Avoid pages of intimidating orange warning text on Toolshed install

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
The Toolshed should install with minimal logged output unless it fails in which case detailed output would help.

This "Errors maybe have occurred..." and the massive pip standard error and standard out logged in orange is very intimidating and almost all useless except for debugging.  And in this case the install seemed to succeed.

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed install /Users/goddard/Downloads/ChimeraX_ArtiaX-0.1-py3-none-
> any.whl

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application Support/ChimeraX/1.4/site-
packages  
sysconfig: /Users/goddard/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application Support/ChimeraX/1.4/site-
packages  
sysconfig: /Users/goddard/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application
Support/ChimeraX/include/python3.9/pandas  
sysconfig: /Users/goddard/Library/Python/3.9/include/pandas  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application Support/ChimeraX/bin  
sysconfig: /Users/goddard/Library/Python/3.9/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application Support/ChimeraX  
sysconfig: /Users/goddard/Library/Python/3.9  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application
Support/ChimeraX/include/python3.9/superqt  
sysconfig: /Users/goddard/Library/Python/3.9/include/superqt  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application
Support/ChimeraX/include/python3.9/starfile  
sysconfig: /Users/goddard/Library/Python/3.9/include/starfile  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-ArtiaX  
sysconfig: /Users/goddard/Library/Python/3.9/include/ChimeraX-ArtiaX  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/goddard/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /Users/goddard/Library/Python/3.9/include/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 22.2.1 is
available.  
You should consider upgrading via the
'/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip
install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /Users/goddard/Downloads/ChimeraX_ArtiaX-0.1-py3-none-any.whl  
Requirement already satisfied: ChimeraX-SaveCommand>=1.5 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.5.1)  
Collecting starfile  
Downloading starfile-0.4.11-py3-none-any.whl (27 kB)  
Requirement already satisfied: ChimeraX-Log>=1.1.4 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.1.5)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.1 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.1)  
Requirement already satisfied: ChimeraX-Markers~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-ModelPanel>=1.2.1 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.3.2)  
Collecting superqt  
Downloading superqt-0.3.3-py3-none-any.whl (59 kB)  
Requirement already satisfied: ChimeraX-Core>=1.3 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.4)  
Requirement already satisfied: ChimeraX-UI>=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.18.3)  
Requirement already satisfied: ChimeraX-Geometry>=1.1 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.2)  
Requirement already satisfied: ChimeraX-BILD~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.1 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.1)  
Requirement already satisfied: ChimeraX-Atomic>=1.1 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.39.1)  
Requirement already satisfied: ChimeraX-IMOD~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.1 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.1)  
Requirement already satisfied: ChimeraX-OpenCommand>=1.7 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ArtiaX==0.1) (1.9)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.1) (2.0.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.1) (2.7)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.1) (2.0.2)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.1) (2.6.6)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.1) (1.0.2)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.1) (7.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-BILD~=1.0->ChimeraX-ArtiaX==0.1) (1.2.2)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-BILD~=1.0->ChimeraX-ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.1->ChimeraX-ArtiaX==0.1) (2.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.1->ChimeraX-ArtiaX==0.1) (2.0)  
Requirement already satisfied: ChimeraX-StdCommands>=1.3.1,~=1.3 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.1) (1.8)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-OpenCommand>=1.7->ChimeraX-ArtiaX==0.1) (1.0.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI>=1.0->ChimeraX-ArtiaX==0.1) (1.0)  
Collecting pandas  
Downloading pandas-1.4.3-cp39-cp39-macosx_10_9_x86_64.whl (11.5 MB)  
Requirement already satisfied: qtpy>=1.1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from superqt->ChimeraX-ArtiaX==0.1) (2.1.0)  
Requirement already satisfied: typing-extensions>=3.10.0.0 in
/Users/goddard/Library/Application Support/ChimeraX/1.4/site-packages (from
superqt->ChimeraX-ArtiaX==0.1) (4.1.1)  
Requirement already satisfied: packaging in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from superqt->ChimeraX-ArtiaX==0.1) (21.0)  
Requirement already satisfied: pygments>=2.4.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from superqt->ChimeraX-ArtiaX==0.1) (2.11.2)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.1->ChimeraX-
ArtiaX==0.1) (2.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI>=1.0->ChimeraX-
ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands>=1.3.1,~=1.3->ChimeraX-
ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.1) (2.0)  
Requirement already satisfied: pyparsing>=2.0.2 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from packaging->superqt->ChimeraX-ArtiaX==0.1) (3.0.9)  
Requirement already satisfied: pytz>=2020.1 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->starfile->ChimeraX-ArtiaX==0.1) (2022.1)  
Requirement already satisfied: python-dateutil>=2.8.1 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->starfile->ChimeraX-ArtiaX==0.1) (2.8.2)  
Requirement already satisfied: numpy>=1.18.5 in
/Users/goddard/Library/Application Support/ChimeraX/1.4/site-packages (from
pandas->starfile->ChimeraX-ArtiaX==0.1) (1.20.3)  
Requirement already satisfied: six>=1.5 in
./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from python-dateutil>=2.8.1->pandas->starfile->ChimeraX-ArtiaX==0.1)
(1.16.0)  
Installing collected packages: pandas, superqt, starfile, ChimeraX-ArtiaX  
Successfully installed ChimeraX-ArtiaX-0.1 pandas-1.4.3 starfile-0.4.11
superqt-0.3.3  
\---  

Successfully installed ChimeraX-ArtiaX-0.1 pandas-1.4.3 starfile-0.4.11
superqt-0.3.3  
Installed ChimeraX-ArtiaX (0.1)  




OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 451.120.7.0.0
      OS Loader Version: 540.120.3~6
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 65 days 24 minutes

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.1
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-DeepSSETracer: 0.1
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    importlib-metadata: 4.0.1
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.20.3
    openvr: 1.16.802
    packaging: 21.0
    pandas: 1.4.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    starfile: 0.4.11
    suds-community: 1.0.0
    superqt: 0.3.3
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    torch: 1.8.1
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    zipp: 3.7.0

[Greg Couch]

I don't see a good way to make pip less verbose and still be able to debug problems. I suspect that as pip matures, this will be less of an issue. What's problematic here are the lines:

WARNING: Value for scheme.platlib does not match. Please report this to <​https://github.com/pypa/pip/issues/10151>

That is a debugging message for the pip maintainers. Unfortunately, the version of pip used, 21.3.1, is already out of date.

Looking closer at the error, it seems that ChimeraX's Python is finding /Users/goddard/Library/Python/3.9/lib/python/site-packages. That should not happen.

Tom, can you check if your environment might be screwing things up? ChimeraX's application launcher explicitly passes the -I argument, so that shouldn't be the issue. But it might. There is also the chance that some other code in the Python standard library is screwing things up (most likely site.py).

[Zach Pearson]

I saw this error when I was adding a pip bundle (and then moved pip.py to core.commands).

​https://github.com/pypa/pip/issues/10151#issuecomment-1169028558

There's a comment in pip.py from me that says:

                # If we don't add this flag then pip complains that distutils and sysconfig
                # don't report the same location for the user's site packages directory. The
                # error tells programmers to report the error to
                # https://github.com/pypa/pip/issues/10151
                pip_cmd.extend(["--no-warn-script-location"])

so it's just pypa collecting data for where distutils (which they're trying to deprecate) and sysconfig (which they'd much rather you use over distutils.sysconfig) disagree.

toolshed_utils could use the core pip code or add the flag to its own invocations of pip. For simplicity's sake I like the former, but for expediency's sake the latter is fine. Packages go to the correct directories either way.

[Greg Couch]

I'm still worried about the /Users/goddard/Library/Application Support/ChimeraX/1.4/site-packages versus /Users/goddard/Library/Python/3.9/lib/python/site-packages. The latter should not be there.

[Zach Pearson]

May be a non-issue. I commented out the argument in my ChimeraX and attempted to install Pandas:

pip install pandasCollecting pandas
Downloading pandas-1.4.4-cp39-cp39-macosx_11_0_arm64.whl (10.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.5/10.5 MB 38.5 MB/s eta 0:00:00
Requirement already satisfied: numpy>=1.20.0 in /Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from pandas) (1.23.3)
Requirement already satisfied: pytz>=2020.1 in /Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from pandas) (2022.2.1)
Requirement already satisfied: python-dateutil>=2.8.1 in /Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from pandas) (2.8.2)
Requirement already satisfied: six>=1.5 in /Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas) (1.16.0)
Installing collected packages: pandas
Successfully installed pandas-1.4.4

and got no wall of text.

Tom, can you upgrade your ChimeraX's version of pip and see if the issue persists?

[goddard@…]

Here is the Log output installing ArtiaX in today's ChimeraX daily build with clean preferences / cache on the same machine this bug was reported on.  I used menu Tools / More Tools.... Nice concise output.  So I think this problem has been fixed already.  In the bug report ArtiaX was not yet on the Toolshed and so I got a wheel file from the developer and used the command "toolshed install artiax-zzz.whl".  Maybe that command still gives verbose output.  I did not try it.

toolshed show
Downloading bundle ChimeraX_ArtiaX-0.1-py3-none-any.whl
Successfully installed ChimeraX-ArtiaX-0.1 pandas-1.4.4 starfile-0.4.11 superqt-0.3.5 typing-extensions-4.3.0
Installed ChimeraX-ArtiaX (0.1)

[Tom Goddard]

Ticket #7594 shows the same "Errors may have occurred..." with lots of warnings when installing Clipper in ChimeraX 1.4 on Linux.

Install the Clipper bundle to open "MTZ" format files.  
Opener for format 'MTZ' is not installed; see log for more info  
Downloading bundle ChimeraX_Clipper-0.18.0-cp39-cp39-manylinux_2_17_x86_64.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /home/urovsnik/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /home/urovsnik/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/include/python3.9/ChimeraX-
Clipper  
sysconfig: /home/urovsnik/.local/include/python3.9/ChimeraX-Clipper  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/bin  
sysconfig: /home/urovsnik/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX  
sysconfig: /home/urovsnik/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/urovsnik/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 22.2.2 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
./Downloads/ChimeraX_Clipper-0.18.0-cp39-cp39-manylinux_2_17_x86_64.whl  
Requirement already satisfied: ChimeraX-Core~=1.4.dev202203030220 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
Clipper==0.18.0) (1.4)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Clipper==0.18.0) (7.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.36 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Clipper==0.18.0) (1.39.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Clipper==0.18.0) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.2)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.7)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.0.2)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.0.2)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.1)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.6.6)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.2.2)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.5.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.9)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.18.3)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0)  
Requirement already satisfied: ChimeraX-IO~=1.0.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-PDB~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0.1)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.8)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)  
Installing collected packages: ChimeraX-Clipper  
Successfully installed ChimeraX-Clipper-0.18.0  
\---  

Successfully installed ChimeraX-Clipper-0.18.0  
Installed ChimeraX-Clipper (0.18.0)  
Installed ChimeraX-Registration (1.1)  

[Zach Pearson]

The ChimeraX in that ticket has pip 21.3.1, but the version in recent distributions is 22.2.2.

I installed ArtiaX in a daily build:

toolshed install ArtiaX
Successfully installed ChimeraX-ArtiaX-0.1 starfile-0.4.11 superqt-0.3.5 typing-extensions-4.3.0
Installed ChimeraX-ArtiaX (0.1)

toolshed uninstall ArtiaX
unloading module chimerax.artiax
Successfully uninstalled ChimeraX-ArtiaX-0.1
Removed ChimeraX-ArtiaX (0.1)

toolshed install /Users/zjp/Downloads/ChimeraX_ArtiaX-0.1-py3-none-any.whlSuccessfully installed ChimeraX-ArtiaX-0.1
Installed ChimeraX-ArtiaX (0.1)
Replacing data format 'Artiatomi Motivelist' as defined by ChimeraX-ArtiaX with definition from ChimeraX-ArtiaX
Replacing data format 'Generic Particle List' as defined by ChimeraX-ArtiaX with definition from ChimeraX-ArtiaX
Replacing data format 'Dynamo Table' as defined by ChimeraX-ArtiaX with definition from ChimeraX-ArtiaX
Replacing data format 'RELION STAR file' as defined by ChimeraX-ArtiaX with definition from ChimeraX-ArtiaX
Replacing data format 'Coords file' as defined by ChimeraX-ArtiaX with definition from ChimeraX-ArtiaX
Replacing data format 'PEET mod/csv' as defined by ChimeraX-ArtiaX with definition from ChimeraX-ArtiaX
Overriding existing toolbar provider for toolbar provider 'Launch' in bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Help' in bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'XY' in bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'XZ' in bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'YZ' in bundle 'ChimeraX-ArtiaX'

The toolshed code paths used do not include the --no-warn-script-location flag, so I think pip 22.2.2 fixes the error output.

[Zach Pearson]

Or, actually they do. I was going off the error output above and assumed.

[goddard@…]

Looks good with pip 22.2.2!