Clipper installation

[Tristan Croll]

The following bug report has been submitted:
Platform:        macOS-12.7-arm64-arm-64bit
ChimeraX Version: 1.7.dev202309270131 (2023-09-27 01:31:04 UTC)
Description
Something seems to be wrong with Toolshed dependency resolution in the latest Mac daily builds (seems fine in Linux and Windows). Despite the fact that Clipper 0.22.0 is installed and working, trying to "toolshed install" the matching ISOLDE version fails with "Error: No matching distribution found for ChimeraX-Clipper ~=0.22.0". I did notice the below little bit of weirdness ("No bundles were installed") when doing "devel install" on Clipper from the command line, but I'm not sure if that's actually related. I do note that the directory layout has changed since 1.6, and wonder if that has something to do with it:

~/Library/Application\ Support/ChimeraX/1.6/site-packages/ 
~/Library/Application\ Support/ChimeraX/1.7/lib/python/site-packages/ 

removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in ./dist/ChimeraX_Clipper-0.22.0-cp311-cp311-macosx_10_13_universal2.whl
Installing bundle
Executing: toolshed install ./dist/ChimeraX_Clipper-0.22.0-cp311-cp311-macosx_10_13_universal2.whl reinstall true
No bundles were installed
Installed ChimeraX-Clipper (0.22.0)


Executing: exit
Exiting ... 

Log:
> isolde shorthand

Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand  
UCSF ChimeraX version: 1.7.dev202309270131 (2023-09-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed install
> ./ChimeraX_ISOLDE-1.7.dev0-cp311-cp311-macosx_10_13_universal2.whl

ERROR: Could not find a version that satisfies the requirement ChimeraX-
Clipper~=0.22.0 (from chimerax-isolde) (from versions: none)  
ERROR: No matching distribution found for ChimeraX-Clipper~=0.22.0  
  

> open 3io0 structureFactors true

Summary of feedback from opening 3io0 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Resolution: 3.003  
Launching live xmap mgr took 1.1706490516662598 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 28,26,26, pixel 0.963, shown at
level 0.0948, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 28,26,26, pixel 0.963, shown at
level -0.0565,0.0565, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 28,26,26, pixel 0.963,
shown at level 0.346, step 1, values float32  
3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description | UniProt  
1.2/A | EtuB protein | A5N734_CLOK5 75-304  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> toolshed list

List of installed bundles:  

  * AddCharge (1.5.11): Add partial charges to atoms
  * AddH (2.2.5): Add hydrogens
  * AlignmentAlgorithms (2.0.1): Sequence alignment algorithms
  * AlignmentHdrs (3.4.1): Alignment header support
  * AlignmentMatrices (2.1): Sequence alignment similarity matrices
  * Alignments (2.11.1): Sequence alignment support
  * AlphaFold (1.0): Predict or fetch AlphaFold structures
  * AltlocExplorer (1.1.1): Examine/change alternate atomic locations
  * AmberInfo (1.0): Provide information about AmberTools installation
  * Arrays (1.1): C++ library for parsing numpy arrays
  * Atomic (1.48): Atomic-structure functionality
  * AtomicLibrary (10.1): Atomic-structure C++ library
  * AtomSearch (2.0.1): 3D atom search
  * AxesPlanes (2.3.2): Depict axes or planes
  * BasicActions (1.1.2): Basic actions for user-defined specifier names
  * BILD (1.0): BILD file reader
  * BlastProtein (2.1.2): Search PDB/NR/AlphaFold using BLAST
  * BondRot (2.0.4): Bond rotation support
  * BugReporter (1.0.1): Report bugs when an error occurs
  * BuildStructure (2.10.5): Create/modify structures
  * Bumps (1.0): Find protrusions in density maps
  * ButtonPanel (1.0.1): Create custom user interface panels
  * CageBuilder (1.0.1): Build polygonal meshes for oligomeric molecular assemblies
  * CellPack (1.0): Fetch cellPACK models from web
  * Centroids (1.3.2): Depict centroid of atoms
  * ChangeChains (1.0.3): Change chain IDs
  * CheckWaters (1.3.1): Check water placement in maps
  * ChemGroup (2.0.1): Detect chemically functional groups
  * Clashes (2.2.4): Find clashes/contacts in structures
  * Clipper (0.22.0): Clipper: Efficient handling of volumetric data and symmetry
  * ColorActions (1.0.3): Simple interface for coloring objects
  * ColorGlobe (1.0): Show directional resolution colored sphere
  * ColorKey (1.5.4): Add color key to graphics
  * CommandLine (1.2.5): Command line support
  * ConnectStructure (2.0.1): Add bonds to structures that lack them
  * Contacts (1.0.1): Display chain contact maps
  * Core (1.7.dev202309270131): ChimeraX Core Package
  * CoreFormats (1.2): ChimeraX session support
  * coulombic (1.4.2): Compute/show electrostatic potential
  * Crosslinks (1.0): Analyze crosslinks
  * Crystal (1.0): Crystal symmetries
  * CrystalContacts (1.0.1): Show contacting asymmetric units in a crystal
  * DataFormats (1.2.3): Data format management
  * Dicom (1.2): Read medical imaging and segmentations in DICOM format
  * DistMonitor (1.4): Interactive distance display
  * DockPrep (1.1.2): Prepare structures for docking
  * Dssp (2.0): Compute/assign secondary structure
  * EMDB-SFF (1.0): EMDB SFF file reader
  * ESMFold (1.0): Predict or fetch ESMFold structures
  * FileHistory (1.0.1): File History Panel
  * FunctionKey (1.0.1): Assign function keys to run commands
  * Geometry (1.3): Vector and coordinate system routines
  * gltf (1.0): Read/write glTF 3d scene files
  * Graphics (1.1.1): OpenGL graphics rendering
  * Hbonds (2.4): Identify hydrogen bonds in and among structures
  * Help (1.2.2): Show ChimeraX Help
  * HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
  * IHM (1.1): Integrative Hybrid Models file reader
  * ImageFormats (1.2): Support for saving images
  * IMOD (1.0): IMOD model file reader
  * IO (1.0.1): Python convenience input/output functions
  * ItemsInspection (1.0.1): Inspection of attributes of a set of items
  * IUPAC (1.0): IUPAC fetch
  * Label (1.1.8): Add text labels to graphics
  * ListInfo (1.2.1): Report attributes for selected atomic data
  * Log (1.1.6): Log support
  * LookingGlass (1.1): LookingGlass holographic display
  * Maestro (1.9.1): Maestro reader
  * Map (1.1.4): Density maps
  * MapData (2.0): Volume data file formats
  * MapEraser (1.0.1): Map eraser
  * MapFilter (2.0.1): Operations on maps
  * MapFit (2.0): Fit molecules into maps
  * MapSeries (2.1.1): Volume series
  * Markers (1.0.1): Place markers on density maps
  * Mask (1.0.2): Mask a volume to a surface
  * MatchMaker (2.1.2): Superimpose structures
  * MCopy (1.0): Copy atomic structure attributes to another structure
  * MDcrds (2.6): Molecular dynamics support
  * MedicalToolbar (1.0.2): Toolbar for medical image analysis
  * Meeting (1.0.1): Shared interactive VR sessions.
  * MLP (1.1.1): Molecular lipophilicity calculation
  * mmCIF (2.12.1): mmCIF format read/write
  * MMTF (2.2): MMTF format read/write
  * Modeller (1.5.12): Interface to Modeller
  * ModelPanel (1.4): ChimeraX Model Panel
  * ModelSeries (1.0.1): Display sequences of models one by one
  * Mol2 (2.0.3): Mol2 reader/writer
  * Mole (1.0): Open JSON tunnel files from Mole
  * Morph (1.0.2): Morph atomic structures
  * MouseModes (1.2): Provide right button mouse mode tool
  * Movie (1.0): Commands to record movies
  * Neuron (1.0): Read SWC neuron trace files
  * Nifti (1.1): Read medical images in NIfTI format
  * NRRD (1.1): Read medical images in NRRD format
  * Nucleotides (2.0.3): Create nucleotide-specific displays
  * OpenCommand (1.11): Manages 'open' command extensibility
  * PDB (2.7.2): PDB format read/write
  * PDBBio (1.0.1): PDB biological assembly fetch
  * PDBLibrary (1.0.2): C++ PDB support
  * PDBMatrices (1.0): Crystal and biological unit matrices
  * PickBlobs (1.0.1): Measure and color blobs
  * Positions (1.0): Read and write model position matrices
  * PresetMgr (1.1): Preset management
  * PubChem (2.1): PubChem fetch
  * ReadPbonds (1.0.1): Read in pseudobonds from a file
  * Registration (1.1.2): Register ChimeraX
  * RemoteControl (1.0): Control ChimeraX from other apps
  * RenderByAttr (1.1): Depict attribute values on structures
  * RenumberResidues (1.1): Renumber residues
  * ResidueFit (1.0.1): Display fit of residues to density map
  * RestServer (1.2): Starts REST server to execute commands from network requests
  * RNALayout (1.0): Make RNA models
  * RotamerLibMgr (4.0): Manage rotamer libraries
  * RotamerLibsDunbrack (2.0): Dunbrack rotamer library
  * RotamerLibsDynameomics (2.0): Dynameomics rotamer library
  * RotamerLibsRichardson (2.0): Richardson rotamer libraries
  * SaveCommand (1.5.1): Manages 'save' command extensibility
  * SchemeMgr (1.0): HTTP scheme management
  * SDF (2.0.1): SDF file reader
  * Segger (1.0): Segment map
  * Segment (1.0.1): Watershed segment calculation
  * SelInspector (1.0): Inspect contents of selection
  * SeqView (2.10): Sequence viewer
  * Shape (1.0.1): Make models for geometric shapes
  * Shell (1.0.1): Interactive Python shell
  * Shortcuts (1.1.1): Button and keyboard shortcuts
  * ShowSequences (1.0.2): Choose/show structure sequences
  * SideView (1.0.1): Side view of scene
  * Smiles (2.1.2): SMILES fetch
  * SmoothLines (1.0): Smooth network of lines
  * SpaceNavigator (1.0): Space Navigator device support
  * StdCommands (1.12.2): Standard commands
  * STL (1.0.1): STL file read/write
  * Storm (1.0): STORM file reader
  * StructMeasure (1.1.2): Structure measurement user interface
  * Struts (1.0.1): struts for 3D printing
  * Surface (1.0.1): Surface calculations
  * SwapAA (2.0.1): Swap amino acid
  * SwapRes (2.2.2): Swap residue side chains
  * TapeMeasure (1.0): Tape measure mouse mode
  * TaskManager (1.0): Manage background tasks in ChimeraX
  * Test (1.0): simple regression test
  * Toolbar (1.1.2): Toolbar
  * ToolshedUtils (1.2.4): Toolshed bundle utilities
  * Topography (1.0): Show a topographic surface for a 2D image
  * ToQuest (1.0): Copy scenes to VR Quest headset
  * Tug (1.0.1): Tug on atoms with molecular dynamics
  * UI (1.32.2): ChimeraX user interface
  * uniprot (2.3): UniProt database support
  * UnitCell (1.0.1): Show crystal unit cell
  * ViewDockX (1.3.1): Analyze ligand-receptor docking results
  * VIPERdb (1.0): Read Virus Particle Explorer .vdb files
  * Vive (1.1): Virtual reality headset support
  * VolumeMenu (1.0.1): Volume menu
  * VTK (1.0): Legacy VTK file reader and writer
  * WavefrontOBJ (1.0): Wavefront OBJ file read/write
  * WebCam (1.0.2): Combine camera video with graphics
  * WebServices (1.1.2): Web service and HTTP request support
  * Zone (1.0.1): Mouse mode to show atom and map zones

  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 7459.141.1.700.1

Software:

    System Software Overview:

      System Version: macOS 12.7 (21G816)
      Kernel Version: Darwin 21.6.0
      Time since boot: 25 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        HP Z27k G3:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.0
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.11.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.48
    ChimeraX-AtomicLibrary: 10.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.3
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.4
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202309270131
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.1
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.12
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.11
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.10
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.32.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.4
    contourpy: 1.1.1
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.42.1
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.10.0
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.0
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.2
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.0.5
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Tristan Croll]

toolshed list from within ChimeraX lists Clipper as installed, but /Applications/ChimeraX_Daily.app/Contents/bin/pip list doesn't:

ChimeraX-ChemGroup              2.0.1
ChimeraX-Clashes                2.2.4
ChimeraX-ColorActions           1.0.3
ChimeraX-ColorGlobe             1.0
ChimeraX-ColorKey               1.5.4

[Greg Couch]

The pip binary doesn't know about the ChimeraX toolshed. You need to run:

/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip list.

[Tristan Croll]

I don’t think this ticket is ready to be closed. The “pip list” post was me
attempting to start on debugging the real problem: on the Mac ISOLDE is
refusing to install because the dependency resolution is failing to find
Clipper.

On Wed, 27 Sep 2023 at 18:27, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Tristan Croll]

To add some detail to the original bug report: once I’ve built and
installed Clipper, then “devel install .” in the ISOLDE directory
successfully builds the ISOLDE wheel (so passes the ToolShed’s up-front
dependency checks), but fails on the final “toolshed install” when pip
fails to find Clipper.

On Wed, 27 Sep 2023 at 18:34, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Greg Couch]

There is a bug in the toolshed database right now that might be confusing things. There appears to be two ISODE releases with the same date and platform. It's going to take me a while to track it down.

[Tristan Croll]

Pretty sure I found the problem: chimerax.core.python_utils.chimerax_python_executable() returns '/Applications/ChimeraX_Daily.app/Contents/bin/python3.11' - so calls to run_pip() don't know about the user bundle directory:

from chimerax.core.python_utils import run_logged_pip
run_logged_pip(['list'], session.logger)

# truncated output
ChimeraX-ChemGroup              2.0.1
ChimeraX-Clashes                2.2.4
ChimeraX-ColorActions           1.0.3
# truncated output

... i.e. it doesn't know that ChimeraX-Clipper is installed. This is the resulting traceback I get after running make app-install in the ISOLDE directory:

adding 'ChimeraX_ISOLDE-1.7.dev0.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in ./dist/ChimeraX_ISOLDE-1.7.dev0-cp311-cp311-macosx_10_13_universal2.whl
Installing bundle
Executing: toolshed install ./dist/ChimeraX_ISOLDE-1.7.dev0-cp311-cp311-macosx_10_13_universal2.whl
Traceback (most recent call last):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 512, in _pip_install
    results = run_logged_pip(command, logger)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/python_utils.py", line 108, in run_logged_pip
    raise RuntimeError(s)
RuntimeError: ERROR: Could not find a version that satisfies the requirement ChimeraX-Clipper~=0.22.0 (from chimerax-isolde) (from versions: none)
ERROR: No matching distribution found for ChimeraX-Clipper~=0.22.0


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/devel.py", line 174, in _run
    unbound_method(bb, *args, **kw)
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 154, in make_install
    run(session, cmd)
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38, in run
    results = command.run(text, log=log, return_json=return_json)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/toolshed.py", line 301, in toolshed_install
    ts.install_bundle(bundles, logger, **kw)
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 916, in install_bundle
    _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps)
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 246, in _install_bundle
    results = _pip_install(
              ^^^^^^^^^^^^^
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 515, in _pip_install
    raise UserError(str(e))
chimerax.core.errors.UserError: ERROR: Could not find a version that satisfies the requirement ChimeraX-Clipper~=0.22.0 (from chimerax-isolde) (from versions: none)
ERROR: No matching distribution found for ChimeraX-Clipper~=0.22.0

[Tristan Croll]

If I hack chimerax_python_executable() to simply return realpath(sys.executable) then ISOLDE installs successfully.

[Greg Couch]

We switched to the Python executable for source code package dependencies to install correctly. _pip_install adds the --extra-index-url argument to the toolshed's pypi server, so the the ChimeraX-Clipper packages should be found. Can you send me the wheel for testing?

[Tristan Croll]

I can - but to be clear, the situation I’m working with here is builds that
*aren’t* on the toolshed server yet. They’re my latest local dev builds.
The correct version of Clipper is installed on my local machine, but Python
executed without the ChimeraX wrapper doesn’t know how to find it.

I’ve just left for today, but will send my latest Mac Clipper and ISOLDE
wheels tomorrow.

On Thu, 28 Sep 2023 at 17:43, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Tristan Croll]

Woke up with a cold so I'm home on sick leave and won't be able to send
these today. Hopefully on Monday.

On Thu, Sep 28, 2023 at 5:49 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Tristan Croll]

Turns out that "cold" morphed into a pretty nasty case of the 'flu over the
weekend, and I still haven't made it back to the office. Now looking like
Thursday at the earliest.

On Fri, Sep 29, 2023 at 11:05 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Tom Goddard]

Rest up and get well Tristan.

[Tom Goddard]

These bugs that block our outside developers have high priority.

[Tristan Croll]

I've attached my current Clipper and ISOLDE wheels. What should happen:

• "toolshed install {clipper wheel file}" should proceed without issue, and Clipper itself will work fine (test by doing "open 1a0m structurefactors true")
• "toolshed install {isolde wheel file}" should fail with: "ERROR: No matching distribution found for ChimeraX-Clipper~=0.22.0"

[Tristan Croll]

After some head-scratching, I think I've found the true root cause - it's the subprocess._args_from_interpreter_flags() call in ​https://github.com/RBVI/ChimeraX/blob/965cd6284b39ab071d494c4e3c6ff27de66afb00/src/bundles/core/src/python_utils.py#L86.

In the ChimeraX shell:

import subprocess

subprocess._args_from_interpreter_flags()
Out[4]: ['-I', '-X', 'faulthandler']

From python --help in the terminal:

-I     : isolate Python from the user's environment (implies -E and -s)

-s     : don't add user site directory to sys.path; also PYTHONNOUSERSITE

If I remove that call to make the line read:

    pip_cmd = [prog] + ["-m", "pip"]

... then things start to work as expected:

from chimerax.core import python_utils

print(python_utils.run_pip(['list', '--user', '-v']).stdout.decode())
Package          Version  Location                                                                        Installer
---------------- -------- ------------------------------------------------------------------------------- ---------
ChimeraX-Clipper 0.22.1   /Users/tcroll/Library/Application Support/ChimeraX/1.7/lib/python/site-packages pip
ChimeraX-ISOLDE  1.7.dev0 /Users/tcroll/Library/Application Support/ChimeraX/1.7/lib/python/site-packages pip

... and make app-install for ISOLDE goes through without error.

Strangely enough, essentially the same problem is present in today's Linux build (subprocess._args_from_interpreter_flags() returns the same values, and python_utils.run_pip(['list']) fails to find the user bundles - but for some reason ISOLDE installation still manages to go ahead there. Weird.

[Greg Couch]

I believe this is essentially a duplicate of #9877. And is resolved in the next daily build.