Toolshed install of wiggle wheel file error installing dependencies

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.6-arm64-arm-64bit
ChimeraX Version: 1.5rc202210180220 (2022-10-18 02:20:12 UTC)
Description
Trying to install the wiggle bundle from a .whl file now gets this error while isntalling the dependencies.  I'll attach the whl file and the bundle_info.xml.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.5rc202210180220 (2022-10-18)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed install /Users/goddard/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-
> any.whl

Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing
/Users/goddard/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-any.whl Collecting
pyqtgraph Downloading pyqtgraph-0.13.1-py3-none-any.whl (966 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 966.1/966.1 kB 10.1 MB/s eta 0:00:00
Requirement already satisfied: ChimeraX-Core~=1.3 in ./ChimeraX RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from wiggle==0.2.2) (1.5rc202210180220) Collecting mrcfile
Downloading mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.9/43.9 kB 1.3 MB/s eta 0:00:00
Collecting umap-learn Downloading umap-learn-0.5.3.tar.gz (88 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.2/88.2 kB 3.2 MB/s eta 0:00:00
Preparing metadata (setup.py): started Preparing metadata (setup.py): finished
with status 'done' Collecting scikit-image Downloading
scikit_image-0.19.3-cp39-cp39-macosx_12_0_arm64.whl (12.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.5/12.5 MB 30.8 MB/s eta 0:00:00
Collecting torch Downloading torch-1.12.1-cp39-none-macosx_11_0_arm64.whl
(49.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.1/49.1 MB 19.5 MB/s eta
0:00:00 Requirement already satisfied: ChimeraX-UI~=1.0 in ./ChimeraX RC Oct
19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from wiggle==0.2.2) (1.24.2) Collecting phate Downloading
phate-1.0.8-py3-none-any.whl (23 kB) Collecting scikit-learn Downloading
scikit_learn-1.1.2-cp39-cp39-macosx_12_0_arm64.whl (7.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.7/7.7 MB 20.4 MB/s eta 0:00:00
Collecting pyyaml Downloading PyYAML-6.0-cp39-cp39-macosx_11_0_arm64.whl (173
kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 174.0/174.0 kB 5.6 MB/s eta
0:00:00 Requirement already satisfied: ChimeraX-MouseModes~=1.0 in ./ChimeraX
RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.1.1) Requirement already
satisfied: ChimeraX-Graphics~=1.0 in ./ChimeraX RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.1) Requirement already
satisfied: ChimeraX-SelInspector~=1.0 in ./ChimeraX RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.0) Requirement already
satisfied: numpy>=1.16.0 in ./ChimeraX RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from mrcfile->wiggle==0.2.2) (1.23.1) Collecting graphtools>=1.3.1
Downloading graphtools-1.5.2-py3-none-any.whl (45 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.3/45.3 kB 1.4 MB/s eta 0:00:00
Collecting scprep>=0.11.1 Downloading scprep-1.2.1-py3-none-any.whl (93 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.8/93.8 kB 3.4 MB/s eta 0:00:00
Collecting future Downloading future-0.18.2.tar.gz (829 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 12.9 MB/s eta 0:00:00
Preparing metadata (setup.py): started Preparing metadata (setup.py): finished
with status 'error' error: subprocess-exited-with-error × python setup.py
egg_info did not run successfully. │ exit code: 1 ╰─> [27 lines of output]
ERROR: Traceback (most recent call last): File
"/Users/goddard/Desktop/ChimeraX RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 197, in _run_module_as_main return _run_code(code, main_globals, None,
File "/Users/goddard/Desktop/ChimeraX RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 87, in _run_code exec(code, run_globals) File
"/Users/goddard/Desktop/ChimeraX RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/__main__.py", line 1031, in <module> exit_code =
init(sys.argv) File "/Users/goddard/Desktop/ChimeraX RC Oct 19
2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/__main__.py", line 831, in init exec(opts.cmd,
global_dict) File "<string>", line 2, in <module> File "<pip-setuptools-
caller>", line 34, in <module> File
"/private/var/folders/xm/39nw5kqs2z14whlsf6ks_bcr0000gn/T/pip-install-
ookqm8j1/future_1c7291db6d9f4cfc865281318affeb99/setup.py", line 86, in
<module> import src.future ModuleNotFoundError: No module named 'src' [end of
output] note: This error originates from a subprocess, and is likely not a
problem with pip. error: metadata-generation-failed × Encountered error while
generating package metadata. ╰─> See above for output. note: This is an issue
with the package mentioned above, not pip. hint: See above for details.
[notice] A new release of pip available: 22.2.2 -> 22.3 [notice] To update,
run: /Users/goddard/Desktop/ChimeraX RC Oct 19
2022.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip  




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

Python: 3.9.11
Locale: 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: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 28 days 1:27

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202210180220
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.37.4
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    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: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.5
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.9.0
File attachment: wiggle-0.2.2-py3-none-any.whl

wiggle-0.2.2-py3-none-any.whl​

[goddard@…]

Added by email2trac

[Tom Goddard]

The bundle_info.xml file used to create this wheel.

[Tom Goddard]

This error is in today's release candidate which has fixes for the previous error #7776 when trying to install wiggle dependencies. Not clear which dependency is causing this latest error.

[Tom Goddard]

Installing the wheel from the shell gives the same error

$ ~/Desktop/ChimeraX\ RC\ Oct\ 19\ 2022.app/Contents/MacOS/ChimeraX -m pip install ~/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-any.whl --user
</MacOS/ChimeraX -m pip install ~/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-any.whl --user
Processing ./dist/wiggle-0.2.2-py3-none-any.whl
Collecting scikit-image
  Downloading scikit_image-0.19.3-cp39-cp39-macosx_12_0_arm64.whl (12.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.5/12.5 MB 3.5 MB/s eta 0:00:00

Collecting scikit-learn
  Downloading scikit_learn-1.1.2-cp39-cp39-macosx_12_0_arm64.whl (7.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.7/7.7 MB 3.5 MB/s eta 0:00:00

Requirement already satisfied: ChimeraX-UI~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from wiggle==0.2.2) (1.24.2)
Collecting mrcfile
  Downloading mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.9/43.9 kB 1.1 MB/s eta 0:00:00

Collecting umap-learn
  Downloading umap-learn-0.5.3.tar.gz (88 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.2/88.2 kB 2.3 MB/s eta 0:00:00

  Preparing metadata (setup.py) ... done
Collecting phate
  Downloading phate-1.0.8-py3-none-any.whl (23 kB)
Collecting torch
  Downloading torch-1.12.1-cp39-none-macosx_11_0_arm64.whl (49.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.1/49.1 MB 4.0 MB/s eta 0:00:00

Requirement already satisfied: ChimeraX-Core~=1.3 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from wiggle==0.2.2) (1.5rc202210180220)
Collecting pyyaml
  Downloading PyYAML-6.0-cp39-cp39-macosx_11_0_arm64.whl (173 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 174.0/174.0 kB 3.0 MB/s eta 0:00:00

Collecting pyqtgraph
  Downloading pyqtgraph-0.13.1-py3-none-any.whl (966 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 966.1/966.1 kB 4.2 MB/s eta 0:00:00

Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.0)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.1.1)
Requirement already satisfied: numpy>=1.16.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from mrcfile->wiggle==0.2.2) (1.23.1)
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 3.8 MB/s eta 0:00:00

  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [27 lines of output]
      ERROR:
      Traceback (most recent call last):
        File "/Users/goddard/Desktop/ChimeraX RC Oct 19
      2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
      line 197, in _run_module_as_main
          return _run_code(code, main_globals, None,
        File "/Users/goddard/Desktop/ChimeraX RC Oct 19
      2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
      line 87, in _run_code
          exec(code, run_globals)
        File "/Users/goddard/Desktop/ChimeraX RC Oct 19
      2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
      packages/chimerax/core/__main__.py", line 1031, in <module>
          exit_code = init(sys.argv)
        File "/Users/goddard/Desktop/ChimeraX RC Oct 19
      2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
      packages/chimerax/core/__main__.py", line 831, in init
          exec(opts.cmd, global_dict)
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/private/var/folders/xm/39nw5kqs2z14whlsf6ks_bcr0000gn/T/pip-
      install-6vjiaukm/future_d13799b050c84ec48f14078b3dd05314/setup.py", line 86,
      in <module>
          import src.future
      ModuleNotFoundError: No module named 'src'
      
      
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

[notice] A new release of pip available: 22.2.2 -> 22.3
[notice] To update, run: /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip
$ 

[Zach Pearson]

Installing future 0.18.2 through python.exe seems to work for me on Windows, but not ChimeraX-Console.exe

pip log below:

~/git/ChimeraX develop* ❯ ./ChimeraX.app/bin/ChimeraX-console.exe -I -m pip install --user future --log pip.log
Collecting future
  Using cached future-0.18.2.tar.gz (829 kB)
  Preparing metadata (setup.py) ...   error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
error
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
~/git/ChimeraX develop* ❯ cat pip.log
2022-10-19T11:58:07,022 Using pip 22.2.2 from C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip (python 3.9)
2022-10-19T11:58:07,023 User install by explicit request
2022-10-19T11:58:07,202 Created temporary directory: C:\Users\zpear\AppData\Local\Temp\pip-ephem-wheel-cache-1gscmb7e
2022-10-19T11:58:07,202 Created temporary directory: C:\Users\zpear\AppData\Local\Temp\pip-build-tracker-9al4o2i5
2022-10-19T11:58:07,202 Initialized build tracking at C:\Users\zpear\AppData\Local\Temp\pip-build-tracker-9al4o2i5
2022-10-19T11:58:07,202 Created build tracker: C:\Users\zpear\AppData\Local\Temp\pip-build-tracker-9al4o2i5
2022-10-19T11:58:07,203 Entered build tracker: C:\Users\zpear\AppData\Local\Temp\pip-build-tracker-9al4o2i5
2022-10-19T11:58:07,204 Created temporary directory: C:\Users\zpear\AppData\Local\Temp\pip-install-l9q2bxys
2022-10-19T11:58:07,212 1 location(s) to search for versions of future:
2022-10-19T11:58:07,212 * https://pypi.org/simple/future/
2022-10-19T11:58:07,212 Fetching project page and analyzing links: https://pypi.org/simple/future/
2022-10-19T11:58:07,212 Getting page https://pypi.org/simple/future/
2022-10-19T11:58:07,213 Found index url https://pypi.org/simple
2022-10-19T11:58:07,272 Fetched page https://pypi.org/simple/future/ as application/vnd.pypi.simple.v1+json
2022-10-19T11:58:07,274   Found link https://files.pythonhosted.org/packages/97/22/1f2ed10053f338c41e622ca0ea155990d5cdb6ffd602c951649554cc9723/future-0.0.1.tar.gz (from https://pypi.org/simple/future/), version: 0.0.1
2022-10-19T11:58:07,274   Found link https://files.pythonhosted.org/packages/6a/d7/8a0dc06421cde141a4f1345e19fd08967901c3ab969c47feb8f1157d81ec/future-0.0.2.tar.gz (from https://pypi.org/simple/future/), version: 0.0.2
2022-10-19T11:58:07,274   Found link https://files.pythonhosted.org/packages/70/3d/8110f3a9eba14fa50ad8773a25715294117ce8364c3cb5b7fec3cec94b45/future-0.0.3.tar.gz (from https://pypi.org/simple/future/), version: 0.0.3
2022-10-19T11:58:07,275   Found link https://files.pythonhosted.org/packages/af/cf/4fbe349bcf9a08f2c329a66cc4d4a417387acc9033ad5238160b3f266e05/future-0.1.0.tar.gz (from https://pypi.org/simple/future/), version: 0.1.0
2022-10-19T11:58:07,275   Found link https://files.pythonhosted.org/packages/47/71/85e86ca16d116369e327aeece8f383d896fb2e55f3033d03753ae3c717a9/future-0.2.0.tar.gz (from https://pypi.org/simple/future/), version: 0.2.0
2022-10-19T11:58:07,275   Found link https://files.pythonhosted.org/packages/8d/96/0c1b5bd252dad69587f2f38f13d4e611bc3582d51f985a2ec3001f5a56e3/future-0.3.0.tar.gz (from https://pypi.org/simple/future/), version: 0.3.0
2022-10-19T11:58:07,275   Found link https://files.pythonhosted.org/packages/0d/e6/37fd66577d0d0f2f647949e8e2d9096b03562e71ffd38046e2a0491e3b6e/future-0.3.1.tar.gz (from https://pypi.org/simple/future/), version: 0.3.1
2022-10-19T11:58:07,275   Found link https://files.pythonhosted.org/packages/1a/fa/e955d2aaa4ea5d518837e5ff45dd3f5e8a7857312c57292232caf8d064f5/future-0.3.2.tar.gz (from https://pypi.org/simple/future/), version: 0.3.2
2022-10-19T11:58:07,275   Found link https://files.pythonhosted.org/packages/36/8d/403c370d25bde232bef32e8e306942b1a95c62e5146b7d3586c2548c6171/future-0.3.3.tar.gz (from https://pypi.org/simple/future/), version: 0.3.3
2022-10-19T11:58:07,276   Found link https://files.pythonhosted.org/packages/ed/52/ed0ce839b5b8cf521e2361296c8a5892a242824a7a7e294a3fdbb8d2d79d/future-0.3.4.tar.gz (from https://pypi.org/simple/future/), version: 0.3.4
2022-10-19T11:58:07,276   Found link https://files.pythonhosted.org/packages/76/49/512ff7efa41f0b63d311bb4f5260d63f547f8bfb0fb8ad2e84268932491e/future-0.3.5.tar.gz (from https://pypi.org/simple/future/), version: 0.3.5
2022-10-19T11:58:07,276   Found link https://files.pythonhosted.org/packages/39/20/35ff22a9737f14d4d036811a3f7f7f06f3a936f176496ac99021de80c2f5/future-0.4.0.tar.gz (from https://pypi.org/simple/future/), version: 0.4.0
2022-10-19T11:58:07,276   Found link https://files.pythonhosted.org/packages/35/34/f3ab317ef4dc8c68a4e263ff2698e56e77a5c6eb2dfaf32c933022dab408/future-0.4.1.tar.gz (from https://pypi.org/simple/future/), version: 0.4.1
2022-10-19T11:58:07,276   Found link https://files.pythonhosted.org/packages/19/af/6e9bcbd4d75c0529e01951cdcc5d4ceea2ff5503c166eceb829c938442b4/future-0.5.0.tar.gz (from https://pypi.org/simple/future/), version: 0.5.0
2022-10-19T11:58:07,277   Found link https://files.pythonhosted.org/packages/bd/f1/3969374107374de0133022284302829ce57bb3aae40d3652954725c730d4/future-0.5.1.tar.gz (from https://pypi.org/simple/future/), version: 0.5.1
2022-10-19T11:58:07,277   Found link https://files.pythonhosted.org/packages/6a/f5/79aed4c3961bd5a33ed259a6d700dfb91cddde963c03f1e0f5fe8c4f9800/future-0.5.2.tar.gz (from https://pypi.org/simple/future/), version: 0.5.2
2022-10-19T11:58:07,277   Found link https://files.pythonhosted.org/packages/1f/b8/b1c98f9a79016720b87516e83281278c470140a15621531ab32b13ffe243/future-0.6.0.tar.gz (from https://pypi.org/simple/future/), version: 0.6.0
2022-10-19T11:58:07,277   Found link https://files.pythonhosted.org/packages/02/d7/f598e05b40dab77125a08d79409e2993b464a72bd8f6e30748fb25c8d2ff/future-0.7.0.tar.gz (from https://pypi.org/simple/future/), version: 0.7.0
2022-10-19T11:58:07,277   Found link https://files.pythonhosted.org/packages/57/57/970dcbc3d2ea887f286a4d3caa03ad772fba910de2bb0da83a3b960614aa/future-0.8.0.tar.gz (from https://pypi.org/simple/future/), version: 0.8.0
2022-10-19T11:58:07,278   Found link https://files.pythonhosted.org/packages/2f/b1/202444d6c09a6d7af12fe2a8aa1ca82231497fbd3c4db0851c13af773ad1/future-0.8.1.tar.gz (from https://pypi.org/simple/future/), version: 0.8.1
2022-10-19T11:58:07,278   Found link https://files.pythonhosted.org/packages/39/62/85c024887fe4c3740856e4ee5b7fa69f73fe4e3edce06f7435d90dc5fbdf/future-0.8.2.tar.gz (from https://pypi.org/simple/future/), version: 0.8.2
2022-10-19T11:58:07,278   Found link https://files.pythonhosted.org/packages/f7/19/0a60b692f34dae382bff5ca243dd5727b0205d8ee7ace62dee8348e5751e/future-0.9.0.tar.gz (from https://pypi.org/simple/future/), version: 0.9.0
2022-10-19T11:58:07,278   Found link https://files.pythonhosted.org/packages/14/7b/a841b12ed2fd1da2db3833943a077acc7882a5657bb0cdfab6a22f9ed2c4/future-0.10.0.tar.gz (from https://pypi.org/simple/future/), version: 0.10.0
2022-10-19T11:58:07,278   Found link https://files.pythonhosted.org/packages/c9/77/a67f45ce02080d57bb6da0577e85cfcde8bf155c90dbedbcd4d43d21591a/future-0.10.1.tar.gz (from https://pypi.org/simple/future/), version: 0.10.1
2022-10-19T11:58:07,279   Found link https://files.pythonhosted.org/packages/4b/26/efbffa48a3ddd910c039b62fdc1b619f1e995eeff46a895ac14f7accafb8/future-0.10.2.tar.gz (from https://pypi.org/simple/future/), version: 0.10.2
2022-10-19T11:58:07,279   Found link https://files.pythonhosted.org/packages/5e/05/b1c3543d934e289d879e91a5ba4d8d53dd97f794a23c555b13757b2c6bf6/future-0.11.0.tar.gz (from https://pypi.org/simple/future/), version: 0.11.0
2022-10-19T11:58:07,279   Found link https://files.pythonhosted.org/packages/50/ee/213a1d99b19b9b37e26698ef20b704a27bfaaa7fd98de67464f15f36af1c/future-0.11.1.tar.gz (from https://pypi.org/simple/future/), version: 0.11.1
2022-10-19T11:58:07,279   Found link https://files.pythonhosted.org/packages/fe/4a/5697d5a9681607f9c34b87af13782cb8eb832bc3a4ea2747b9433a2d7e52/future-0.11.2.tar.gz (from https://pypi.org/simple/future/), version: 0.11.2
2022-10-19T11:58:07,279   Found link https://files.pythonhosted.org/packages/48/04/0f72f4e005490d07b25ce5b8ac023ecf4bfb2d38ece2bc55b0f03f1ae45d/future-0.11.3.tar.gz (from https://pypi.org/simple/future/), version: 0.11.3
2022-10-19T11:58:07,280   Found link https://files.pythonhosted.org/packages/9e/be/c3adca8bdf3e452622e085e0cf9cb5c9f45e9e14a8ff77f7e7ae9cd34604/future-0.11.4.tar.gz (from https://pypi.org/simple/future/), version: 0.11.4
2022-10-19T11:58:07,280   Found link https://files.pythonhosted.org/packages/02/f8/f284a56149af9e72da9605cb178175f4acdfedc4655aabee19a138acd6fe/future-0.12.0.tar.gz (from https://pypi.org/simple/future/), version: 0.12.0
2022-10-19T11:58:07,280   Found link https://files.pythonhosted.org/packages/db/74/22c98655ae91486061cd2fe3058bd8a8422e213a36d3ae315bef023d062b/future-0.12.1.tar.gz (from https://pypi.org/simple/future/), version: 0.12.1
2022-10-19T11:58:07,280   Found link https://files.pythonhosted.org/packages/9d/47/5cdb58d1ce9035d6f6b4bde347354f262d2cddd568c51c3053baa88fc59d/future-0.12.2.tar.gz (from https://pypi.org/simple/future/), version: 0.12.2
2022-10-19T11:58:07,280   Found link https://files.pythonhosted.org/packages/ac/7f/f925ed0e29af42ed3273a1eceaf90b9c3d6bd51bca8aaba49725e9c0d9b5/future-0.12.3.tar.gz (from https://pypi.org/simple/future/), version: 0.12.3
2022-10-19T11:58:07,281   Found link https://files.pythonhosted.org/packages/ea/a9/8f9d4a952a681b860b4d08759dc3fa768b8d611c72048497c872bee6e54b/future-0.12.4.tar.gz (from https://pypi.org/simple/future/), version: 0.12.4
2022-10-19T11:58:07,281   Found link https://files.pythonhosted.org/packages/08/94/9f023d3443f00f62d5f3e44e6daaef059bd28300d92d59c60bedfdc298da/future-0.13.0.tar.gz (from https://pypi.org/simple/future/), version: 0.13.0
2022-10-19T11:58:07,281   Found link https://files.pythonhosted.org/packages/b4/e6/07e207c894654762689a37c1b697c16aee1360df6eeafcbd66d3a16b9812/future-0.13.1.tar.gz (from https://pypi.org/simple/future/), version: 0.13.1
2022-10-19T11:58:07,281   Found link https://files.pythonhosted.org/packages/4b/ab/3e42d1f0227e3a23d02338506e24007a1d9c21bda028735efb19285578f9/future-0.14.0.tar.gz (from https://pypi.org/simple/future/), version: 0.14.0
2022-10-19T11:58:07,281   Found link https://files.pythonhosted.org/packages/dc/a6/57718937bc25e602367d82ff86a6689b677f18e29e30ff9bab58cc17f5dc/future-0.14.1.tar.gz (from https://pypi.org/simple/future/), version: 0.14.1
2022-10-19T11:58:07,281   Found link https://files.pythonhosted.org/packages/d6/c1/3e8cee376151bd70744e7f1290212f887333323f260da22eb834c709d236/future-0.14.2.tar.gz (from https://pypi.org/simple/future/), version: 0.14.2
2022-10-19T11:58:07,282   Found link https://files.pythonhosted.org/packages/83/80/8ef3a11a15f8eaafafa0937b20c1b3f73527e69ab6b3fa1cf94a5a96aabb/future-0.14.3.tar.gz (from https://pypi.org/simple/future/), version: 0.14.3
2022-10-19T11:58:07,282   Found link https://files.pythonhosted.org/packages/7c/eb/1d7403c6d187ec097394685b0ea8a69faadaeb63f222d6c9b85ae165f915/future-0.15.0.tar.gz (from https://pypi.org/simple/future/), version: 0.15.0
2022-10-19T11:58:07,282   Found link https://files.pythonhosted.org/packages/41/b7/b646f0140a752ea87bb0b4c3a4af6a1e6e5fa676b9b1314a702368b75d4b/future-0.15.1.tar.gz (from https://pypi.org/simple/future/), version: 0.15.1
2022-10-19T11:58:07,282   Found link https://files.pythonhosted.org/packages/5a/f4/99abde815842bc6e97d5a7806ad51236630da14ca2f3b1fce94c0bb94d3d/future-0.15.2.tar.gz (from https://pypi.org/simple/future/), version: 0.15.2
2022-10-19T11:58:07,282   Found link https://files.pythonhosted.org/packages/00/2b/8d082ddfed935f3608cc61140df6dcbf0edea1bc3ab52fb6c29ae3e81e85/future-0.16.0.tar.gz (from https://pypi.org/simple/future/), version: 0.16.0
2022-10-19T11:58:07,283   Found link https://files.pythonhosted.org/packages/85/aa/ba2e24dcb889d7e98733f87515d80b3512418b80ba79d82d2ddcd43fadf3/future-0.17.0.tar.gz (from https://pypi.org/simple/future/) (requires-python:>=2.6, !=3.0.*, !=3.1.*, !=3.2.*), version: 0.17.0
2022-10-19T11:58:07,283   Found link https://files.pythonhosted.org/packages/90/52/e20466b85000a181e1e144fd8305caf2cf475e2f9674e797b222f8105f5f/future-0.17.1.tar.gz (from https://pypi.org/simple/future/) (requires-python:>=2.6, !=3.0.*, !=3.1.*, !=3.2.*), version: 0.17.1
2022-10-19T11:58:07,283   Skipping link: none of the wheel's tags (cp27-none-any) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f7/1b/f7b288e12c7233323e0d0662031a5f7870b06e46c566aa0fbc8b0904391f/future-0.18.0-cp27-none-any.whl (from https://pypi.org/simple/future/) (requires-python:>=2.6, !=3.0.*, !=3.1.*, !=3.2.*)
2022-10-19T11:58:07,284   Skipping link: none of the wheel's tags (cp36-none-any) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/9e/cf/95b17d4430942dbf291fa5411d8189374a2e6dba91d9ef077e7fb8e869bc/future-0.18.0-cp36-none-any.whl (from https://pypi.org/simple/future/) (requires-python:>=2.6, !=3.0.*, !=3.1.*, !=3.2.*)
2022-10-19T11:58:07,284   Found link https://files.pythonhosted.org/packages/f6/85/c273089eb6efa5644c0a1382ea553554bc0d40e00a46d989ec67f123f8b5/future-0.18.0.tar.gz (from https://pypi.org/simple/future/) (requires-python:>=2.6, !=3.0.*, !=3.1.*, !=3.2.*), version: 0.18.0
2022-10-19T11:58:07,284   Found link https://files.pythonhosted.org/packages/3f/bf/57733d44afd0cf67580658507bd11d3ec629612d5e0e432beb4b8f6fbb04/future-0.18.1.tar.gz (from https://pypi.org/simple/future/) (requires-python:>=2.6, !=3.0.*, !=3.1.*, !=3.2.*), version: 0.18.1
2022-10-19T11:58:07,285   Found link https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz (from https://pypi.org/simple/future/) (requires-python:>=2.6, !=3.0.*, !=3.1.*, !=3.2.*), version: 0.18.2
2022-10-19T11:58:07,285 Skipping link: not a file: https://pypi.org/simple/future/
2022-10-19T11:58:07,285 Given no hashes to check 50 links for project 'future': discarding no candidates
2022-10-19T11:58:07,287 Collecting future
2022-10-19T11:58:07,288   Created temporary directory: C:\Users\zpear\AppData\Local\Temp\pip-unpack-dhq19s_j
2022-10-19T11:58:07,290   Using cached future-0.18.2.tar.gz (829 kB)
2022-10-19T11:58:07,545   Added future from https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz to build tracker 'C:\\Users\\zpear\\AppData\\Local\\Temp\\pip-build-tracker-9al4o2i5'
2022-10-19T11:58:07,545   Running setup.py (path:C:\Users\zpear\AppData\Local\Temp\pip-install-l9q2bxys\future_f2a1ed2c9144448d9a3e8faab3b4f2db\setup.py) egg_info for package future
2022-10-19T11:58:07,546   Created temporary directory: C:\Users\zpear\AppData\Local\Temp\pip-pip-egg-info-3w16j234
2022-10-19T11:58:07,546   Running command python setup.py egg_info
2022-10-19T11:58:08,179   ERROR:
2022-10-19T11:58:08,179   Traceback (most recent call last):
2022-10-19T11:58:08,179     File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\runpy.py", line 197,
2022-10-19T11:58:08,179   in _run_module_as_main
2022-10-19T11:58:08,179       return _run_code(code, main_globals, None,
2022-10-19T11:58:08,180     File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\runpy.py", line 87,
2022-10-19T11:58:08,180   in _run_code
2022-10-19T11:58:08,180       exec(code, run_globals)
2022-10-19T11:58:08,180     File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-
2022-10-19T11:58:08,180   packages\chimerax\core\\__main__.py", line 1039, in <module>
2022-10-19T11:58:08,180       exit_code = init(sys.argv)
2022-10-19T11:58:08,180     File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-
2022-10-19T11:58:08,180   packages\chimerax\core\\__main__.py", line 831, in init
2022-10-19T11:58:08,181       exec(opts.cmd, global_dict)
2022-10-19T11:58:08,181     File "<string>", line 2, in <module>
2022-10-19T11:58:08,181     File "<pip-setuptools-caller>", line 34, in <module>
2022-10-19T11:58:08,181     File "C:\Users\zpear\AppData\Local\Temp\pip-
2022-10-19T11:58:08,181   install-l9q2bxys\future_f2a1ed2c9144448d9a3e8faab3b4f2db\setup.py", line 86,
2022-10-19T11:58:08,181   in <module>
2022-10-19T11:58:08,181       import src.future
2022-10-19T11:58:08,181   ModuleNotFoundError: No module named 'src'


2022-10-19T11:58:08,223   ERROR: [present-rich] python setup.py egg_info exited with 1
2022-10-19T11:58:08,227   [bold magenta]full command[/]: [blue]'C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\ChimeraX-console.exe' -c '
2022-10-19T11:58:08,227   exec(compile('"'"''"'"''"'"'
2022-10-19T11:58:08,227   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2022-10-19T11:58:08,227   #
2022-10-19T11:58:08,227   # - It imports setuptools before invoking setup.py, to enable projects that directly
2022-10-19T11:58:08,227   #   import from `distutils.core` to work with newer packaging standards.
2022-10-19T11:58:08,227   # - It provides a clear error message when setuptools is not installed.
2022-10-19T11:58:08,227   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2022-10-19T11:58:08,227   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2022-10-19T11:58:08,227   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2022-10-19T11:58:08,227   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2022-10-19T11:58:08,227   import os, sys, tokenize
2022-10-19T11:58:08,227
2022-10-19T11:58:08,227   try:
2022-10-19T11:58:08,227       import setuptools
2022-10-19T11:58:08,227   except ImportError as error:
2022-10-19T11:58:08,227       print(
2022-10-19T11:58:08,227           "ERROR: Can not execute `setup.py` since setuptools is not available in "
2022-10-19T11:58:08,227           "the build environment.",
2022-10-19T11:58:08,227           file=sys.stderr,
2022-10-19T11:58:08,227       )
2022-10-19T11:58:08,227       sys.exit(1)
2022-10-19T11:58:08,227
2022-10-19T11:58:08,227   __file__ = %r
2022-10-19T11:58:08,227   sys.argv[0] = __file__
2022-10-19T11:58:08,227
2022-10-19T11:58:08,227   if os.path.exists(__file__):
2022-10-19T11:58:08,227       filename = __file__
2022-10-19T11:58:08,227       with tokenize.open(__file__) as f:
2022-10-19T11:58:08,227           setup_py_code = f.read()
2022-10-19T11:58:08,227   else:
2022-10-19T11:58:08,227       filename = "<auto-generated setuptools caller>"
2022-10-19T11:58:08,227       setup_py_code = "from setuptools import setup; setup()"
2022-10-19T11:58:08,227
2022-10-19T11:58:08,227   exec(compile(setup_py_code, filename, "exec"))
2022-10-19T11:58:08,227   '"'"''"'"''"'"' % ('"'"'C:\\Users\\zpear\\AppData\\Local\\Temp\\pip-install-l9q2bxys\\future_f2a1ed2c9144448d9a3e8faab3b4f2db\\setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' egg_info --egg-base 'C:\Users\zpear\AppData\Local\Temp\pip-pip-egg-info-3w16j234'[/]
2022-10-19T11:58:08,228   [bold magenta]cwd[/]: C:\Users\zpear\AppData\Local\Temp\pip-install-l9q2bxys\future_f2a1ed2c9144448d9a3e8faab3b4f2db\
2022-10-19T11:58:08,228 ERROR: [present-rich] metadata generation failed
2022-10-19T11:58:08,230 Exception information:
2022-10-19T11:58:08,230 Traceback (most recent call last):
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\operations\build\metadata_legacy.py", line 64, in generate_metadata
2022-10-19T11:58:08,230     call_subprocess(
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\utils\subprocess.py", line 224, in call_subprocess
2022-10-19T11:58:08,230     raise error
2022-10-19T11:58:08,230 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1
2022-10-19T11:58:08,230
2022-10-19T11:58:08,230 The above exception was the direct cause of the following exception:
2022-10-19T11:58:08,230
2022-10-19T11:58:08,230 Traceback (most recent call last):
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\cli\base_command.py", line 167, in exc_logging_wrapper
2022-10-19T11:58:08,230     status = run_func(*args)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\cli\req_command.py", line 247, in wrapper
2022-10-19T11:58:08,230     return func(self, options, args)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\commands\install.py", line 369, in run
2022-10-19T11:58:08,230     requirement_set = resolver.resolve(
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\resolver.py", line 92, in resolve
2022-10-19T11:58:08,230     result = self._result = resolver.resolve(
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 481, in resolve
2022-10-19T11:58:08,230     state = resolution.resolve(requirements, max_rounds=max_rounds)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 348, in resolve
2022-10-19T11:58:08,230     self._add_to_criteria(self.state.criteria, r, parent=None)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 172, in _add_to_criteria
2022-10-19T11:58:08,230     if not criterion.candidates:
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_vendor\resolvelib\structs.py", line 151, in __bool__
2022-10-19T11:58:08,230     return bool(self._sequence)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\found_candidates.py", line 155, in __bool__
2022-10-19T11:58:08,230     return any(self)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\found_candidates.py", line 143, in <genexpr>
2022-10-19T11:58:08,230     return (c for c in iterator if id(c) not in self._incompatible_ids)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\found_candidates.py", line 47, in _iter_built
2022-10-19T11:58:08,230     candidate = func()
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\factory.py", line 206, in _make_candidate_from_link
2022-10-19T11:58:08,230     self._link_candidate_cache[link] = LinkCandidate(
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 297, in __init__
2022-10-19T11:58:08,230     super().__init__(
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 162, in __init__
2022-10-19T11:58:08,230     self.dist = self._prepare()
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 231, in _prepare
2022-10-19T11:58:08,230     dist = self._prepare_distribution()
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 308, in _prepare_distribution
2022-10-19T11:58:08,230     return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\operations\prepare.py", line 438, in prepare_linked_requirement
2022-10-19T11:58:08,230     return self._prepare_linked_requirement(req, parallel_builds)
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\operations\prepare.py", line 524, in _prepare_linked_requirement
2022-10-19T11:58:08,230     dist = _get_prepared_distribution(
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\operations\prepare.py", line 68, in _get_prepared_distribution
2022-10-19T11:58:08,230     abstract_dist.prepare_distribution_metadata(
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\distributions\sdist.py", line 61, in prepare_distribution_metadata
2022-10-19T11:58:08,230     self.req.prepare_metadata()
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\req\req_install.py", line 539, in prepare_metadata
2022-10-19T11:58:08,230     self.metadata_directory = generate_metadata_legacy(
2022-10-19T11:58:08,230   File "C:\Users\zpear\git\ChimeraX\ChimeraX.app\bin\lib\site-packages\pip\_internal\operations\build\metadata_legacy.py", line 71, in generate_metadata
2022-10-19T11:58:08,230     raise MetadataGenerationFailed(package_details=details) from error
2022-10-19T11:58:08,230 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed
2022-10-19T11:58:08,237 Remote version of pip: 22.2.2
2022-10-19T11:58:08,237 Local version of pip:  22.2.2
2022-10-19T11:58:08,238 Was pip installed by pip? True
2022-10-19T11:58:08,238 Removed future from https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz from build tracker 'C:\\Users\\zpear\\AppData\\Local\\Temp\\pip-build-tracker-9al4o2i5'
2022-10-19T11:58:08,238 Removed build tracker: 'C:\\Users\\zpear\\AppData\\Local\\Temp\\pip-build-tracker-9al4o2i5'

[Tom Goddard]

The wheel and its dependencies install correctly using the ChimeraX python3.9 executable from the shell instead of the ChimeraX launcher on the same Mac M1 computer where the other install methods fail.

$ ~/Desktop/ChimeraX\ RC\ Oct\ 19\ 2022.app/Contents/bin/python3.9 -m pip install ~/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-any.whl --user
</bin/python3.9 -m pip install ~/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-any.whl --user
Processing ./dist/wiggle-0.2.2-py3-none-any.whl
Collecting umap-learn
  Downloading umap-learn-0.5.3.tar.gz (88 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.2/88.2 kB 1.8 MB/s eta 0:00:00

  Preparing metadata (setup.py) ... done
Collecting pyqtgraph
  Downloading pyqtgraph-0.13.1-py3-none-any.whl (966 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 966.1/966.1 kB 4.7 MB/s eta 0:00:00

Requirement already satisfied: ChimeraX-Core~=1.3 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from wiggle==0.2.2) (1.5rc202210180220)
Collecting mrcfile
  Downloading mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.9/43.9 kB 1.5 MB/s eta 0:00:00

Requirement already satisfied: ChimeraX-UI~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from wiggle==0.2.2) (1.24.2)
Collecting scikit-learn
  Downloading scikit_learn-1.1.2-cp39-cp39-macosx_12_0_arm64.whl (7.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.7/7.7 MB 3.1 MB/s eta 0:00:00

Collecting phate
  Downloading phate-1.0.8-py3-none-any.whl (23 kB)
Collecting torch
  Downloading torch-1.12.1-cp39-none-macosx_11_0_arm64.whl (49.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.1/49.1 MB 3.2 MB/s eta 0:00:00

Collecting pyyaml
  Downloading PyYAML-6.0-cp39-cp39-macosx_11_0_arm64.whl (173 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 174.0/174.0 kB 2.3 MB/s eta 0:00:00

Collecting scikit-image
  Downloading scikit_image-0.19.3-cp39-cp39-macosx_12_0_arm64.whl (12.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.5/12.5 MB 3.2 MB/s eta 0:00:00

Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.0)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.1.1)
Requirement already satisfied: numpy>=1.16.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from mrcfile->wiggle==0.2.2) (1.23.1)
Collecting Deprecated
  Downloading Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB)
Collecting tasklogger>=1.0
  Downloading tasklogger-1.2.0-py3-none-any.whl (14 kB)
Requirement already satisfied: matplotlib>=3.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from phate->wiggle==0.2.2) (3.5.2)
Requirement already satisfied: scipy>=1.1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from phate->wiggle==0.2.2) (1.9.0)
Collecting graphtools>=1.3.1
  Downloading graphtools-1.5.2-py3-none-any.whl (45 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.3/45.3 kB 1.5 MB/s eta 0:00:00

Collecting s-gd2>=1.5
  Downloading s_gd2-1.8.tar.gz (53 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.7/53.7 kB 1.7 MB/s eta 0:00:00

  Preparing metadata (setup.py) ... done
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 2.6 MB/s eta 0:00:00

  Preparing metadata (setup.py) ... done
Collecting scprep>=0.11.1
  Downloading scprep-1.2.1-py3-none-any.whl (93 kB)
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Collecting joblib>=1.0.0
  Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
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Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Requirement already satisfied: packaging>=20.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scikit-image->wiggle==0.2.2) (21.3)
Collecting imageio>=2.4.1
  Downloading imageio-2.22.2-py3-none-any.whl (3.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 3.2 MB/s eta 0:00:00

Requirement already satisfied: tifffile>=2019.7.26 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scikit-image->wiggle==0.2.2) (2022.7.31)
Requirement already satisfied: pillow!=7.1.0,!=7.1.1,!=8.3.0,>=6.1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scikit-image->wiggle==0.2.2) (9.2.0)
Requirement already satisfied: networkx>=2.2 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scikit-image->wiggle==0.2.2) (2.8.5)
Collecting PyWavelets>=1.1.1
  Downloading PyWavelets-1.4.1-cp39-cp39-macosx_11_0_arm64.whl (4.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.3/4.3 MB 4.3 MB/s eta 0:00:00

Requirement already satisfied: typing-extensions in /Users/goddard/Library/Python/3.9/lib/python/site-packages (from torch->wiggle==0.2.2) (4.3.0)
Collecting numba>=0.49
  Downloading numba-0.56.3-cp39-cp39-macosx_11_0_arm64.whl (2.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 3.9 MB/s eta 0:00:00

Collecting pynndescent>=0.5
  Downloading pynndescent-0.5.7.tar.gz (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 3.8 MB/s eta 0:00:00

  Preparing metadata (setup.py) ... done
Collecting tqdm
  Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 1.7 MB/s eta 0:00:00

Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->wiggle==0.2.2) (1.2)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->wiggle==0.2.2) (1.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->wiggle==0.2.2) (1.0.1)
Collecting pygsp>=0.5.1
  Downloading PyGSP-0.5.1-py2.py3-none-any.whl (1.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 3.4 MB/s eta 0:00:00

Requirement already satisfied: pyparsing>=2.2.1 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (3.0.9)
Requirement already satisfied: python-dateutil>=2.7 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (2.8.2)
Requirement already satisfied: fonttools>=4.22.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (4.37.4)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (1.4.4)
Requirement already satisfied: cycler>=0.10 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (0.11.0)
Requirement already satisfied: setuptools in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from numba>=0.49->umap-learn->wiggle==0.2.2) (65.1.1)
Collecting llvmlite<0.40,>=0.39.0dev0
  Downloading llvmlite-0.39.1-cp39-cp39-macosx_11_0_arm64.whl (23.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.1/23.1 MB 3.3 MB/s eta 0:00:00

Requirement already satisfied: decorator>=4.3.0 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scprep>=0.11.1->phate->wiggle==0.2.2) (5.1.1)
Collecting pandas<1.4,>=0.25
  Downloading pandas-1.3.5.tar.gz (4.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 3.0 MB/s eta 0:00:00

  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting wrapt<2,>=1.10
  Downloading wrapt-1.14.1-cp39-cp39-macosx_11_0_arm64.whl (35 kB)
Requirement already satisfied: pytz>=2017.3 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from pandas<1.4,>=0.25->scprep>=0.11.1->phate->wiggle==0.2.2) (2022.5)
Requirement already satisfied: six>=1.5 in /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=3.0->phate->wiggle==0.2.2) (1.16.0)
Building wheels for collected packages: umap-learn, pynndescent, s-gd2, future, pandas
  Building wheel for umap-learn (setup.py) ... done
  Created wheel for umap-learn: filename=umap_learn-0.5.3-py3-none-any.whl size=82814 sha256=a79e0a3018ea9ab128caa25c84bea5cdbc48a06d07985ebc2b296ba93f7db77a
  Stored in directory: /Users/goddard/Library/Caches/pip/wheels/f4/3e/1c/596d0a463d17475af648688443fa4846fef624d1390339e7e9
  Building wheel for pynndescent (setup.py) ... done
  Created wheel for pynndescent: filename=pynndescent-0.5.7-py3-none-any.whl size=54269 sha256=438877e668a9f532653c8c1b3818fa8cf6f543c13aa2a4c67086bc646b02d6c7
  Stored in directory: /Users/goddard/Library/Caches/pip/wheels/5b/f5/6e/aac11d69fe2115d9ac871d6c148b361f0d3f8a35ed7354fa03
  Building wheel for s-gd2 (setup.py) ... done
  Created wheel for s-gd2: filename=s_gd2-1.8-cp39-cp39-macosx_10_9_universal2.whl size=106543 sha256=831c48336ad3c530161f176468557cf26714cd3ebe8d546c888b71cf0d311d4d
  Stored in directory: /Users/goddard/Library/Caches/pip/wheels/d4/5b/da/1cdff95cb7d01665f44e60a61abf7ebaa8e475c79884c590fe
  Building wheel for future (setup.py) ... done
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=354652f170f649c993205e383191a87ed80939195091646ee0dc61b8ce735f28
  Stored in directory: /Users/goddard/Library/Caches/pip/wheels/2f/a0/d3/4030d9f80e6b3be787f19fc911b8e7aa462986a40ab1e4bb94
  Building wheel for pandas (pyproject.toml) ... done
  Created wheel for pandas: filename=pandas-1.3.5-cp39-cp39-macosx_10_9_universal2.whl size=17331847 sha256=d181cf17ddcb6552695848777a574fe3c86a394850d3ba170d9eb7578d467ce9
  Stored in directory: /Users/goddard/Library/Caches/pip/wheels/46/1f/09/be8c6f216f000b48aaef3009dc7017707a1b18ef30ba548b8d
Successfully built umap-learn pynndescent s-gd2 future pandas
Installing collected packages: wrapt, tqdm, torch, threadpoolctl, s-gd2, pyyaml, PyWavelets, pyqtgraph, mrcfile, llvmlite, joblib, imageio, future, scikit-learn, scikit-image, pygsp, pandas, numba, Deprecated, tasklogger, scprep, pynndescent, umap-learn, graphtools, phate, wiggle
  WARNING: The script tqdm is installed in '/Users/goddard/Library/Python/3.9/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts convert-caffe2-to-onnx, convert-onnx-to-caffe2 and torchrun are installed in '/Users/goddard/Library/Python/3.9/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts mrcfile-header and mrcfile-validate are installed in '/Users/goddard/Library/Python/3.9/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts imageio_download_bin and imageio_remove_bin are installed in '/Users/goddard/Library/Python/3.9/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts futurize and pasteurize are installed in '/Users/goddard/Library/Python/3.9/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script skivi is installed in '/Users/goddard/Library/Python/3.9/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed Deprecated-1.2.13 PyWavelets-1.4.1 future-0.18.2 graphtools-1.5.2 imageio-2.22.2 joblib-1.2.0 llvmlite-0.39.1 mrcfile-1.4.3 numba-0.56.3 pandas-1.3.5 phate-1.0.8 pygsp-0.5.1 pynndescent-0.5.7 pyqtgraph-0.13.1 pyyaml-6.0 s-gd2-1.8 scikit-image-0.19.3 scikit-learn-1.1.2 scprep-1.2.1 tasklogger-1.2.0 threadpoolctl-3.1.0 torch-1.12.1 tqdm-4.64.1 umap-learn-0.5.3 wiggle-0.2.2 wrapt-1.14.1

[notice] A new release of pip available: 22.2.2 -> 22.3
[notice] To update, run: /Users/goddard/Desktop/ChimeraX RC Oct 19 2022.app/Contents/bin/python3.9 -m pip install --upgrade pip
$ 

[Zach Pearson]

PHATE is the package that depends on future.

​https://pypi.org/proj

​https://github.com/KrishnaswamyLab/PHATEect/phate/

future is a compatibility layer between Python 2 and 3, but PHATE only claims to be compatible with Python >= 3.5. Perhaps we can open a PR?

[goddard@…]

We should focus on the underlying issue of why the python executable installs correctly but the ChimeraX launcher does not.

[Greg Couch]

It turns out that a recursive call to sys.executable by pip sometimes leaves out the -I. In that case, it is expecting to be first on sys.path. ChimeraX always uses -I to avoid the environment and current directory contents from screwing up ChimeraX. Workaround this by adding back to sys.path when running a Python command via -c.

[Tom Goddard]

I was able to install wiggle in the current ChimeraX 1.5 release candidate with command

toolshed install ~/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-any.whl

and the PyPi dependencies were installed automatically using the attached wiggle bundle_info.xml to build the .whl file. I did not add the PyPi "cupy" dependency to bundle_info.xml because it depends on the CUDA version (e.g. cupy-cuda100). The plan for installing cupy is to do it when Wiggle is first run. It will look for CUDA and raise a dialog asking if they user wants to install the correct cupy, or warn about missing functionality no CUDA is available.

I will update the Wiggle Github issue about getting Wiggle on Toolshed to describe this progress.

​https://github.com/charbj/wiggle/issues/3

Here is the log output from installing the .whl file.

UCSF ChimeraX version: 1.5rc202211032258 (2022-11-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
toolshed install /Users/goddard/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
---

[notice] A new release of pip available: 22.2.2 -> 22.3.1
[notice] To update, run: /Users/goddard/Desktop/ChimeraX-1.5-rc2022.11.03.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip
---
pip standard output:
---
Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/goddard/ucsf/wiggle/dist/wiggle-0.2.2-py3-none-any.whl
Collecting pyyaml
Using cached PyYAML-6.0-cp39-cp39-macosx_10_9_x86_64.whl (197 kB)
Collecting scikit-image
Using cached scikit_image-0.19.3-cp39-cp39-macosx_10_13_x86_64.whl (13.3 MB)
Collecting torch
Using cached torch-1.13.0-cp39-none-macosx_10_9_x86_64.whl (137.9 MB)
Collecting scikit-learn
Using cached scikit_learn-1.1.3-cp39-cp39-macosx_10_9_x86_64.whl (8.7 MB)
Collecting phate
Using cached phate-1.0.9-py3-none-any.whl (23 kB)
Collecting umap-learn
Using cached umap-learn-0.5.3.tar.gz (88 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: ChimeraX-Core~=1.3 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from wiggle==0.2.2) (1.5rc202211032258)
Collecting mrcfile
Using cached mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
Collecting pyqtgraph
Using cached pyqtgraph-0.13.1-py3-none-any.whl (966 kB)
Requirement already satisfied: ChimeraX-UI~=1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from wiggle==0.2.2) (1.24.3)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.0)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->wiggle==0.2.2) (1.1.1)
Requirement already satisfied: numpy>=1.16.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from mrcfile->wiggle==0.2.2) (1.23.1)
Collecting tasklogger>=1.0
Using cached tasklogger-1.2.0-py3-none-any.whl (14 kB)
Collecting scprep>=0.11.1
Using cached scprep-1.2.1-py3-none-any.whl (93 kB)
Collecting s-gd2>=1.8.1
Using cached s_gd2-1.8.1-cp39-cp39-macosx_10_15_x86_64.whl (57 kB)
Requirement already satisfied: scipy>=1.1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from phate->wiggle==0.2.2) (1.9.0)
Collecting future
Using cached future-0.18.2.tar.gz (829 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting Deprecated
Using cached Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB)
Collecting graphtools>=1.3.1
Using cached graphtools-1.5.2-py3-none-any.whl (45 kB)
Requirement already satisfied: matplotlib>=3.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from phate->wiggle==0.2.2) (3.5.2)
Collecting threadpoolctl>=2.0.0
Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting joblib>=1.0.0
Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.0/298.0 kB 22.6 MB/s eta 0:00:00
Collecting PyWavelets>=1.1.1
Downloading PyWavelets-1.4.1-cp39-cp39-macosx_10_13_x86_64.whl (4.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 76.7 MB/s eta 0:00:00
Requirement already satisfied: packaging>=20.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scikit-image->wiggle==0.2.2) (21.3)
Requirement already satisfied: tifffile>=2019.7.26 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scikit-image->wiggle==0.2.2) (2022.7.31)
Requirement already satisfied: pillow!=7.1.0,!=7.1.1,!=8.3.0,>=6.1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scikit-image->wiggle==0.2.2) (9.2.0)
Requirement already satisfied: networkx>=2.2 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scikit-image->wiggle==0.2.2) (2.8.5)
Collecting imageio>=2.4.1
Downloading imageio-2.22.4-py3-none-any.whl (3.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 80.8 MB/s eta 0:00:00
Requirement already satisfied: typing-extensions in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from torch->wiggle==0.2.2) (4.4.0)
Collecting numba>=0.49
Downloading numba-0.56.4-cp39-cp39-macosx_10_14_x86_64.whl (2.4 MB)
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Collecting pynndescent>=0.5
Downloading pynndescent-0.5.8.tar.gz (1.1 MB)
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Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting tqdm
Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
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Requirement already satisfied: ChimeraX-Geometry~=1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->wiggle==0.2.2) (1.2)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->wiggle==0.2.2) (1.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->wiggle==0.2.2) (1.0.1)
Collecting pygsp>=0.5.1
Downloading PyGSP-0.5.1-py2.py3-none-any.whl (1.8 MB)
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Requirement already satisfied: fonttools>=4.22.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (4.38.0)
Requirement already satisfied: python-dateutil>=2.7 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (2.8.2)
Requirement already satisfied: pyparsing>=2.2.1 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (3.0.9)
Requirement already satisfied: cycler>=0.10 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (0.11.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from matplotlib>=3.0->phate->wiggle==0.2.2) (1.4.4)
Collecting llvmlite<0.40,>=0.39.0dev0
Downloading llvmlite-0.39.1-cp39-cp39-macosx_10_9_x86_64.whl (25.5 MB)
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Requirement already satisfied: setuptools in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from numba>=0.49->umap-learn->wiggle==0.2.2) (65.1.1)
Requirement already satisfied: decorator>=4.3.0 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from scprep>=0.11.1->phate->wiggle==0.2.2) (5.1.1)
Collecting pandas<1.4,>=0.25
Downloading pandas-1.3.5-cp39-cp39-macosx_10_9_x86_64.whl (11.3 MB)
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Collecting wrapt<2,>=1.10
Downloading wrapt-1.14.1-cp39-cp39-macosx_10_9_x86_64.whl (35 kB)
Requirement already satisfied: pytz>=2017.3 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from pandas<1.4,>=0.25->scprep>=0.11.1->phate->wiggle==0.2.2) (2022.6)
Requirement already satisfied: six>=1.5 in ./ChimeraX-1.5-rc2022.11.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=3.0->phate->wiggle==0.2.2) (1.16.0)
Building wheels for collected packages: umap-learn, pynndescent, future
Building wheel for umap-learn (setup.py): started
Building wheel for umap-learn (setup.py): finished with status 'done'
Created wheel for umap-learn: filename=umap_learn-0.5.3-py3-none-any.whl size=82814 sha256=ae4621c09a71b5fd863bd74fd1e20c0ba5f8b8d0102722341ddde31de52ed4c4
Stored in directory: /Users/goddard/Library/Caches/pip/wheels/f4/3e/1c/596d0a463d17475af648688443fa4846fef624d1390339e7e9
Building wheel for pynndescent (setup.py): started
Building wheel for pynndescent (setup.py): finished with status 'done'
Created wheel for pynndescent: filename=pynndescent-0.5.8-py3-none-any.whl size=55496 sha256=a6cb8aa1894dfd42a850e7f62676f6e521e0ba5527002fef3d9320a7d800265a
Stored in directory: /Users/goddard/Library/Caches/pip/wheels/b9/89/cc/59ab91ef5b21dc2ab3635528d7d227f49dfc9169905dcb959d
Building wheel for future (setup.py): started
Building wheel for future (setup.py): finished with status 'done'
Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=ad6c806e6fcb5d8b740efdd1a971b93eebfd8cda8ff738eacabca1e23ae75573
Stored in directory: /Users/goddard/Library/Caches/pip/wheels/2f/a0/d3/4030d9f80e6b3be787f19fc911b8e7aa462986a40ab1e4bb94
Successfully built umap-learn pynndescent future
Installing collected packages: wrapt, tqdm, torch, threadpoolctl, s-gd2, pyyaml, PyWavelets, pyqtgraph, mrcfile, llvmlite, joblib, imageio, future, scikit-learn, scikit-image, pygsp, pandas, numba, Deprecated, tasklogger, scprep, pynndescent, umap-learn, graphtools, phate, wiggle
Successfully installed Deprecated-1.2.13 PyWavelets-1.4.1 future-0.18.2 graphtools-1.5.2 imageio-2.22.4 joblib-1.2.0 llvmlite-0.39.1 mrcfile-1.4.3 numba-0.56.4 pandas-1.3.5 phate-1.0.9 pygsp-0.5.1 pynndescent-0.5.8 pyqtgraph-0.13.1 pyyaml-6.0 s-gd2-1.8.1 scikit-image-0.19.3 scikit-learn-1.1.3 scprep-1.2.1 tasklogger-1.2.0 threadpoolctl-3.1.0 torch-1.13.0 tqdm-4.64.1 umap-learn-0.5.3 wiggle-0.2.2 wrapt-1.14.1
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Successfully installed Deprecated-1.2.13 PyWavelets-1.4.1 future-0.18.2 graphtools-1.5.2 imageio-2.22.4 joblib-1.2.0 llvmlite-0.39.1 mrcfile-1.4.3 numba-0.56.4 pandas-1.3.5 phate-1.0.9 pygsp-0.5.1 pynndescent-0.5.8 pyqtgraph-0.13.1 pyyaml-6.0 s-gd2-1.8.1 scikit-image-0.19.3 scikit-learn-1.1.3 scprep-1.2.1 tasklogger-1.2.0 threadpoolctl-3.1.0 torch-1.13.0 tqdm-4.64.1 umap-learn-0.5.3 wiggle-0.2.2 wrapt-1.14.1
Installed wiggle (0.2.2)
ui tool show wiggle