make install in bundles should reinstall even if version did not change

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202101220301 (2021-01-22 03:01:58 UTC)
Description
Using "make install" in bundles/read_pbonds gives an error saying it is already installed.  This  should not be an error -- it should reinstall it.  I have been fighting with our build system the last half hour -- very bad.  I guess it sees the version has not changed so it doesn't install now.  This is a major pain and should be returned to the previous working behavior.


make install
../../../ChimeraX.app/Contents/bin/ChimeraX --nogui --safemode --exit --cmd "devel install . user false exit true  "
0.00% done: Initializing core
50.00% done: Initializing bundles
Executing: devel install . user false exit true  
Bundle renamed to 'ChimeraX-Read-Pbonds' after replacing underscores with hyphens.
running build
running build_py
creating build
creating build/lib
creating build/lib/chimerax
creating build/lib/chimerax/read_pbonds
copying src/__init__.py -> build/lib/chimerax/read_pbonds
copying src/readpbonds.py -> build/lib/chimerax/read_pbonds
running bdist_wheel
installing to build/bdist.macosx-10.9-x86_64/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-x86_64
creating build/bdist.macosx-10.9-x86_64/wheel
creating build/bdist.macosx-10.9-x86_64/wheel/chimerax
creating build/bdist.macosx-10.9-x86_64/wheel/chimerax/read_pbonds
copying build/lib/chimerax/read_pbonds/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/chimerax/read_pbonds
copying build/lib/chimerax/read_pbonds/readpbonds.py -> build/bdist.macosx-10.9-x86_64/wheel/chimerax/read_pbonds
running install_egg_info
running egg_info
creating ChimeraX_Read_Pbonds.egg-info
writing ChimeraX_Read_Pbonds.egg-info/PKG-INFO
writing dependency_links to ChimeraX_Read_Pbonds.egg-info/dependency_links.txt
writing requirements to ChimeraX_Read_Pbonds.egg-info/requires.txt
writing top-level names to ChimeraX_Read_Pbonds.egg-info/top_level.txt
writing manifest file 'ChimeraX_Read_Pbonds.egg-info/SOURCES.txt'
reading manifest file 'ChimeraX_Read_Pbonds.egg-info/SOURCES.txt'
writing manifest file 'ChimeraX_Read_Pbonds.egg-info/SOURCES.txt'
Copying ChimeraX_Read_Pbonds.egg-info to build/bdist.macosx-10.9-x86_64/wheel/ChimeraX_Read_Pbonds-1.0-py3.8.egg-info
running install_scripts
creating build/bdist.macosx-10.9-x86_64/wheel/ChimeraX_Read_Pbonds-1.0.dist-info/WHEEL
creating 'dist/ChimeraX_Read_Pbonds-1.0-py3-none-any.whl' and adding 'build/bdist.macosx-10.9-x86_64/wheel' to it
adding 'chimerax/read_pbonds/__init__.py'
adding 'chimerax/read_pbonds/readpbonds.py'
adding 'ChimeraX_Read_Pbonds-1.0.dist-info/METADATA'
adding 'ChimeraX_Read_Pbonds-1.0.dist-info/WHEEL'
adding 'ChimeraX_Read_Pbonds-1.0.dist-info/top_level.txt'
adding 'ChimeraX_Read_Pbonds-1.0.dist-info/RECORD'
removing build/bdist.macosx-10.9-x86_64/wheel
Distribution is in ./dist/ChimeraX_Read_Pbonds-1.0-py3-none-any.whl
Executing: toolshed install ./dist/ChimeraX_Read_Pbonds-1.0-py3-none-any.whl userOnly false
Traceback (most recent call last):
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/devel.py", line 162, in _run
    unbound_method(bb, *args, **kw)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/bundle_builder/bundle_builder.py", line 118, in make_install
    run(session, cmd)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36, in run
    results = command.run(text, log=log, return_json=return_json)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run
    result = ci.function(session, **kw_args)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/toolshed.py", line 301, in toolshed_install
    ts.install_bundle(bundles, logger, **kw)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/toolshed/__init__.py", line 898, in install_bundle
    _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/toolshed_utils/__init__.py", line 219, in _install_bundle
    raise ToolshedInstalledError("bundle %r already installed" % bundle_name)
chimerax.core.toolshed.ToolshedInstalledError: bundle './dist/ChimeraX_Read_Pbonds-1.0-py3-none-any.whl' already installed


make: *** [install] Error 1
$ 

Log:
UI Theme  
UCSF ChimeraX version: 1.2.dev202101220301 (2021-01-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 42 days 21:34

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PySide2 version: 5.15.2
Qt version: 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    biopython: 1.78
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.3.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.10.5
    ChimeraX-AtomicLibrary: 1.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202101220301
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    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-themes: 0.3
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.4.1
    ChimeraX-uniprot: 2.1
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
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    h5py: 2.10.0
    html2text: 2020.1.16
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    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
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    ipython-genutils: 0.2.0
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    msgpack: 1.0.0
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    networkx: 2.5
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    pip: 20.3.1
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    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

[Greg Couch]

It works when reinstalling the help viewer bundle. Will investigate.

[Greg Couch]

The bug due to code in toolshed.find_bundle that changes ChimeraX-Read-Pbonds to ChimeraX-ReadPbonds, ie., no second dash. The comment is: "put the below kludge in to allow sessions saved before some bundles got renamed to restore". That was added by Eric on 2020-05-20. Since ChimeraX-Read-Pbonds was never renamed, I've deleted that line. I'm not sure why those kludges are there since there is a supersedes attribute for <BundleInfo> for that scenario.

[Eric Pettersen]

I made those changes so that bundles uniformly used camel case for their bundle name, so that I didn't have to keep referring back to other bundles to see if their names used dashes, underscores, or no spaces in their name while I was declaring dependencies for my own bundle.

There is no documented supersedes attribute for the <BundleInfo> tag. There is one for the obsolete Bundle ChimeraX metadata classifier. The actual toolshed code says that the supersedes tag is deprecated.

For consistency I will probably restore the ReadPbonds kludge and change the bundle name.

[Eric Pettersen]

Went ahead and renamed Read-Pbonds to ReadPbonds