envs/pyleo310/lib/python3.10/site-packages/jupyter_sphinx/ast.py", line 46, in load_content
    raise OSError(f"File {filename} not found or reading it failed")
OSError: File /Users/julieneg/Documents/GitHub/jupyter-sphinx/doc/source/python not found or reading it failed

Sorry if this is trivial or useless to you ; it seems like a path is not correctly specified, but I cannot figure out how to fix this. The pyleoclim package is already imported in conf.py, but perhaps autodoc requires the source code to be in the same folder? Do you know what is going on? I'd appreciate any help.
Best,
Julien

Answer 5 · 2022-12-19T19:58:16.000Z

I still cannot reproduce the issue.

I've done the following:

Add sphinx.ext.autodoc to conf.py of jupyter-sphinx.
Add .. autoclass:: jupyter_sphinx.ast.JupyterWidgetStateNode somewhere in the index.rst
Extend the docstring of jupyter_sphinx.ast.JupyterWidgetStateNode with

  .. jupyter-execute::

      print("hello")

I then build the docs and see

Answer 6 · 2022-12-19T20:00:42.000Z

Come to think of it, the code branch that yields the errors is a part of the literal include option; are you doing anything with literal includes?

Answer 7 · 2022-12-19T21:17:59.000Z

With apologies for the silly question: what do you mean by "literal includes"?

Answer 8 · 2022-12-19T21:26:01.000Z

Nvm. I found this, which seems relevant. My doc build obviously is triggering that branch of load_content(), but I am not consciously using any literal includes, so my autoclass call (or something else in pyleoclim's docstrings) must be calling that under the hood.

Here's what I added to the jupyter-sphinx index.rst:

Jupyter Sphinx Extension
========================

.. toctree::
   :maxdepth: 2
   :caption: Contents:

Jupyter-sphinx is a Sphinx extension that executes embedded code in a Jupyter
kernel, and embeds outputs of that code in the document. It has support
for rich output such as images, Latex math and even javascript widgets, and
it allows to enable `thebelab <https://thebelab.readthedocs.io/>`_ for live
code execution with minimal effort.

Installation
------------
Get jupyter-sphinx from pip:

.. code-block:: bash

  pip install jupyter-sphinx

or conda:

.. code-block:: bash

  conda install jupyter_sphinx -c conda-forge

SsaRes (pyleoclim.SsaRes)
-------------------------

.. autoclass:: pyleoclim.core.ssares.SsaRes
   :members:


Enabling the extension
----------------------

To enable the extension, add ``jupyter_sphinx`` to your enabled extensions in
``conf.py``:

.. code-block:: python

   extensions = [
      'jupyter_sphinx',
   ]

Answer 9 · 2022-12-19T21:31:06.000Z

(in between Installation and Enabling the extension).
If you want to see how the docstrings of SsaRes are defined, look here

Answer 10 · 2023-12-05T06:50:25.000Z

@CommonClimate is this issue still a problem or can it be considered as solved ?

Answer 11 · 2023-12-05T18:30:42.000Z

Thank you for following up. My amazing student @jordanplanders managed to resolve this issue back in June, and our documentation now proudly uses jupyter-sphinx. Thanks for the amazing work!