[Documentation] Error when trying to build PDF documentation file #5281
Description
The documentation of MDAnalyis is utilizing the Sphinx software, consist of ".rst" files, and contains both "conf.py" and "Makefile". It seems that all conditions to create a PDF file containing a user guide are fulfilled. A single PDF file is very useful for printing and when there is a need to work offline.
To create a single PDF file, I performed the following steps:
conda create -n mda-docs python=3.11
conda activate mda-docs
git clone https://github.com/MDAnalysis/mdanalysis.git
cd mdanalysis
git checkout release-2.10.0
cd package
pip install -e .
pip install sphinx sphinx-sitemap "mdanalysis-sphinx-theme>=1.3.0" sphinxcontrib-bibtex pybtex pybtex-docutils
cd doc/sphinx
make SPHINXOPTS="" latexpdf
Unfortunately, the last command produced a lot of warning messages and finally errors:
Running Sphinx v9.0.4
loading translations [en]... locale_dir /home/dboczar/mdanalysis/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist
locale_dir /home/dboczar/mdanalysis/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist
done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
checking bibtex cache... out of date
parsing bibtex file /home/dboczar/mdanalysis/package/doc/sphinx/source/references.bib... parsed 69 entries
locale_dir /home/dboczar/mdanalysis/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist
loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ...
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ...
loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv ...
loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ...
loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv ...
loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ...
loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ...
loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ...
loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ...
loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ...
loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ...
loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
loading intersphinx inventory 'imdclient' from https://imdclient.readthedocs.io/en/stable/objects.inv ...
intersphinx inventory has moved: https://mdanalysis.org/GridDataFormats/objects.inv -> https://www.mdanalysis.org/GridDataFormats/objects.inv
intersphinx inventory has moved: https://mdanalysis.org/pmda/objects.inv -> https://www.mdanalysis.org/pmda/objects.inv
locale_dir /home/dboczar/mdanalysis/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist
building [mo]: targets for 0 po files that are out of date
writing output...
building [latex]: all documents
updating environment: locale_dir /home/dboczar/mdanalysis/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist
[new config] 179 added, 0 changed, 0 removed
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WARNING:root:sklearn.cluster could not be imported: some functionality will not be available in encore.fit_clusters()
/home/dboczar/mdanalysis/package/MDAnalysis/analysis/encore/__init__.py:45: DeprecationWarning: Deprecation in version 2.8.0
MDAnalysis.analysis.encore is deprecated in favour of the MDAKit mdaencore (https://www.mdanalysis.org/mdaencore/) and will be removed in MDAnalysis version 3.0.0.
warnings.warn(wmsg, category=DeprecationWarning)
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/home/dboczar/mdanalysis/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:54: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0.
warnings.warn(wmsg, category=DeprecationWarning)
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/home/dboczar/mdanalysis/package/MDAnalysis/analysis/hole2/__init__.py:50: UserWarning: Please install the mdahole2 mdakit to use it in MDAnalysis.
More details can be found here: https://www.mdanalysis.org/mdahole2/getting_started.html
warnings.warn(wmsg, category=UserWarning)
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/home/dboczar/mdanalysis/package/MDAnalysis/analysis/psa.py:72: UserWarning: Please install the PathSimAnalysis mdakit to use it in MDAnalysis.
More details can be found here: https://www.mdanalysis.org/PathSimAnalysis/getting_started.html
warnings.warn(wmsg, category=UserWarning)
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/home/dboczar/mdanalysis/package/MDAnalysis/analysis/waterdynamics.py:57: UserWarning: Please install the waterdynamics mdakit to use it in MDAnalysis.
More details can be found here: https://www.mdanalysis.org/waterdynamics/getting_started.html
warnings.warn(wmsg, category=UserWarning)
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/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:52: DeprecationWarning: Deprecated in version 2.8.0
MDAnalysis.topology.tables has been moved to MDAnalysis.guesser.tables. This import point will be removed in MDAnalysis version 3.0.0
warnings.warn(wmsg, category=DeprecationWarning)
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/home/dboczar/mdanalysis/package/MDAnalysis/analysis/dssp/dssp.py:docstring of MDAnalysis.analysis.dssp.dssp:25: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils]
WARNING: autodoc: failed to import 'utils' from module 'MDAnalysis.analysis.hole2'; the following exception was raised:
Traceback (most recent call last):
File "/home/dboczar/miniconda3/envs/mda-docs/lib/python3.11/site-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 131, in _import_from_module_and_path
module = _import_module(module_name, try_reload=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dboczar/miniconda3/envs/mda-docs/lib/python3.11/site-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 218, in _import_module
raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'MDAnalysis.analysis.hole2.utils'
[autodoc.import_object]
WARNING: autodoc: failed to import 'templates' from module 'MDAnalysis.analysis.hole2'; the following exception was raised:
Traceback (most recent call last):
File "/home/dboczar/miniconda3/envs/mda-docs/lib/python3.11/site-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 131, in _import_from_module_and_path
module = _import_module(module_name, try_reload=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dboczar/miniconda3/envs/mda-docs/lib/python3.11/site-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 218, in _import_module
raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'MDAnalysis.analysis.hole2.templates'
[autodoc.import_object]
/home/dboczar/mdanalysis/package/MDAnalysis/analysis/msd.py:docstring of MDAnalysis.analysis.msd.EinsteinMSD:40: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/analysis/rdf.py:docstring of MDAnalysis.analysis.rdf.nested_array_sum:13: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/analysis/rdf.py:docstring of MDAnalysis.analysis.rdf.nested_array_sum:14: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/coordinates/PDB.py:docstring of MDAnalysis.coordinates.PDB.PDBReader:68: WARNING: Inline emphasis start-string without end-string. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: ERROR: Unexpected section title.
Notes
----- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:6: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:17: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:31: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:41: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:51: ERROR: Unexpected section title.
Note
---- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:16: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:30: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:39: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:49: ERROR: Unexpected section title.
Note
---- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:30: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:42: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:24: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:36: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:48: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.groups.AtomGroup.fragments:21: ERROR: Unexpected section title.
Note
---- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:16: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:26: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:23: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:28: ERROR: Unexpected section title.
Notes
----- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:19: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:31: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:43: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:29: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:41: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:53: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:6: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:9: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:20: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:9: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:20: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: ERROR: Unexpected section title.
Notes
----- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:6: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:17: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:31: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:41: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:51: ERROR: Unexpected section title.
Note
---- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:16: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:30: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:39: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:49: ERROR: Unexpected section title.
Note
---- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:5: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:16: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:30: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:42: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:24: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:36: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:48: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:16: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:26: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:23: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:28: ERROR: Unexpected section title.
Notes
----- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:9: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:5: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:14: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:5: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:14: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:19: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:31: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:43: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:29: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:41: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:53: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:44: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:64: ERROR: Unexpected section title.
Raises
------ [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:6: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:9: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:20: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:9: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:20: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: ERROR: Unexpected section title.
Notes
----- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:6: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:17: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:31: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:41: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:51: ERROR: Unexpected section title.
Note
---- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:16: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:30: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:39: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:49: ERROR: Unexpected section title.
Note
---- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:30: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:42: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:24: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:36: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:48: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:16: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:26: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:23: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:28: ERROR: Unexpected section title.
Notes
----- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:19: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:31: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:43: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:29: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:41: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:53: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:4: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:6: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:9: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:20: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:9: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:20: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:14: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:25: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:9: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:18: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:5: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:14: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:5: ERROR: Unexpected section title.
Parameters
---------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/groups.py:docstring of MDAnalysis.core.topologyattrs._build_stub.<locals>.stub_method:14: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Inline strong start-string without end-string. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe.models:12: ERROR: Unexpected section title.
Returns
------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/guesser/default_guesser.py:docstring of MDAnalysis.guesser.default_guesser.DefaultGuesser:5: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/doc/sphinx/source/documentation_pages/references.rst:232: ERROR: Unknown directive type "comment".
.. comment::
If you use IMD capability with :mod:`MDAnalysis.coordinates.IMD.py`, please cite [IMDv3paper]_.
.. [IMDv3paper] Authors (YEAR).
IMDv3 Manuscript Title.
*Journal*, 185. doi:`insert-doi-here <https://doi.org/>`_ [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/ExtendedPDBParser.py:docstring of MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser:29: ERROR: Unexpected section title.
See Also
-------- [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/TPRParser.py:docstring of MDAnalysis.topology.TPRParser:46: WARNING: Footnote [*] is not referenced. [ref.footnote]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.atomelements:3: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.atomelements:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.atomelements:7: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.atomelements:8: WARNING: Inline strong start-string without end-string. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.masses:3: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.masses:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.masses:7: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.masses:8: WARNING: Inline strong start-string without end-string. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.vdwradii:3: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.vdwradii:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.vdwradii:7: ERROR: Unexpected indentation. [docutils]
/home/dboczar/mdanalysis/package/MDAnalysis/topology/tables.py:docstring of MDAnalysis.topology.tables.vdwradii:8: WARNING: Inline strong start-string without end-string. [docutils]
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pickling environment... done
checking consistency... done
preparing documents... WARNING: "latex_documents" config value references unknown document MDAnalysis.tex
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build finished with problems, 162 warnings (with warnings treated as errors).
make: *** [Makefile:103: latexpdf] Error 1
'''
Afterwards, I tried another approach, but also without a success :(
MDAnalysis/UserGuide#435
What can I do to fix it and generate a correct PDF file containing the MDAnalysis user guide?