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.
$ make latexpdf
./source/scripts/generate_all.sh
/home/dboczar/miniconda3/envs/mda-user-guide/bin/python
2.11.0-dev0
2.11.0-dev0
Wrote /home/dboczar/UserGuide/doc/source/formats/format_overview.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMAPP.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMTOPOLOGY.txt
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Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/XPDB.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/XTC.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/DMS.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/DCD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/DATA.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/NCDF.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TNG.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/GSD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/LAMMPSDUMP.txt
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Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/CONFIG.txt
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Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/INPCRD.txt
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Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PQR.txt
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Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/HISTORY.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/H5MD.txt
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Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMSIMULATION.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRC.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/MOL2.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/COOR.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/XYZ.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PDBQT.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/RDKIT.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/CRD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PSF.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRJ.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/LAMMPS.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PARMED.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/CHEMFILES.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/IMD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/selection_exporter_formats.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/protein.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/protein_backbone.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/nucleic.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/nucleic_backbone.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/base.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/nucleic_sugar.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/topology/groupmethods.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/topology/defaults.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/topology_parsers.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/topology/topologyattrs.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/topology/connectivityattrs.txt
Wrote generated/units_table.txt
Running Sphinx v9.1.0
/home/dboczar/miniconda3/envs/mda-user-guide/bin/python
2.11.0-dev0
2.11.0-dev0
Wrote /home/dboczar/UserGuide/doc/source/formats/format_overview.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMAPP.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMSIMULATION.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRC.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PARMED.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/IN.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/H5MD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/NCDF.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/INPCRD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/RDKIT.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PQR.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/DCD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/CRD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/COOR.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/GRO.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TOP.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/HISTORY.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/DMS.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/XYZ.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/LAMMPSDUMP.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/MMTF.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/GMS.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRJ.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/OPENMMTOPOLOGY.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TPR.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/ITP.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TXYZ.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TNG.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/MOL2.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/CONFIG.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/LAMMPS.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PSF.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PDBQT.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/GSD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/XPDB.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/XML.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PDB.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/CHEMFILES.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/DATA.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRZ.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/IMD.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/XTC.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRR.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/selection_exporter_formats.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/protein.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/protein_backbone.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/nucleic.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/nucleic_backbone.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/base.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/selections/nucleic_sugar.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/topology/groupmethods.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/topology/defaults.txt
Wrote /home/dboczar/UserGuide/doc/source/formats/topology_parsers.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/topology/topologyattrs.txt
Wrote /home/dboczar/UserGuide/doc/source/generated/topology/connectivityattrs.txt
Wrote generated/units_table.txt
loading translations [en]... done
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/dboczar/UserGuide/doc/source/references.bib... parsed 35 entries
[autosummary] generating autosummary for: advanced_topology.rst, atomgroup.rst, contributing.rst, contributing_code.rst, contributing_docs.rst, datasets.rst, examples/README.rst, examples/analysis/README.rst, examples/analysis/alignment_and_rms/README.rst, examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb, ..., releases.md, selections.rst, standard_selections.rst, testing.rst, topology_system.rst, trajectories/slicing_trajectories.rst, trajectories/trajectories.rst, trajectories/transformations.rst, units.rst, universe.rst
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
loading intersphinx inventory 'mdanalysis' from https://docs.mdanalysis.org/2.11.0-dev0/objects.inv ...
loading intersphinx inventory 'pytest' from https://docs.pytest.org/en/latest/objects.inv ...
loading intersphinx inventory 'chemfiles' from https://chemfiles.org/chemfiles.py/latest/objects.inv ...
loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ...
myst v5.0.0: 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)
building [mo]: targets for 0 po files that are out of date
writing output... building [latex]: all documents
updating environment: [new config] 116 added, 0 changed, 0 removed
reading sources... [ 20%] examples/analysis/distances_and_contacts/distances_between_atomgrreading sources... [ 21%] examples/analysis/distances_and_contacts/distances_between_selectreading sources... [ 22%] examples/analysis/distances_and_contacts/distances_within_selectireading sources... [ 37%] examples/analysis/trajectory_similarity/clustering_ensemble_similreading sources... [ 39%] examples/analysis/trajectory_similarity/dimension_reduction_ensemreading sources... [ 40%] examples/analysis/trajectory_similarity/harmonic_ensemble_similar/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/auxiliary/EDR.py:350: UserWarning: Could not find unit type for the following units: ['K', 'bar', '', 'nm^3', 'kg/m^3', 'bar nm']
warnings.warn(
reading sources... [100%] universe
/home/dboczar/UserGuide/doc/source/contributing_code.rst:586: WARNING: Duplicate explicit target name: "black". [docutils]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:465: ERROR: Duplicate target name, cannot be used as a unique reference: "black". [docutils]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:465: ERROR: Duplicate target name, cannot be used as a unique reference: "black". [docutils]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:578: ERROR: Duplicate target name, cannot be used as a unique reference: "black". [docutils]
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/README.rst:7: WARNING: duplicate label alignment-and-rms, other instance in /home/dboczar/UserGuide/doc/source/examples/analysis/README.rst
/home/dboczar/UserGuide/doc/source/examples/analysis/hydrogen_bonds/README.rst:7: WARNING: duplicate label hydrogen-bonds, other instance in /home/dboczar/UserGuide/doc/source/examples/analysis/README.rst
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/README.rst:6: WARNING: duplicate label trajectory-similarity, other instance in /home/dboczar/UserGuide/doc/source/examples/analysis/README.rst
WARNING: >>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/formats/auxiliary.rst at block ending on line 282
Specify :okwarning: as an option in the ipython:: block to suppress this message
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<ipython-input-49-1eb00ff78cf2>:1: UserWarning: FigureCanvasAgg is non-interactive, and thus cannot be shown
plt.show()
<<<-------------------------------------------------------------------------
/home/dboczar/UserGuide/doc/source/formats/coordinates.rst:4: WARNING: duplicate label coordinate-readers, other instance in /home/dboczar/UserGuide/doc/source/formats/coordinates.rst
WARNING: >>>-------------------------------------------------------------------------
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/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:296: UserWarning: No coordinate reader found for /home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
warnings.warn(
<<<-------------------------------------------------------------------------
WARNING: >>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line 35
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/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:1940: UserWarning: This Universe has no coordinates
warnings.warn(str(e))
<<<-------------------------------------------------------------------------
WARNING: >>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line 53
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/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:296: UserWarning: No coordinate reader found for /home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
warnings.warn(
<<<-------------------------------------------------------------------------
WARNING: >>>-------------------------------------------------------------------------
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/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:296: UserWarning: No coordinate reader found for /home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
warnings.warn(
<<<-------------------------------------------------------------------------
WARNING: >>>-------------------------------------------------------------------------
Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line None
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/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/coordinates/DCD.py:171: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.
warnings.warn("DCDReader currently makes independent timesteps"
<<<-------------------------------------------------------------------------
/home/dboczar/UserGuide/doc/source/preparing_releases_and_hotfixes.rst:214: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils]
WARNING: >>>-------------------------------------------------------------------------
Warning in <rst_epilogue> at block ending on line 1
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/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/coordinates/DCD.py:171: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.
warnings.warn("DCDReader currently makes independent timesteps"
<<<-------------------------------------------------------------------------
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/dboczar/UserGuide/doc/source/formats/guessers/default.rst: WARNING: document isn't included in any toctree [toc.not_included]
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/aligning_structure_to_another
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/aligning_trajectory.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/aligning_trajectory
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/aligning_trajectory_to_frame.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/aligning_trajectory_to_frame
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/pairwise_rmsd
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/rmsd.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/rmsd
/home/dboczar/UserGuide/doc/source/examples/analysis/alignment_and_rms/rmsf.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/alignment_and_rms/README'], selecting: examples/analysis/alignment_and_rms/README <- examples/analysis/alignment_and_rms/rmsf
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/contacts_custom.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/contacts_custom
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/contacts_native_fraction.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/contacts_native_fraction
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/contacts_q1q2.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/contacts_q1q2
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/contacts_within_cutoff.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/contacts_within_cutoff
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/distances_between_atomgroups.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/distances_between_atomgroups
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/distances_between_selections.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/distances_between_selections
/home/dboczar/UserGuide/doc/source/examples/analysis/distances_and_contacts/distances_within_selection.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/distances_and_contacts/README'], selecting: examples/analysis/distances_and_contacts/README <- examples/analysis/distances_and_contacts/distances_within_selection
/home/dboczar/UserGuide/doc/source/examples/analysis/hydrogen_bonds/hbonds.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/hydrogen_bonds/README'], selecting: examples/analysis/hydrogen_bonds/README <- examples/analysis/hydrogen_bonds/hbonds
/home/dboczar/UserGuide/doc/source/examples/analysis/hydrogen_bonds/hbonds-lifetimes.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/hydrogen_bonds/README'], selecting: examples/analysis/hydrogen_bonds/README <- examples/analysis/hydrogen_bonds/hbonds-lifetimes
/home/dboczar/UserGuide/doc/source/examples/analysis/hydrogen_bonds/hbonds-selections.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/hydrogen_bonds/README'], selecting: examples/analysis/hydrogen_bonds/README <- examples/analysis/hydrogen_bonds/hbonds-selections
/home/dboczar/UserGuide/doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/polymers_and_membranes/README'], selecting: examples/analysis/polymers_and_membranes/README <- examples/analysis/polymers_and_membranes/hole2
/home/dboczar/UserGuide/doc/source/examples/analysis/polymers_and_membranes/polymer.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/polymers_and_membranes/README'], selecting: examples/analysis/polymers_and_membranes/README <- examples/analysis/polymers_and_membranes/polymer
/home/dboczar/UserGuide/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/reduced_dimensions/README'], selecting: examples/analysis/reduced_dimensions/README <- examples/analysis/reduced_dimensions/diffusion_map
/home/dboczar/UserGuide/doc/source/examples/analysis/reduced_dimensions/pca.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/reduced_dimensions/README'], selecting: examples/analysis/reduced_dimensions/README <- examples/analysis/reduced_dimensions/pca
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/average_rdf.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/average_rdf
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/dihedrals.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/dihedrals
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/elastic_network.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/elastic_network
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/helanal.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/helanal
/home/dboczar/UserGuide/doc/source/examples/analysis/structure/site_specific_rdf.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/structure/README'], selecting: examples/analysis/structure/README <- examples/analysis/structure/site_specific_rdf
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/clustering_ensemble_similarity.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/clustering_ensemble_similarity
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/convergence.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/convergence
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/harmonic_ensemble_similarity.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/harmonic_ensemble_similarity
/home/dboczar/UserGuide/doc/source/examples/analysis/trajectory_similarity/psa.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/trajectory_similarity/README'], selecting: examples/analysis/trajectory_similarity/README <- examples/analysis/trajectory_similarity/psa
/home/dboczar/UserGuide/doc/source/examples/analysis/volumetric/density_analysis.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/volumetric/README'], selecting: examples/analysis/volumetric/README <- examples/analysis/volumetric/density_analysis
/home/dboczar/UserGuide/doc/source/examples/analysis/volumetric/linear_density.ipynb: document is referenced in multiple toctrees: ['examples/analysis/README', 'examples/analysis/volumetric/README'], selecting: examples/analysis/volumetric/README <- examples/analysis/volumetric/linear_density
/home/dboczar/UserGuide/doc/source/examples/quickstart.ipynb: document is referenced in multiple toctrees: ['examples/README', 'index'], selecting: index <- examples/quickstart
done
preparing documents... done
copying assets... copying TeX support files... Writing evaluated template result to /home/dboczar/UserGuide/doc/build/latex/Makefile
Writing evaluated template result to /home/dboczar/UserGuide/doc/build/latex/latexmkrc
Writing evaluated template result to /home/dboczar/UserGuide/doc/build/latex/make.bat
Writing evaluated template result to /home/dboczar/UserGuide/doc/build/latex/latexmkjarc
done
copying assets: done
processing mdanalysisuserguide.tex... index
installation
examples/quickstart
faq
examples/README
examples/constructing_universe
examples/transformations/README
examples/transformations/center_protein_in_box
examples/other/README
examples/other/parmed_sim
examples/analysis/alignment_and_rms/README
examples/analysis/alignment_and_rms/aligning_structure_to_another
examples/analysis/alignment_and_rms/aligning_trajectory
examples/analysis/alignment_and_rms/aligning_trajectory_to_frame
examples/analysis/alignment_and_rms/rmsd
examples/analysis/alignment_and_rms/pairwise_rmsd
examples/analysis/alignment_and_rms/rmsf
examples/analysis/distances_and_contacts/README
examples/analysis/distances_and_contacts/distances_between_atomgroups
examples/analysis/distances_and_contacts/distances_between_selections
examples/analysis/distances_and_contacts/distances_within_selection
examples/analysis/distances_and_contacts/contacts_native_fraction
examples/analysis/distances_and_contacts/contacts_q1q2
examples/analysis/distances_and_contacts/contacts_within_cutoff
examples/analysis/distances_and_contacts/contacts_custom
examples/analysis/trajectory_similarity/README
examples/analysis/trajectory_similarity/psa
examples/analysis/trajectory_similarity/harmonic_ensemble_similarity
examples/analysis/trajectory_similarity/clustering_ensemble_similarity
examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity
examples/analysis/trajectory_similarity/convergence
examples/analysis/structure/README
examples/analysis/structure/elastic_network
examples/analysis/structure/average_rdf
examples/analysis/structure/site_specific_rdf
examples/analysis/structure/dihedrals
examples/analysis/structure/helanal
examples/analysis/reduced_dimensions/README
examples/analysis/reduced_dimensions/pca
examples/analysis/reduced_dimensions/diffusion_map
examples/analysis/polymers_and_membranes/README
examples/analysis/polymers_and_membranes/polymer
examples/analysis/polymers_and_membranes/hole2
examples/analysis/volumetric/README
examples/analysis/volumetric/linear_density
examples/analysis/volumetric/density_analysis
releases
universe
atomgroup
groups_of_atoms
selections
topology_system
guessing
trajectories/trajectories
trajectories/slicing_trajectories
trajectories/transformations
units
reading_and_writing
formats/index
formats/auxiliary
formats/selection_exporters
formats/format_reference
formats/reference/chemfiles
formats/reference/config
formats/reference/coor
formats/reference/crd
formats/reference/data
formats/reference/dcd
formats/reference/dcd_lammps
formats/reference/dms
formats/reference/gms
formats/reference/gro
formats/reference/gsd
formats/reference/in
formats/reference/inpcrd
formats/reference/itp
formats/reference/lammpsdump
formats/reference/mmtf
formats/reference/mol2
formats/reference/ncdf
formats/reference/parmed
formats/reference/pdb
formats/reference/pdbqt
formats/reference/pqr
formats/reference/psf
formats/reference/tng
formats/reference/top
formats/reference/tpr
formats/reference/trj
formats/reference/trr
formats/reference/trz
formats/reference/txyz
formats/reference/xml
formats/reference/xpdb
formats/reference/xtc
formats/reference/xyz
examples/analysis/README
examples/analysis/hydrogen_bonds/hbonds
examples/analysis/hydrogen_bonds/hbonds-selections
examples/analysis/hydrogen_bonds/hbonds-lifetimes
examples/analysis/custom_trajectory_analysis
examples/analysis/custom_parallel_analysis
standard_selections
advanced_topology
datasets
contributing
contributing_code
contributing_docs
preparing_releases_and_hotfixes
module_imports
testing
references
resolving references...
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:24: WARNING: undefined label: 'h5md-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:26: WARNING: undefined label: 'imd-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:38: WARNING: undefined label: 'openmmapp-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:39: WARNING: undefined label: 'openmmsimulation-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:40: WARNING: undefined label: 'openmmtopology-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:48: WARNING: undefined label: 'rdkit-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/format_overview.txt:53: WARNING: undefined label: 'trc-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:24: WARNING: undefined label: 'h5md-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:26: WARNING: undefined label: 'imd-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:37: WARNING: undefined label: 'openmmapp-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:38: WARNING: undefined label: 'openmmsimulation-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:43: WARNING: undefined label: 'rdkit-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/formats/coordinate_readers.txt:47: WARNING: undefined label: 'trc-format' [ref.ref]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:719: WARNING: undefined label: 'travis' [ref.ref]
/home/dboczar/UserGuide/doc/source/contributing_code.rst:719: WARNING: undefined label: 'appveyor' [ref.ref]
/home/dboczar/UserGuide/doc/source/testing.rst:108: WARNING: undefined label: 'appveyor' [ref.ref]
/home/dboczar/UserGuide/doc/source/testing.rst:110: WARNING: undefined label: 'travis' [ref.ref]
WARNING: Could not fetch remote image: https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true [429]
WARNING: Could not fetch remote image: https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true [404]
processing mdanalysisuserguide.tex: failed
sphinx-sitemap: No pages generated for sitemap.xml
Versions
========
* Platform: linux; (Linux-6.14.0-37-generic-x86_64-with-glibc2.39)
* Python version: 3.12.13 (CPython)
* Sphinx version: 9.1.0
* Docutils version: 0.22.4
* Jinja2 version: 3.1.6
* Pygments version: 2.19.2
Last Messages
=============
contributing_code
contributing_docs
preparing_releases_and_hotfixes
module_imports
testing
references
resolving references...
processing mdanalysisuserguide.tex: failed
sphinx-sitemap: No pages generated for sitemap.xml
Loaded Extensions
=================
* sphinx.ext.mathjax (9.1.0)
* alabaster (1.0.0)
* sphinxcontrib.applehelp (2.0.0)
* sphinxcontrib.devhelp (2.0.0)
* sphinxcontrib.htmlhelp (2.1.0)
* sphinxcontrib.serializinghtml (1.1.10)
* sphinxcontrib.qthelp (2.0.0)
* sphinx.ext.autodoc (9.1.0)
* sphinx.ext.autosummary (9.1.0)
* sphinx.ext.intersphinx (9.1.0)
* sphinx.ext.ifconfig (9.1.0)
* sphinx.ext.viewcode (9.1.0)
* sphinx.ext.napoleon (9.1.0)
* sphinx.ext.githubpages (9.1.0)
* sphinx_sitemap (2.9.0)
* nbsphinx (0.9.8)
* IPython.sphinxext.ipython_console_highlighting (unknown version)
* IPython.sphinxext.ipython_directive (unknown version)
* sphinxcontrib.bibtex (2.6.5)
* matplotlib.sphinxext.plot_directive (3.10.8)
* mdanalysis_sphinx_theme (1.3.1)
* myst_parser (5.0.0)
Traceback
=========
File "/home/dboczar/miniconda3/envs/mda-user-guide/lib/python3.12/site-packages/sphinx/builders/latex/transforms.py", line 487, in get_footnote_by_reference
raise ValueError(__('No footnote was found for given reference node %r') % node)
ValueError: No footnote was found for given reference node <footnote_reference: <#text: '1'>>
The full traceback has been saved in:
/tmp/sphinx-err-7vm4s53_.log
To report this error to the developers, please open an issue at <https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message can be provided next time.
make: *** [Makefile:31: latexpdf] Error 1
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:
The last command resulted in obtaining many warning and error messages:
Can I easily fix it?