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: ``` git clone https://github.com/MDAnalysis/UserGuide cd UserGuide conda env create --file environment.yml --quiet conda activate mda-user-guide cd doc make latexpdf ``` The last command resulted in obtaining many warning and error messages: ``` $ 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 Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/GRO.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TPR.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRZ.txt 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 Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/ITP.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/CONFIG.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TXYZ.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/IN.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/GMS.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/INPCRD.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TOP.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/XML.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PQR.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/TRR.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/HISTORY.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/H5MD.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/PDB.txt Wrote /home/dboczar/UserGuide/doc/source/formats/reference/classes/MMTF.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/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 ---------------------------------------------------------------------------- <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: >>>------------------------------------------------------------------------- Warning in /home/dboczar/UserGuide/doc/source/guessing.rst at block ending on line 35 Specify :okwarning: as an option in the ipython:: block to suppress this message ---------------------------------------------------------------------------- /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 Specify :okwarning: as an option in the ipython:: block to suppress this message ---------------------------------------------------------------------------- /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 Specify :okwarning: as an option in the ipython:: block to suppress this message ---------------------------------------------------------------------------- /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 77 Specify :okwarning: as an option in the ipython:: block to suppress this message ---------------------------------------------------------------------------- /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 Specify :okwarning: as an option in the ipython:: block to suppress this message ---------------------------------------------------------------------------- /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 Specify :okwarning: as an option in the ipython:: block to suppress this message ---------------------------------------------------------------------------- /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 ``` Can I easily fix it?