Opened 4 years ago

Last modified 4 years ago

#5675 assigned defect

Problems with links in Sphinx-generated help

Reported by: Tristan Croll Owned by: Greg Couch
Priority: normal Milestone:
Component: Documentation Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202111182158 (2021-11-18 21:58:36 UTC)
Description
New issue with auto-linking commands to their documentation: for a command including capitals (e.g. the camel-case "isolde write phenixRefineInput" the link generated in the log by "usage isolde" wants to go to user/commands/isolde.html#write-phenixRefineInput ... but defining this target in RestructuredText:

.. _`write phenixRefineInput`:


isolde write phenixRefineInput
==============================


... leads to an all-lowercase anchor in the generated html:

<section id="isolde-write-phenixrefineinput">
<span id="write-phenixrefineinput"></span><h2>isolde write phenixRefineInput<a class="headerlink" href="#isolde-write-phenixrefineinput" title="Permalink to this headline">¶</a></h2>

I guess I can work around this by making the different options into an enum argument to a generic "isolde write" command.


Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> usage isolde write

isolde write phenixRefineInput model [modelFileName a file name]
[paramFileName a file name] [includeHydrogens true or false] [numProcessors an
integer] [numMacrocycles an integer] [nqhFlips true or false] [scatteringType
scatteringType]  
— Write input files for phenix.refine, restraining the model to its current
geometry.  
scatteringType: one of electron, neutron, or xray

isolde write phenixRsrInput model resolution volume [modelFileName a file
name] [paramFileName a file name] [restrainPositions true or false]
[includeHydrogens true or false]  
— Write input files for phenix.real_space_refine, restraining the model to its
current geometry.  
resolution: a number

isolde write refmacRestraints model [distanceCutoff a number] [includeWaters
true or false] [fileName a file name]  
— Write REFMAC input to restrain a model to its current geometry  

> usage isolde

Subcommands are:

  * isolde add aa
  * isolde add ligand
  * isolde add water
  * isolde adjust bfactors
  * isolde adjust distances
  * isolde adjust torsions
  * isolde cisflip
  * isolde demo
  * isolde ignore
  * isolde ~ignore
  * isolde jumpto
  * isolde mod his
  * isolde parameterise
  * isolde pepflip
  * isolde release distances
  * isolde release torsions
  * isolde remote rest info
  * isolde remote rest start
  * isolde remote rest stop
  * isolde remote xmlrpc
  * isolde replace ligand
  * isolde report
  * isolde reset forcefield
  * isolde restrain distances
  * isolde restrain ligands
  * isolde restrain single distance
  * isolde restrain torsions
  * isolde select
  * isolde set
  * isolde shorthand
  * isolde sim
  * isolde start
  * isolde stepto
  * isolde tutorial
  * isolde write phenixRefineInput
  * isolde write phenixRsrInput
  * isolde write refmacRestraints

  

> ui tool show Shell




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    -himerax-clipper: 0.17.0
    -himerax-isolde: 1.3.dev33
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.2
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202111182158
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev33
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.22
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    python-igraph: 0.9.7
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    texttable: 1.6.4
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (6)

in reply to:  1 ; comment:1 by Tristan Croll, 4 years ago 

Easier workaround: can insert the necessary tag into the RestructuredText file as raw html:

.. raw:: html

  <span id="write-phenixRefineInput"></span>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 24 November 2021 13:07
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #5675: ChimeraX bug report submission

#5675: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Windows-10-10.0.19041
 ChimeraX Version: 1.3rc202111182158 (2021-11-18 21:58:36 UTC)
 Description
 New issue with auto-linking commands to their documentation: for a command
 including capitals (e.g. the camel-case "isolde write phenixRefineInput"
 the link generated in the log by "usage isolde" wants to go to
 user/commands/isolde.html#write-phenixRefineInput ... but defining this
 target in RestructuredText:

 .. _`write phenixRefineInput`:


 isolde write phenixRefineInput
 ==============================


 ... leads to an all-lowercase anchor in the generated html:

 <section id="isolde-write-phenixrefineinput">
 <span id="write-phenixrefineinput"></span><h2>isolde write
 phenixRefineInput<a class="headerlink" href="#isolde-write-
 phenixrefineinput" title="Permalink to this headline">¶</a></h2>

 I guess I can work around this by making the different options into an
 enum argument to a generic "isolde write" command.


 Log:
 > isolde shorthand


     Initialising ISOLDE-specific command aliases:
     Alias       Equivalent full command
     -------------------------------------------------
     st  isolde step {arguments}
     aw  isolde add water {arguments}
     awsf        isolde add water {arguments} sim false
     al  isolde add ligand {arguments}
     aa  isolde add aa $1 sel {arguments}
     ht  isolde mod his sel {arguments}
     so  setattr sel atoms occupancy {arguments}
     ab  isolde adjust bfactors {arguments}
     ss  isolde sim start sel
     rt  isolde release torsions sel {arguments}
     rd  isolde release distances sel {arguments}
     ra  rd; rt
     pf  isolde pepflip sel
     cf  isolde cisflip sel
     cbb color bfactor {arguments}
     cbo color byattr occupancy {arguments}
     cbc color {arguments} bychain; color {arguments} byhet
     cs  clipper set contourSensitivity {arguments}



 UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > usage isolde write

 isolde write phenixRefineInput model [modelFileName a file name]
 [paramFileName a file name] [includeHydrogens true or false]
 [numProcessors an
 integer] [numMacrocycles an integer] [nqhFlips true or false]
 [scatteringType
 scatteringType]
 — Write input files for phenix.refine, restraining the model to its
 current
 geometry.
 scatteringType: one of electron, neutron, or xray

 isolde write phenixRsrInput model resolution volume [modelFileName a file
 name] [paramFileName a file name] [restrainPositions true or false]
 [includeHydrogens true or false]
 — Write input files for phenix.real_space_refine, restraining the model to
 its
 current geometry.
 resolution: a number

 isolde write refmacRestraints model [distanceCutoff a number]
 [includeWaters
 true or false] [fileName a file name]
 — Write REFMAC input to restrain a model to its current geometry

 > usage isolde

 Subcommands are:

   * isolde add aa
   * isolde add ligand
   * isolde add water
   * isolde adjust bfactors
   * isolde adjust distances
   * isolde adjust torsions
   * isolde cisflip
   * isolde demo
   * isolde ignore
   * isolde ~ignore
   * isolde jumpto
   * isolde mod his
   * isolde parameterise
   * isolde pepflip
   * isolde release distances
   * isolde release torsions
   * isolde remote rest info
   * isolde remote rest start
   * isolde remote rest stop
   * isolde remote xmlrpc
   * isolde replace ligand
   * isolde report
   * isolde reset forcefield
   * isolde restrain distances
   * isolde restrain ligands
   * isolde restrain single distance
   * isolde restrain torsions
   * isolde select
   * isolde set
   * isolde shorthand
   * isolde sim
   * isolde start
   * isolde stepto
   * isolde tutorial
   * isolde write phenixRefineInput
   * isolde write phenixRsrInput
   * isolde write refmacRestraints



 > ui tool show Shell




 OpenGL version: 3.3.0 NVIDIA 471.11
 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Notebook
 Model: P7xxTM1
 OS: Microsoft Windows 10 Education (Build 19041)
 Memory: 68,654,501,888
 MaxProcessMemory: 137,438,953,344
 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
 OSLanguage: en-GB
 Locale: ('en_GB', 'cp1252')
 PyQt5 5.15.2, Qt 5.15.2
 Installed Packages:
     -himerax-clipper: 0.17.0
     -himerax-isolde: 1.3.dev33
     alabaster: 0.7.12
     appdirs: 1.4.4
     Babel: 2.9.1
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2021.10.8
     cftime: 1.5.1.1
     charset-normalizer: 2.0.7
     ChimeraX-AddCharge: 1.2
     ChimeraX-AddH: 2.1.10
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.2.3
     ChimeraX-AlphaFold: 1.0
     ChimeraX-AltlocExplorer: 1.0.1
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.30.2
     ChimeraX-AtomicLibrary: 4.1.5
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 2.0
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.6
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.1
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.2
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.2.2
     ChimeraX-Clipper: 0.17.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.5
     ChimeraX-CommandLine: 1.1.5
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.3rc202111182158
     ChimeraX-CoreFormats: 1.1
     ChimeraX-coulombic: 1.3.1
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.2.2
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.5
     ChimeraX-DistUI: 1.0
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0
     ChimeraX-FunctionKey: 1.0
     ChimeraX-Geometry: 1.1
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 1.1
     ChimeraX-Hbonds: 2.1.2
     ChimeraX-Help: 1.2
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.1
     ChimeraX-ImageFormats: 1.2
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0.1
     ChimeraX-ISOLDE: 1.3.dev33
     ChimeraX-ItemsInspection: 1.0
     ChimeraX-Label: 1.1
     ChimeraX-ListInfo: 1.1.1
     ChimeraX-Log: 1.1.4
     ChimeraX-LookingGlass: 1.1
     ChimeraX-Maestro: 1.8.1
     ChimeraX-Map: 1.1
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.1
     ChimeraX-Markers: 1.0
     ChimeraX-Mask: 1.0
     ChimeraX-MatchMaker: 2.0.4
     ChimeraX-MDcrds: 2.6
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.4
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.2.6
     ChimeraX-ModelPanel: 1.2.1
     ChimeraX-ModelSeries: 1.0
     ChimeraX-Mol2: 2.0
     ChimeraX-Morph: 1.0
     ChimeraX-MouseModes: 1.1
     ChimeraX-Movie: 1.0
     ChimeraX-Neuron: 1.0
     ChimeraX-Nucleotides: 2.0.2
     ChimeraX-OpenCommand: 1.7
     ChimeraX-PDB: 2.6.5
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0.2
     ChimeraX-PDBMatrices: 1.0
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0.1
     ChimeraX-PubChem: 2.1
     ChimeraX-ReadPbonds: 1.0.1
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.1
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0.1
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.5
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.4.6
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0
     ChimeraX-Shortcuts: 1.1
     ChimeraX-ShowAttr: 1.0
     ChimeraX-ShowSequences: 1.0
     ChimeraX-SideView: 1.0
     ChimeraX-Smiles: 2.1
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.6.1
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-Struts: 1.0
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.1
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.1
     ChimeraX-ToolshedUtils: 1.2
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.13.7
     ChimeraX-uniprot: 2.2
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.0.1
     ChimeraX-VIPERdb: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.4
     comtypes: 1.1.10
     cxservices: 1.1
     cycler: 0.11.0
     Cython: 0.29.24
     decorator: 5.1.0
     docutils: 0.17.1
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 3.6.0
     html2text: 2020.1.16
     idna: 3.3
     ihm: 0.21
     imagecodecs: 2021.4.28
     imagesize: 1.3.0
     ipykernel: 5.5.5
     ipython: 7.23.1
     ipython-genutils: 0.2.0
     jedi: 0.18.0
     Jinja2: 3.0.1
     jupyter-client: 6.1.12
     jupyter-core: 4.9.1
     kiwisolver: 1.3.2
     lxml: 4.6.3
     lz4: 3.1.3
     MarkupSafe: 2.0.1
     matplotlib: 3.4.3
     matplotlib-inline: 0.1.3
     msgpack: 1.0.2
     netCDF4: 1.5.7
     networkx: 2.6.3
     numexpr: 2.7.3
     numpy: 1.21.2
     openvr: 1.16.801
     packaging: 21.3
     ParmEd: 3.2.0
     parso: 0.8.2
     pickleshare: 0.7.5
     Pillow: 8.3.2
     pip: 21.2.4
     pkginfo: 1.7.1
     prompt-toolkit: 3.0.22
     psutil: 5.8.0
     pycollada: 0.7.1
     pydicom: 2.1.2
     Pygments: 2.10.0
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 3.0.6
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.2
     python-igraph: 0.9.7
     pytz: 2021.3
     pywin32: 228
     pyzmq: 22.3.0
     qtconsole: 5.1.1
     QtPy: 1.11.2
     RandomWords: 0.3.0
     requests: 2.26.0
     scipy: 1.7.1
     setuptools: 57.5.0
     sfftk-rw: 0.7.1
     six: 1.16.0
     snowballstemmer: 2.2.0
     sortedcontainers: 2.4.0
     Sphinx: 4.2.0
     sphinx-autodoc-typehints: 1.12.0
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     sphinxcontrib-devhelp: 1.0.2
     sphinxcontrib-htmlhelp: 2.0.0
     sphinxcontrib-jsmath: 1.0.1
     sphinxcontrib-qthelp: 1.0.3
     sphinxcontrib-serializinghtml: 1.1.5
     suds-jurko: 0.6
     tables: 3.6.1
     texttable: 1.6.4
     tifffile: 2021.4.8
     tinyarray: 1.2.3
     tornado: 6.1
     traitlets: 5.1.1
     urllib3: 1.26.7
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.37.0
     wheel-filename: 1.3.0
     WMI: 1.5.1

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5675>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Tristan Croll, 4 years ago

Platform: → all
Project: → ChimeraX

In a similar vein, Sphinx also doesn't like "~" in reference names:

.. _`~ignore`

... just gets converted to a generic <span id="id2"></span>

Not really ChimeraX bugs, I suppose - just limitations of Sphinx that need to be worked around by people using that to generate their documentation.

comment:3 by pett, 4 years ago

Cc: chimera-programmers added
Component: Unassigned → Documentation
Owner: set to Greg Couch
Status: new → assigned
Summary: ChimeraX bug report submission → Problems with links in Sphinx-generated help

comment:4 by Tom Goddard, 4 years ago

I strongly suggest not twisting your code (ie changing your isolde command parsing) in order to work around bugs in Sphinx. There must be better ways to handle it. For instance, ChimeraX generates the links it puts in the log and can look for the camel-case Sphinx links and make them lower case.

in reply to:  5 ; comment:5 by Tristan Croll, 4 years ago 

Yeah - I changed my mind on that pretty quickly. But it’s easy enough to add the offending anchors as raw html in the .rst.

in reply to:  6 ; comment:6 by goddard@…, 4 years ago 

Yeah, adding the raw anchors in .rst may be the best short-term solution.  Filing a bug report with Sphinx would be a good community service if time permits.
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