Broken public website
WillemWybo opened this issue · comments
The 'Reference' doesn't show any docstrings, even though my locally built version does.
Can you send me the log output when you build the documentation? It will tell me what is built.
I have no idea, I don't build it, the public website https://neatdend.readthedocs.io/en/latest/. I thought it builds automatically?
But you compared to your local build. That would be interesting. Then I can compare that to the automatic build of rtd such that I can see what is missing.
This is the build log (output of `sh renew-sphinxdoc.sh > log.txt'
rm -rf build/*
rm -rf ghpages_build
rm -rf auto_examples modules
rm -rf reference/generated reference/algorithms/generated reference/classes/generated reference/readwrite/generated
File source/neat.rst already exists, skipping.
File source/neat.channels.rst already exists, skipping.
File source/neat.channels.channelcollection.rst already exists, skipping.
File source/neat.tools.rst already exists, skipping.
File source/neat.tools.fittools.rst already exists, skipping.
File source/neat.tools.plottools.rst already exists, skipping.
File source/neat.tools.simtools.rst already exists, skipping.
File source/neat.tools.simtools.net.rst already exists, skipping.
File source/neat.tools.simtools.neuron.rst already exists, skipping.
File source/neat.tools.simtools.neuron.mech.rst already exists, skipping.
File source/neat.trees.rst already exists, skipping.
File source/modules.rst already exists, skipping.
sphinx-build -b html -d build/doctrees . build/html
Running Sphinx v2.4.3
Copy example notebooks into docs/_tutorials
making output directory... done
[autosummary] generating autosummary for: _tutorials/models.ipynb, _tutorials/morphologies.ipynb, bibliography.rst, citing.rst, credits.rst, developer/code_of_conduct.rst, developer/contribute.rst, developer/gitwash/configure_git.rst, developer/gitwash/development_workflow.rst, developer/gitwash/following_latest.rst, ..., source/neat.rst, source/neat.tools.fittools.rst, source/neat.tools.plottools.rst, source/neat.tools.rst, source/neat.tools.simtools.net.rst, source/neat.tools.simtools.neuron.mech.rst, source/neat.tools.simtools.neuron.rst, source/neat.tools.simtools.rst, source/neat.trees.rst, tutorial.rst
Failed to import 'neat.channels.ionchannels_simplified': no module named neat.channels.ionchannels_simplified
--> Writing mod files
Failed to import 'neat.tools.simtools.net.netsim': no module named neat.tools.simtools.net.netsim
[autosummary] generating autosummary for: /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.createTreeGF.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.createTreeSOV.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.evalChannel.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.fitCapacitance.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.fitChannels.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.fitEEq.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.fitModel.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.fitPassive.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.fitPassiveLeak.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.CompartmentFitter.fitSynRescale.rst, ..., /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.pathBetweenNodes.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.pathBetweenNodesDepthFirst.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.pathToRoot.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.removeNode.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.removeSingleNode.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.resetIndices.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.root.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.sisterLeafs.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.softRemoveNode.rst, /Users/wybo/Code/NEAT_public/docs/reference/generated/neat.STree.upBifurcationNode.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 42 source files that are out of date
updating environment: [new config] 206 added, 0 changed, 0 removed
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build succeeded, 57 warnings.
The HTML pages are in build/html.
Build finished. The HTML pages are in build/html.
Somehow the script still printed stuff to the terminal:
/Users/wybo/Code/NEAT_public/docs/index.rst:113: WARNING: toctree contains reference to nonexisting document 'auto_examples/index'
../INSTALL.rst:14: WARNING: Unexpected indentation.
../INSTALL.rst:25: WARNING: Unexpected indentation.
../INSTALL.rst:29: WARNING: Unexpected indentation.
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.IonChannel.computeDerivatives:12: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.IonChannel.computeDerivativesConc:9: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.IonChannel.setDefaultParams:1: WARNING: Inline strong start-string without end-string.
/Users/wybo/Code/NEAT_public/neat/trees/morphtree.py:docstring of neat.MorphTree._convertNodeArgToNodes:15: WARNING: Unexpected indentation.
/Users/wybo/Code/NEAT_public/neat/trees/morphtree.py:docstring of neat.MorphTree._convertNodeArgToNodes:16: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/trees/netree.py:docstring of neat.NET.getReducedTree:1: WARNING: Inline literal start-string without end-string.
/Users/wybo/Code/NEAT_public/docs/reference/trees.rst:110:<autosummary>:1: WARNING: Inline literal start-string without end-string.
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.IonChannel:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.IonChannel:38: WARNING: Unexpected section title.
Parameters
----------
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.IonChannel:75: WARNING: Unexpected section title.
Examples
--------
/Users/wybo/Code/NEAT_public/docs/reference/trees.rst:352:<autosummary>:1: WARNING: Inline strong start-string without end-string.
WARNING: autodoc: failed to import class 'netsim.NETSim' from module 'neat'; the following exception was raised:
No module named 'neat.netsim'
/Users/wybo/Code/NEAT_public/docs/release/index.rst:17: WARNING: toctree contains reference to nonexisting document 'release/api_0.1'
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.channels.ionchannels.IonChannel:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.channels.ionchannels.IonChannel:38: WARNING: Unexpected section title.
Parameters
----------
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.channels.ionchannels.IonChannel:75: WARNING: Unexpected section title.
Examples
--------
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.channels.ionchannels.IonChannel.computeDerivatives:12: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.channels.ionchannels.IonChannel.computeDerivativesConc:9: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/Users/wybo/Code/NEAT_public/neat/channels/ionchannels.py:docstring of neat.channels.ionchannels.IonChannel.setDefaultParams:1: WARNING: Inline strong start-string without end-string.
WARNING: autodoc: failed to import module 'ionchannels_simplified' from module 'neat.channels'; the following exception was raised:
No module named 'neat.channels.ionchannels_simplified'
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp:12: WARNING: Unexpected indentation.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp:14: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp:18: WARNING: Definition list ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp:28: WARNING: Unexpected indentation.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp:29: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp_vector:9: WARNING: Unexpected indentation.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp_vector:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp_vector:12: WARNING: Unexpected indentation.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp_vector:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp_vector:23: WARNING: Unexpected indentation.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp_vector:24: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.fExpFitter.fitFExp_vector:26: WARNING: Definition list ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.kernelExtractor:15: WARNING: Unknown target name: "vdend".
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.kernelExtractor:15: WARNING: Unknown target name: "vsoma".
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.kernelExtractor:15: WARNING: Unknown target name: "vdend".
/Users/wybo/Code/NEAT_public/neat/tools/kernelextraction.py:docstring of neat.tools.kernelextraction.kernelExtractor:15: WARNING: Unknown target name: "vdend".
/Users/wybo/Code/NEAT_public/neat/tools/fittools/zerofinding.py:docstring of neat.tools.fittools.zerofinding.pf_is_left_vec:10: WARNING: Definition list ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/fittools/zerofinding.py:docstring of neat.tools.fittools.zerofinding.poleFinder.find_zeros_and_poles_:7: WARNING: Unexpected indentation.
/Users/wybo/Code/NEAT_public/neat/tools/fittools/zerofinding.py:docstring of neat.tools.fittools.zerofinding.poleFinder.find_zeros_and_poles_:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/fittools/zerofinding.py:docstring of neat.tools.fittools.zerofinding.poleFinder.find_zeros_and_poles_:10: WARNING: Definition list ends without a blank line; unexpected unindent.
/Users/wybo/Code/NEAT_public/neat/tools/plottools/scalebars.py:docstring of neat.tools.plottools.scalebars.addScalebar:10: WARNING: Inline strong start-string without end-string.
WARNING: autodoc: failed to import module 'netsim' from module 'neat.tools.simtools.net'; the following exception was raised:
No module named 'neat.tools.simtools.net.netsim'
/Users/wybo/Code/NEAT_public/neat/trees/netree.py:docstring of neat.trees.netree.NET.getReducedTree:1: WARNING: Inline literal start-string without end-string.
/Users/wybo/Code/NEAT_public/docs/source/neat.trees.rst:2: WARNING: duplicate object description of neat.trees, other instance in reference/trees, use :noindex: for one of them
/Users/wybo/Code/NEAT_public/docs/release/release_0.1.rst: WARNING: document isn't included in any toctree
/Users/wybo/Code/NEAT_public/docs/source/contents.rst: WARNING: document isn't included in any toctree
/Users/wybo/Code/NEAT_public/docs/source/modules.rst: WARNING: document isn't included in any toctree
/Users/wybo/Code/NEAT_public/docs/index.rst:91: WARNING: unknown document: GNU General Public License
/Users/wybo/Code/NEAT_public/docs/index.rst:133: WARNING: undefined label: glossary (if the link has no caption the label must precede a section header)
/Users/wybo/Code/NEAT_public/neat/trees/stree.py:docstring of neat.STree:: WARNING: more than one target found for cross-reference 'STree.root': neat.STree.root, neat.trees.stree.STree.root
/Users/wybo/Code/NEAT_public/neat/trees/morphtree.py:docstring of neat.MorphTree:: WARNING: more than one target found for cross-reference 'MorphTree.root': neat.MorphTree.root, neat.trees.morphtree.MorphTree.root
/Users/wybo/Code/NEAT_public/neat/trees/morphtree.py:docstring of neat.trees.morphtree.MorphTree:: WARNING: more than one target found for cross-reference 'MorphTree.root': neat.MorphTree.root, neat.trees.morphtree.MorphTree.root
/Users/wybo/Code/NEAT_public/neat/trees/stree.py:docstring of neat.trees.stree.STree:: WARNING: more than one target found for cross-reference 'STree.root': neat.STree.root, neat.trees.stree.STree.root
/usr/local/lib/python3.7/site-packages/sphinx_rtd_theme/search.html:21: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a <script> tag directly in your theme instead.
{% endblock %}
The problem is as simple as that:
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
WARNING: [autosummary] failed to import 'neat.CompartmentFitter.fitChannels': no module named neat.CompartmentFitter.fitChannels
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
WARNING: [autosummary] failed to import 'neat.CompartmentFitter.fitEEq': no module named neat.CompartmentFitter.fitEEq
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py:39: UserWarning: NEURON not available
warnings.warn('NEURON not available', UserWarning)
Source: https://readthedocs.org/projects/neatdend/builds/10987756/
Can you spot it?
Hint: NEURON is not available on the readthedocs build platform.
The problem is that the code comment inspection fails on that in several cases:
File "/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/tools/simtools/neuron/neuronmodel.py", line 10, in <module>
import neuron
ModuleNotFoundError: No module named 'neuron'
There is a typo or something:
File "/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/__init__.py", line 45, in <module>
from .tools.fittools.compartmentfitter import CompartmentFitter
File "/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/tools/fittools/compartmentfitter.py", line 24, in <module>
warnings.warn('NEURON not available', UserWarning)
NameError: name 'warnings' is not defined
There are other warnings about not found imports, but I think it is a consequence of the missing neuron module.
How can we deal with systems which have no neuron module (that means no installation of the neuron simulator, right?)? I think you already had a strategy for that, no?
@jakobj @WillemWybo
I think if we fix this, most of the other errors will go away.
Hmm can we tell readthedocs to ingore this somehow? I'm not sure if there is an easy way to get readthedocs to have NEURON available. Our current strategy is to prevent the import of the NEURON-dependent components when NEURON is not installed.
But why would readthedocs need it to be installed? All it has to do is collect docstrings no?
Nono, it is not meant to be installed there. It seems that you guys import it somewhere as 'import neuron' such that it fails on the readthedocs side. The problem is that python needs to run the code in order to inspect them. So imports are definitely run.
File "/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/tools/fittools/compartmentfitter.py", line 22, in <module>
from ...tools.simtools.neuron import neuronmodel as neurm
File "/home/docs/checkouts/readthedocs.org/user_builds/neatdend/checkouts/latest/neat/tools/simtools/neuron/neuronmodel.py", line 10, in <module>
import neuron
ModuleNotFoundError: No module named 'neuron'
If you want to document the compartmentfitter, it seems that it includes neuron in a too agressive way (without dropping a warning or something). It seems that it is related to the fact that warnings.warn is not available there. I will quickly check if I see the problem and can fix it.
Ok, warnings was not imported before it was used there, so I fixed this quickly without PR.
Checking what happens now when the docs build continues.
Ok, documentation ist back as far as I can see.
The problem of the incorrect latex representations persists.