Wrong parent model assigned when shape command modelId given

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005262323 (2020-05-26 23:23:04 UTC)
Description
shape icos model #1.1

creates a model whose parent should be model #1, but in fact it gets assigned  parent which is the root model. So for instance moving model #1 does not move #1.1.

Log:
Startup Messages  
---  
warnings | QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already
registered  
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "help" already registered  
QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered  
8 messages similar to the above omitted  
Replacing file-saver for 'DCD coordinates' from MDcrds bundle with that from
MD-crds bundle  
Replacing opener for 'Gromacs full-precision coordinates' from MDcrds bundle
with that from MD-crds bundle  
Replacing opener for 'Gromacs compressed coordinates' from MDcrds bundle with
that from MD-crds bundle  
Replacing opener for 'DCD coordinates' from MDcrds bundle with that from MD-
crds bundle  
notes | Replacing data format 'Gromacs full-precision coordinates' as defined
by ChimeraX-MDcrds bundle with definition from ChimeraX-MD-crds bundle  
Replacing data format 'Gromacs compressed coordinates' as defined by ChimeraX-
MDcrds bundle with definition from ChimeraX-MD-crds bundle  
Replacing data format 'DCD coordinates' as defined by ChimeraX-MDcrds bundle
with definition from ChimeraX-MD-crds bundle  
  
UCSF ChimeraX version: 1.0rc202005262323 (2020-05-26)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> shape icosahedron

> shape icosahedron modelId #1.1

> ui mousemode right "translate selected models"




OpenGL version: 4.1 ATI-3.8.24
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: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 17 days 22:05

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

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tom Goddard]

This bug probably effects all commands where a model id can be specified by the user. The Models class when adding a Model with an already set id is not using the id to set the parent. It simply sees the model has no parent and sets its parent to the root model.

[Tom Goddard]

These commands take a model_id argument (ModelIdArg).
shape, marker, volume subcommands that make volumes, struts, measure center, measure inertia, rename

[Tom Goddard]

Fixed in ChimeraX 1.1

Rewrote Models.add() and added extensive error checking to assure model hierarchy is not corrupted.