Toolshed install fails on umap-learn PyPi dependency

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.6-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202210050037 (2022-10-05 00:37:42 UTC)
Description
Trying to install a wheel for the ChimeraX wiggle bundle in ChimeraX 1.5 it gives an error apparently due to the umap-learn PyPi dependency and something about having no setuptools.  I'll attach the wheel file.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.5.dev202210050037 (2022-10-05)  
© 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 Using cached pyqtgraph-0.13.1-py3-none-any.whl (966 kB) 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
phate Using cached phate-1.0.8-py3-none-any.whl (23 kB) Collecting torch Using
cached torch-1.12.1-cp39-none-macosx_10_9_x86_64.whl (133.8 MB) Requirement
already satisfied: ChimeraX-UI~=1.0 in
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from wiggle==0.2.2) (1.24.1) Collecting scikit-learn Using cached
scikit_learn-1.1.2-cp39-cp39-macosx_10_9_x86_64.whl (8.7 MB) 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
'error' error: subprocess-exited-with-error × python setup.py egg_info did not
run successfully. │ exit code: 1 ╰─> [36 lines of output] invalid command name
' exec(compile(''' # This is <pip-setuptools-caller> \-- a caller that pip
uses to run setup.py # # - It imports setuptools before invoking setup.py, to
enable projects that directly # import from `distutils.core` to work with
newer packaging standards. # - It provides a clear error message when
setuptools is not installed. # - It sets `sys.argv[0]` to the underlying
`setup.py`, when invoking `setup.py` so # setuptools doesn't think the script
is `-c`. This avoids the following warning: # manifest_maker: standard file
'-c' not found". # - It generates a shim setup.py, for handling setup.cfg-only
projects. import os, sys, tokenize try: import setuptools except ImportError
as error: print( "ERROR: Can not execute `setup.py` since setuptools is not
available in " "the build environment.", file=sys.stderr, ) sys.exit(1)
__file__ = %r sys.argv[0] = __file__ if os.path.exists(__file__): filename =
__file__ with tokenize.open(__file__) as f: setup_py_code = f.read() else:
filename = "<auto-generated setuptools caller>" setup_py_code = "from
setuptools import setup; setup()" exec(compile(setup_py_code, filename,
"exec")) ''' % ('/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-
install-1t1qd51a/umap-learn_d87457d0fd2d4d85b30e0f8b29d026c8/setup.py',),
"<pip-setuptools-caller>", "exec"))' [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.  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 451.140.1.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 20 days 18:01

Graphics/Displays:

    Radeon Pro 580:

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


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    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-ArtiaX: 0.1
    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: 1.5.dev202210050037
    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-PhenixUI: 1.0.1
    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: 1.24.1
    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: 1.1.0
    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
    pandas: 1.4.4
    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: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.4
    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
    starfile: 0.4.11
    superqt: 0.3.5
    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: 4.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1
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 error in the Log for ChimeraX 1.5 seems to say setuptools is not available so it apparently can't install umap-learn from source.

In ChimeraX 1.4 toolshed installing the same wheel file fails in umap-learn in a different way -- here is the ChimeraX 1.4 Log output

UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
toolshed install /Users/goddard/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 scikit-learn Using cached scikit_learn-1.1.2-cp39-cp39-macosx_10_9_x86_64.whl (8.7 MB) Requirement already satisfied: ChimeraX-UI~=1.0 in ./ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from wiggle==0.2.2) (1.18.3) 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 phate Using cached phate-1.0.8-py3-none-any.whl (23 kB) Collecting pyqtgraph Using cached pyqtgraph-0.13.1-py3-none-any.whl (966 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 'error' Using cached umap-learn-0.5.2.tar.gz (86 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.5.1.tar.gz (80 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.5.0.tar.gz (81 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.4.6.tar.gz (69 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.4.5.tar.gz (69 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.4.4.tar.gz (69 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.4.3.tar.gz (68 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.4.2.tar.gz (68 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.4.1.tar.gz (68 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.4.0.tar.gz (68 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.10.tar.gz (40 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.9.tar.gz (40 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.8.tar.gz (40 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.7.tar.gz (40 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.6.tar.gz (39 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.5.tar.gz (39 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.4.tar.gz (39 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.2.tar.gz (38 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.1.tar.gz (38 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.3.0.tar.gz (38 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.2.5.tar.gz (30 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.2.4.tar.gz (30 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.2.3.tar.gz (30 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.2.2.tar.gz (30 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.2.1.tar.gz (30 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.2.0.tar.gz (29 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.1.5.tar.gz (26 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.1.4.tar.gz (22 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.1.3.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.1.2.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.1.1.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' Using cached umap-learn-0.1.0.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3a99a1ea6f3a47d1a1a1742e8473fe3c/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3a99a1ea6f3a47d1a1a1742e8473fe3c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-w8hof68x cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3a99a1ea6f3a47d1a1a1742e8473fe3c/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3a99a1ea6f3a47d1a1a1742e8473fe3c/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3a99a1ea6f3a47d1a1a1742e8473fe3c/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/e1/eb/dca6cfd872e8542fb57dd56ff2d5d67baed270aee6db739c6414d8d5b3b5/umap-learn-0.5.3.tar.gz#sha256=dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_b32c5c6081d14a0dbf9b597ed2447e96/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_b32c5c6081d14a0dbf9b597ed2447e96/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-a4j_0vkf cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_b32c5c6081d14a0dbf9b597ed2447e96/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_b32c5c6081d14a0dbf9b597ed2447e96/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_b32c5c6081d14a0dbf9b597ed2447e96/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/7e/8f/3521bd0ac15c1de51bc8cbe09b3af3ddf51f22fa05da1749a9dec81380a4/umap-learn-0.5.2.tar.gz#sha256=0ede8921c3ef0e1976cdc91b533b2bce82471c87dbb9fad447f617ca5b881d52 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_287d29051c9146c4b219dec0f66ebc06/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_287d29051c9146c4b219dec0f66ebc06/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-yke8ato5 cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_287d29051c9146c4b219dec0f66ebc06/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_287d29051c9146c4b219dec0f66ebc06/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_287d29051c9146c4b219dec0f66ebc06/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/75/69/85e7f950bb75792ad5d666d86c5f3e62eedbb942848e7e3126513af9999c/umap-learn-0.5.1.tar.gz#sha256=3e3e5e526109866012a9da79f423c922edc379c6cac9bf65ea08fbb9dd93ff3a (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_9fab0a75eaf649a5ab58f7b7c9cabbe3/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_9fab0a75eaf649a5ab58f7b7c9cabbe3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-6clfthhn cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_9fab0a75eaf649a5ab58f7b7c9cabbe3/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_9fab0a75eaf649a5ab58f7b7c9cabbe3/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_9fab0a75eaf649a5ab58f7b7c9cabbe3/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/f1/53/3b1598971f4cfe30841ed3390a09820ce830143fd3374fe4f7707175d219/umap-learn-0.5.0.tar.gz#sha256=769c50629871384e85e952ad6f7086c49895f0390e1da8d2b2d7c60ad03a0ed0 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_a2d651dc1fa74cff9a27279fab8a0bbc/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_a2d651dc1fa74cff9a27279fab8a0bbc/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-masxa_er cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_a2d651dc1fa74cff9a27279fab8a0bbc/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_a2d651dc1fa74cff9a27279fab8a0bbc/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_a2d651dc1fa74cff9a27279fab8a0bbc/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/ac/21/e1eb2eb1c624a84f4a23237adb974e94ff7371ee8c178d246194af83fb80/umap-learn-0.4.6.tar.gz#sha256=4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ab01b8f20f8241c79afff05b4e94e55b/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ab01b8f20f8241c79afff05b4e94e55b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-yz8xn_lb cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ab01b8f20f8241c79afff05b4e94e55b/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ab01b8f20f8241c79afff05b4e94e55b/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ab01b8f20f8241c79afff05b4e94e55b/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/1a/ac/02cb40c535a19b5b956b1d3fdf534612b0f5d0a729fb9bbc8b5a2bf093f3/umap-learn-0.4.5.tar.gz#sha256=b12fb3518b9d8b0270fd0715a837a67f25a46d81cbb5e570bfbfce9b330a6f98 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_50d7e406b1dc42e6be3d7573b24cb442/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_50d7e406b1dc42e6be3d7573b24cb442/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-303o78uo cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_50d7e406b1dc42e6be3d7573b24cb442/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_50d7e406b1dc42e6be3d7573b24cb442/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_50d7e406b1dc42e6be3d7573b24cb442/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/6b/85/8ffd8d76b5f825690535656cd6551a2b64fdc47adbb2bbc5e2fe62194918/umap-learn-0.4.4.tar.gz#sha256=7e4668915d170c5c444760a7d544a3107398a193f07cf420029eb9c732f3a6eb (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_73463fc490864e7c810c4d925e4cca16/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_73463fc490864e7c810c4d925e4cca16/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-6i1z0fpq cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_73463fc490864e7c810c4d925e4cca16/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_73463fc490864e7c810c4d925e4cca16/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_73463fc490864e7c810c4d925e4cca16/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/93/ac/838287c562b8f73448ea0d1a989e696d10ba401ce1eaeb64a227f2bca8c4/umap-learn-0.4.3.tar.gz#sha256=e4ac9f537f05a0f511a318b63a15ad0b26a485a2d51b85c392f832bc1c28c4d9 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_875af1de83174077aae5c28c0acd4aa1/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_875af1de83174077aae5c28c0acd4aa1/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-60hib2s1 cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_875af1de83174077aae5c28c0acd4aa1/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_875af1de83174077aae5c28c0acd4aa1/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_875af1de83174077aae5c28c0acd4aa1/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/70/8a/ff151a059e6dcbe7c482442b92931ae289c052a7c42b9c3772d184cab1ae/umap-learn-0.4.2.tar.gz#sha256=3d9e28ff567f47e20a9e731225eac63618845271bb3cb8d804ed9b81d97f7470 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_16a208e185a64794acbc1ccc0835ccc9/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_16a208e185a64794acbc1ccc0835ccc9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-c8nk_e4n cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_16a208e185a64794acbc1ccc0835ccc9/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_16a208e185a64794acbc1ccc0835ccc9/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_16a208e185a64794acbc1ccc0835ccc9/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/f2/f0/7f8b24669c54adc49356707c20000db8afadc479059721cffa6ceb8352e4/umap-learn-0.4.1.tar.gz#sha256=c2a70e5ed561b98cf5ba810e05b6d0f4c31dac27ac93e6de5ea6cb59a9e2a3bb (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f56fae4887f4451db45e210b86aa2249/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f56fae4887f4451db45e210b86aa2249/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-u1svk8u5 cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f56fae4887f4451db45e210b86aa2249/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f56fae4887f4451db45e210b86aa2249/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f56fae4887f4451db45e210b86aa2249/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/12/45/81a0520de8c5d1de1baa733a02e27dff3adb63e8fc71b34234889f8437a6/umap-learn-0.4.0.tar.gz#sha256=fc33bf6d83baedefbcf3dabd8f61ac4b46c8880ab6e3717964681d821966b223 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_22f1b285dd964d5ca5b25c57d2c35cae/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_22f1b285dd964d5ca5b25c57d2c35cae/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-twosacjl cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_22f1b285dd964d5ca5b25c57d2c35cae/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_22f1b285dd964d5ca5b25c57d2c35cae/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_22f1b285dd964d5ca5b25c57d2c35cae/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/ad/92/36bac74962b424870026cb0b42cec3d5b6f4afa37d81818475d8762f9255/umap-learn-0.3.10.tar.gz#sha256=21ce6b6d7486905318ba6458b5a9ba2cfb935878d30c24e6fba64ee3bd504d09 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ff7415213ada4690bd4e4b3d383f462e/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ff7415213ada4690bd4e4b3d383f462e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-p1cn7i8n cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ff7415213ada4690bd4e4b3d383f462e/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ff7415213ada4690bd4e4b3d383f462e/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ff7415213ada4690bd4e4b3d383f462e/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/d9/15/ced881a7af6184c5556dbffbfc82750904a18c6fdafb248ca84873d0be06/umap-learn-0.3.9.tar.gz#sha256=1afa7036b84c30a466c03d16fabbcda42fe1bea8faebb0cc1e9b2ac3ea28a19c (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_21a0235ef93b4300a528f9c4e8466ea3/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_21a0235ef93b4300a528f9c4e8466ea3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-7f_ps2uo cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_21a0235ef93b4300a528f9c4e8466ea3/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_21a0235ef93b4300a528f9c4e8466ea3/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_21a0235ef93b4300a528f9c4e8466ea3/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/26/7f/f39ff1028f8464ab08ef894f85e783df58e494099103044d008f9385d820/umap-learn-0.3.8.tar.gz#sha256=f688060bce5495c06cb3e52df0982a63bb7b7755393b9f30e08e0c1791520d15 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_8354d9d230c74718b682b7c91e1b4dc5/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_8354d9d230c74718b682b7c91e1b4dc5/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-wk78gt2n cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_8354d9d230c74718b682b7c91e1b4dc5/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_8354d9d230c74718b682b7c91e1b4dc5/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_8354d9d230c74718b682b7c91e1b4dc5/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/4e/ce/33e260133f2a8e6c24a434e22de31f1dff01d58b3beec033d5c1b544bfb7/umap-learn-0.3.7.tar.gz#sha256=9c81c9cdc46cc8a87adf1972eeac5ec69bbe9cec440c0e4995fc68a015aafeb9 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_0b01852665db49b2aa3bfdaa336f89cc/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_0b01852665db49b2aa3bfdaa336f89cc/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-p7mq467d cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_0b01852665db49b2aa3bfdaa336f89cc/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_0b01852665db49b2aa3bfdaa336f89cc/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_0b01852665db49b2aa3bfdaa336f89cc/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/e6/3a/404bd62c29af4cd83b9c7adef88f7e9192e0a5b7768ce4260c3a6a2f41db/umap-learn-0.3.6.tar.gz#sha256=0b6bc94ade352cedb4fb22e59a1cc536b04e686d28d2abd647f5fa0994eeba7c (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_2e9ac901552f4469b7bae7aa88017fd8/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_2e9ac901552f4469b7bae7aa88017fd8/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-ktq5ecw6 cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_2e9ac901552f4469b7bae7aa88017fd8/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_2e9ac901552f4469b7bae7aa88017fd8/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_2e9ac901552f4469b7bae7aa88017fd8/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/aa/f9/338a9fe0ec36be32564ad5c57897c36f16c8b34ba79a16de5e35f394ed98/umap-learn-0.3.5.tar.gz#sha256=309cf6e218ae9c5a38c4469919be9471c3dd7a97312f6e8a72d8a8800997f12d (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_be4ebf8cd8744aa3b612e9f2ed2c5738/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_be4ebf8cd8744aa3b612e9f2ed2c5738/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-viizqo8k cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_be4ebf8cd8744aa3b612e9f2ed2c5738/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_be4ebf8cd8744aa3b612e9f2ed2c5738/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_be4ebf8cd8744aa3b612e9f2ed2c5738/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/01/5d/dd32c47ee2f0b7ee940dc88cab9389c5d33cab7f187c2691b709a66ea898/umap-learn-0.3.4.tar.gz#sha256=dced7ee0677d2506f217d8962444f6b3d4e9808c8e5f9fb35372eb4b8af2d617 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3e0315c9b4244c2084e0ee885caf4c75/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3e0315c9b4244c2084e0ee885caf4c75/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-8_1wpmcr cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3e0315c9b4244c2084e0ee885caf4c75/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3e0315c9b4244c2084e0ee885caf4c75/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_3e0315c9b4244c2084e0ee885caf4c75/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/fc/c8/9c8d3a59ee589f7a81ab19b4cd2a00717edb8f3517b5758fa51222b3a3eb/umap-learn-0.3.2.tar.gz#sha256=1f5d28bb70979a0ba14a2c125194294e58ccd2a6fb4744c0ab472bc04ddc708a (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_c3bedde2b8a345cfb1f0fe603cbb8c2f/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_c3bedde2b8a345cfb1f0fe603cbb8c2f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-otrhtfco cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_c3bedde2b8a345cfb1f0fe603cbb8c2f/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_c3bedde2b8a345cfb1f0fe603cbb8c2f/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_c3bedde2b8a345cfb1f0fe603cbb8c2f/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/25/04/0dc35361e7fd7472784a51f71302ab3d51653fecc0718de1eeac2120f59e/umap-learn-0.3.1.tar.gz#sha256=32a8c14c0f5988865afa8236c8fad6d0c2b781d5993694924ff859a905c7e6e4 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_56027db4bd914eb0b3790979260bde68/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_56027db4bd914eb0b3790979260bde68/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-_3439lqs cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_56027db4bd914eb0b3790979260bde68/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_56027db4bd914eb0b3790979260bde68/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_56027db4bd914eb0b3790979260bde68/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/32/4d/e87008c24f39e498341fea26a41b5c861b24bab4d3ddbe4554bf222c026e/umap-learn-0.3.0.tar.gz#sha256=40d8522a301a7691789601fb009c8696141e0aab1ebb648614d7180a7f792225 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_00c01737ccb1426896f38eaba8f2b89c/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_00c01737ccb1426896f38eaba8f2b89c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-gl_3g7s_ cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_00c01737ccb1426896f38eaba8f2b89c/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_00c01737ccb1426896f38eaba8f2b89c/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_00c01737ccb1426896f38eaba8f2b89c/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/5c/fe/9fab22acd9a33d49a221cc683ac0826b38d85e2b5cf58576bcc2b3ec2660/umap-learn-0.2.5.tar.gz#sha256=34f2f6caa15723312cad760bc970fe6f7dde82b7fa5b8791979588ea4d7311fe (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ce9d3eaf1880478eac2b9199099d6219/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ce9d3eaf1880478eac2b9199099d6219/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-jqhzmc21 cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ce9d3eaf1880478eac2b9199099d6219/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ce9d3eaf1880478eac2b9199099d6219/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_ce9d3eaf1880478eac2b9199099d6219/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/8b/c4/5d4ad1d384847239ebb0e637fd975ab55d63b5708d785cfba0bf802bc141/umap-learn-0.2.4.tar.gz#sha256=5a0cb639a98c64184b79d2f81571443eda588e696e1c28db86ce14cd4bcfba5d (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_305878b4588f41bd9e748ecc1211ab95/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_305878b4588f41bd9e748ecc1211ab95/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-r4jj6xq3 cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_305878b4588f41bd9e748ecc1211ab95/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_305878b4588f41bd9e748ecc1211ab95/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_305878b4588f41bd9e748ecc1211ab95/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/e5/d9/26bf2c04a5689e3bfb25149047c14ad3276bbe67b88b35e415caa8024dde/umap-learn-0.2.3.tar.gz#sha256=87012d966a61d79cad81703dd1a46c4a48d9a602918899f228b67ac6bc98abc5 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_7ad2b211cb4c4a4aaacff4202f145e75/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_7ad2b211cb4c4a4aaacff4202f145e75/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-s8mz5rjz cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_7ad2b211cb4c4a4aaacff4202f145e75/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_7ad2b211cb4c4a4aaacff4202f145e75/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_7ad2b211cb4c4a4aaacff4202f145e75/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/d6/ea/07464043825217aabf2fa661b121e308008e13296b9517e41bc462e35ee6/umap-learn-0.2.2.tar.gz#sha256=126bc480920dd39594a5198486b3fd058074301d820348611d0d62591060d74e (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_69afc7a8071f4919a111d0cbc2ce929a/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_69afc7a8071f4919a111d0cbc2ce929a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-95t74rme cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_69afc7a8071f4919a111d0cbc2ce929a/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_69afc7a8071f4919a111d0cbc2ce929a/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_69afc7a8071f4919a111d0cbc2ce929a/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/63/80/95b670c3c8762aca5b31b8e522a1710b64e4192fe2f3edf51e6882596899/umap-learn-0.2.1.tar.gz#sha256=9504bbd3a627d3ee50a33b9036cc8241bfca4f39ef9b4db60de5933486f1e748 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_4fe955f6eaa4452a96888cdd6727b02e/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_4fe955f6eaa4452a96888cdd6727b02e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-24u71vxg cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_4fe955f6eaa4452a96888cdd6727b02e/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_4fe955f6eaa4452a96888cdd6727b02e/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_4fe955f6eaa4452a96888cdd6727b02e/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/f4/ef/92f55d65ebaa5510aa4ec616e0fa04de27328473be51aca8cdb61d222cbf/umap-learn-0.2.0.tar.gz#sha256=a784932079eba344b3393aa58f7211adfa208aa6cf9744c1c524209b5322c6ed (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f5297c57fdeb404c88218fc255aa5b7d/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f5297c57fdeb404c88218fc255aa5b7d/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-9ekk22lp cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f5297c57fdeb404c88218fc255aa5b7d/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f5297c57fdeb404c88218fc255aa5b7d/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_f5297c57fdeb404c88218fc255aa5b7d/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/6d/b3/76ac6f4898931aac13290d6b2bab12c463674a1311bccab20e2bc7204457/umap-learn-0.1.5.tar.gz#sha256=11ab4df92fb33694a4d5aca91484e778e254de1d04c1112933b70bd9e26c81fb (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_426d6f68a6e9453189922bf17494ecf6/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_426d6f68a6e9453189922bf17494ecf6/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-op0masbc cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_426d6f68a6e9453189922bf17494ecf6/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_426d6f68a6e9453189922bf17494ecf6/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_426d6f68a6e9453189922bf17494ecf6/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/db/67/6f9416edf038cc08b339bbacc9a74e09144498392082b679773e990b17ff/umap-learn-0.1.4.tar.gz#sha256=721e24b14e219b9956e2c38a893e4acc6db5e125af4c8d35abf1cccffb664390 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_505b6114094b4ebdbb129e09963e6ae3/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_505b6114094b4ebdbb129e09963e6ae3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-cjhczt4n cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_505b6114094b4ebdbb129e09963e6ae3/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_505b6114094b4ebdbb129e09963e6ae3/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_505b6114094b4ebdbb129e09963e6ae3/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/7e/43/14c1bd9800b266dec342d26ba52f18dd25828d572f135fc66e700e5fc1df/umap-learn-0.1.3.tar.gz#sha256=539d81a3d8bbb1c9b6ab50cc45f6e1bead5886f909784524fb551a7319825a79 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_1889c8f7f0744df094739c8234e79293/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_1889c8f7f0744df094739c8234e79293/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-j98k67ky cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_1889c8f7f0744df094739c8234e79293/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_1889c8f7f0744df094739c8234e79293/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_1889c8f7f0744df094739c8234e79293/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/e7/aa/f636bc5921e3233cede1722bebe2f436f03eac367ed78ab8060d7199d837/umap-learn-0.1.2.tar.gz#sha256=ff91962b56b03d798fce816b2427c15aac0b27fa44e65f885251b7bb3917f9fb (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_bc2fe80ffc6047f682b55d888df6310a/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_bc2fe80ffc6047f682b55d888df6310a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-4wlwqeho cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_bc2fe80ffc6047f682b55d888df6310a/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_bc2fe80ffc6047f682b55d888df6310a/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_bc2fe80ffc6047f682b55d888df6310a/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/08/5e/6c0b8dc72c739428258d6e63ea7bc034b1007c56abdf8147cc8fe731ccbf/umap-learn-0.1.1.tar.gz#sha256=dd3aa829343288ef7710242966d7c19d7031c875cae3550b2189543b33dc2835 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Command errored out with exit status 1: command: /Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_613955b2266841a8b1b935db668527ac/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_613955b2266841a8b1b935db668527ac/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-pip-egg-info-wiqe0nlc cwd: /private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_613955b2266841a8b1b935db668527ac/ Complete output (1 lines): invalid command name 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_613955b2266841a8b1b935db668527ac/setup.py'; __file__='/private/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/pip-install-hkqkzlnm/umap-learn_613955b2266841a8b1b935db668527ac/setup.py';f = getattr(tokenize, 'open', open)(__file__) if os.path.exists(__file__) else io.StringIO('from setuptools import setup; setup()');code = f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))' ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/11/c8/1243243c66d6aeb74372a2b7ed8759ddca64f7eea96a7ae1e2008ed9ca0b/umap-learn-0.1.0.tar.gz#sha256=6bbe26cfccf54afccb75ff05ca1745f128567a88ec0e509fb3c68a4e7a44f7c1 (from https://pypi.org/simple/umap-learn/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Could not find a version that satisfies the requirement umap-learn (from wiggle) (from versions: 0.1.0, 0.1.1, 0.1.2, 0.1.3, 0.1.4, 0.1.5, 0.2.0, 0.2.1, 0.2.2, 0.2.3, 0.2.4, 0.2.5, 0.3.0, 0.3.1, 0.3.2, 0.3.4, 0.3.5, 0.3.6, 0.3.7, 0.3.8, 0.3.9, 0.3.10, 0.4.0rc1, 0.4.0rc2, 0.4.0rc3, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.4.4, 0.4.5, 0.4.6, 0.5.0rc1, 0.5.0, 0.5.1, 0.5.2, 0.5.3) ERROR: No matching distribution found for umap-learn WARNING: You are using pip version 21.3.1; however, version 22.2.2 is available. You should consider upgrading via the '/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command.

[Tom Goddard]

Bundle info file with dependencies that cause this problem.

[Tom Goddard]

The error seems to be in trying to install umap-learn

"ERROR: Can not execute setup.py since setuptools is not available in the build environment."

[Tom Goddard]

This problem has some priority. I am helping Charles Bayly-Jones try to get his very cool Wiggle bundle (​https://github.com/charbj/wiggle) on the Toolshed. He said he has not put it on Toolshed because he could not get the PyPi dependencies to install. So he explains a multistep install procedure on his github site to use his bundle.

[Greg Couch]

Does ChimeraX.app/contents/bin/python -m pip install umap-learn work?

[Zach Pearson]

It does for me, but it downgrades setuptools in ChimeraX's site-packages directory to 58 in the process.

[Zach Pearson]

I forked the Wiggle source code and made a TOML backed version. Built a wheel with my 1.5 developer build using a Makefile copied from the Bundle template and tried to install it with make install (i.e. through 'toolshed install'). Full traceback:

Installing bundle
Executing: toolshed install /Users/zjp/git/rbvi/wiggle/dist/ChimeraX_wiggle-0.2.2-py3-none-any.whl
Traceback (most recent call last):
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolshed_utils/__init__.py", line 505, in _pip_install
    results = _run_logged_pip(command, logger)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolshed_utils/__init__.py", line 569, in _run_logged_pip
    raise RuntimeError(s)
RuntimeError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./dist/ChimeraX_wiggle-0.2.2-py3-none-any.whl
Collecting torch
  Using cached torch-1.12.1-cp39-none-macosx_11_0_arm64.whl (49.1 MB)
Collecting pyqtgraph
  Using cached pyqtgraph-0.13.1-py3-none-any.whl (966 kB)
Collecting scikit-image
  Using cached scikit_image-0.19.3-cp39-cp39-macosx_12_0_arm64.whl (12.5 MB)
Collecting pyyaml
  Using cached PyYAML-6.0-cp39-cp39-macosx_11_0_arm64.whl (173 kB)
Collecting scikit-learn
  Using cached scikit_learn-1.1.2-cp39-cp39-macosx_12_0_arm64.whl (7.7 MB)
Requirement already satisfied: ChimeraX-UI~=1.0 in /Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-wiggle==0.2.2) (1.24.2)
Collecting phate
  Using cached phate-1.0.8-py3-none-any.whl (23 kB)
Requirement already satisfied: ChimeraX-Core~=1.1 in /Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-wiggle==0.2.2) (1.5.dev202210132255)
Collecting mrcfile
  Using cached mrcfile-1.4.3-py2.py3-none-any.whl (43 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 'error'
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [36 lines of output]
      invalid command name '
      exec(compile('''
      # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
      #
      # - It imports setuptools before invoking setup.py, to enable projects that directly
      #   import from `distutils.core` to work with newer packaging standards.
      # - It provides a clear error message when setuptools is not installed.
      # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
      #   setuptools doesn't think the script is `-c`. This avoids the following warning:
      #     manifest_maker: standard file '-c' not found".
      # - It generates a shim setup.py, for handling setup.cfg-only projects.
      import os, sys, tokenize

      try:
          import setuptools
      except ImportError as error:
          print(
              "ERROR: Can not execute `setup.py` since setuptools is not available in "
              "the build environment.",
              file=sys.stderr,
          )
          sys.exit(1)

      __file__ = %r
      sys.argv[0] = __file__

      if os.path.exists(__file__):
          filename = __file__
          with tokenize.open(__file__) as f:
              setup_py_code = f.read()
      else:
          filename = "<auto-generated setuptools caller>"
          setup_py_code = "from setuptools import setup; setup()"

      exec(compile(setup_py_code, filename, "exec"))
      ''' % ('/private/var/folders/6n/m_fspl_j5n15hgm31nkqhfh40000gn/T/pip-install-r0igph8v/umap-learn_d167f35323b1467383591d095cf57c1f/setup.py',), "<pip-setuptools-caller>", "exec"))'
      [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.


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/zjp/git/rbvi/ChimeraX/src/bundles/core/src/commands/devel.py", line 175, in _run
    unbound_method(bb, *args, **kw)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/bundle_builder/bundle_builder_toml.py", line 402, in make_install
    run(session, cmd)
  File "/Users/zjp/git/rbvi/ChimeraX/src/bundles/core/src/commands/run.py", line 38, in run
    results = command.run(text, log=log, return_json=return_json)
  File "/Users/zjp/git/rbvi/ChimeraX/src/bundles/core/src/commands/cli.py", line 2897, in run
    result = ci.function(session, **kw_args)
  File "/Users/zjp/git/rbvi/ChimeraX/src/bundles/core/src/commands/toolshed.py", line 301, in toolshed_install
    ts.install_bundle(bundles, logger, **kw)
  File "/Users/zjp/git/rbvi/ChimeraX/src/bundles/core/src/toolshed/__init__.py", line 914, in install_bundle
    _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolshed_utils/__init__.py", line 240, in _install_bundle
    results = _pip_install(
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolshed_utils/__init__.py", line 508, in _pip_install
    raise UserError(str(e))
chimerax.core.errors.UserError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./dist/ChimeraX_wiggle-0.2.2-py3-none-any.whl
Collecting torch
  Using cached torch-1.12.1-cp39-none-macosx_11_0_arm64.whl (49.1 MB)
Collecting pyqtgraph
  Using cached pyqtgraph-0.13.1-py3-none-any.whl (966 kB)
Collecting scikit-image
  Using cached scikit_image-0.19.3-cp39-cp39-macosx_12_0_arm64.whl (12.5 MB)
Collecting pyyaml
  Using cached PyYAML-6.0-cp39-cp39-macosx_11_0_arm64.whl (173 kB)
Collecting scikit-learn
  Using cached scikit_learn-1.1.2-cp39-cp39-macosx_12_0_arm64.whl (7.7 MB)
Requirement already satisfied: ChimeraX-UI~=1.0 in /Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-wiggle==0.2.2) (1.24.2)
Collecting phate
  Using cached phate-1.0.8-py3-none-any.whl (23 kB)
Requirement already satisfied: ChimeraX-Core~=1.1 in /Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-wiggle==0.2.2) (1.5.dev202210132255)
Collecting mrcfile
  Using cached mrcfile-1.4.3-py2.py3-none-any.whl (43 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 'error'
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [36 lines of output]
      invalid command name '
      exec(compile('''
      # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
      #
      # - It imports setuptools before invoking setup.py, to enable projects that directly
      #   import from `distutils.core` to work with newer packaging standards.
      # - It provides a clear error message when setuptools is not installed.
      # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
      #   setuptools doesn't think the script is `-c`. This avoids the following warning:
      #     manifest_maker: standard file '-c' not found".
      # - It generates a shim setup.py, for handling setup.cfg-only projects.
      import os, sys, tokenize

      try:
          import setuptools
      except ImportError as error:
          print(
              "ERROR: Can not execute `setup.py` since setuptools is not available in "
              "the build environment.",
              file=sys.stderr,
          )
          sys.exit(1)

      __file__ = %r
      sys.argv[0] = __file__

      if os.path.exists(__file__):
          filename = __file__
          with tokenize.open(__file__) as f:
              setup_py_code = f.read()
      else:
          filename = "<auto-generated setuptools caller>"
          setup_py_code = "from setuptools import setup; setup()"

      exec(compile(setup_py_code, filename, "exec"))
      ''' % ('/private/var/folders/6n/m_fspl_j5n15hgm31nkqhfh40000gn/T/pip-install-r0igph8v/umap-learn_d167f35323b1467383591d095cf57c1f/setup.py',), "<pip-setuptools-caller>", "exec"))'
      [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.



make: *** [install] Error 1
(.venv) wiggle git:(main) Ⲗ

[Tom Goddard]

Looks like the same error message as the bundle_info.xml version only with newlines making it infinitely more readable.

[Zach Pearson]

It's definitely that umap is only available as source code. If we fix toolshed installing source code it should work.

[Tom Goddard]

Also umap-learn is entirely Python code. So the install is nothing complicated. But probably the install of some umap-learn dependency is causing the error.

[Zach Pearson]

Just want to note that if you download the umap-learn tarball and try, for example:

wiggle git:(main) Ⲗ ../ChimeraX/ChimeraX.app/Contents/MacOS/ChimeraX -m pip install ~/Downloads/umap-learn-0.5.3.tar.gz

it also fails, for the exact same reason as it does when trying to install it indirectly as a Wiggle dependency.

I thought something we do to the environment at startup is at play, but maybe not: PyRun_SimpleString("import setuptools") before Py_Main in launcher.c had no effect.

So maybe we're missing some command line argument in core/main

[Zach Pearson]

Still, it's good to be able to narrow down the test case to this one package.

[Tom Goddard]

That is useful to have a simpler test case demonstrating the problem.

Here is a test that correctly installs umap-learn using the ChimeraX python executable. In this test umap-learn is installed in the application site-packages because I did not specify the --user option. I believe if I specify the --user option it installs it in the Python user site-packages location and not the ChimeraX user site-packages.

$ ~/ucsf/chimerax/ChimeraX.app/Contents/bin/python3.9 -m pip install umap-learn
Collecting umap-learn
  Using cached umap-learn-0.5.3.tar.gz (88 kB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy>=1.17 in /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from umap-learn) (1.23.1)
Collecting scikit-learn>=0.22
  Using cached scikit_learn-1.1.2-cp39-cp39-macosx_12_0_arm64.whl (7.7 MB)
Requirement already satisfied: scipy>=1.0 in /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from umap-learn) (1.9.0)
Collecting numba>=0.49
  Downloading numba-0.56.3-cp39-cp39-macosx_11_0_arm64.whl (2.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 14.0 MB/s eta 0:00:00

Collecting pynndescent>=0.5
  Using cached pynndescent-0.5.7-py3-none-any.whl
Collecting tqdm
  Using cached tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
Collecting llvmlite<0.40,>=0.39.0dev0
  Using cached llvmlite-0.39.1-cp39-cp39-macosx_11_0_arm64.whl (23.1 MB)
Requirement already satisfied: setuptools in /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from numba>=0.49->umap-learn) (65.1.1)
Collecting joblib>=0.11
  Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
Collecting threadpoolctl>=2.0.0
  Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Building wheels for collected packages: umap-learn
  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=6362b2b558df1ebd7ecff9f24eb780949a672ce126cdc799bb7fe9b08aa8c402
  Stored in directory: /Users/goddard/Library/Caches/pip/wheels/f4/3e/1c/596d0a463d17475af648688443fa4846fef624d1390339e7e9
Successfully built umap-learn
Installing collected packages: tqdm, threadpoolctl, llvmlite, joblib, scikit-learn, numba, pynndescent, umap-learn
  WARNING: The script tqdm is installed in '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/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 joblib-1.2.0 llvmlite-0.39.1 numba-0.56.3 pynndescent-0.5.7 scikit-learn-1.1.2 threadpoolctl-3.1.0 tqdm-4.64.1 umap-learn-0.5.3
$ 

[Zach Pearson]

Here's a weird case too: if you patch src/core/commands/pip.py's 'install' logic to say:

    if action == 'install':
        if not package:
            raise UserError("Can't possibly install an unspecified package.")
        else:
            if not package.endswith(".tar.gz"):
                try:
                    req = Requirement(package)
                except InvalidRequirement:
                    raise UserError("Can't install package: invalid requirement specified.")
            pip_cmd.extend(["install", "--user"])
            if upgrade:
                pip_cmd.extend(["--upgrade"])
            pip_cmd.extend(["%s" % package])
            # If we don't add this flag then pip complains that distutils and sysconfig
            # don't report the same location for the user's site packages directory. The
            # error tells programmers to report the error to
            # https://github.com/pypa/pip/issues/10151
            pip_cmd.extend(["--no-warn-script-location"])

then installing the tar.gz from the ChimeraX command line works fine.

It's like it only doesn't work from the executable.

[Tom Goddard]

Sounds like Zach and Greg were close to solving this today. It would be nice to get it into 1.5 since that will allow the Wiggle bundle to get into the Toolshed, and maybe other bundle developers has similar problems with PyPi dependencies.

But it also sounds like the change could be risky, so let's only put it in 1.5 if we have high confidence that it is safe. And we should test installing ISOLDE and the other popular bundles on a clean machine to make sure they keep working.

[Zach Pearson]

One more nail in the binary's coffin!

../ChimeraX/ChimeraX.app/Contents/bin/python3.9 -I -m chimerax.core -I -m pip install ~/Downloads/umap-learn-0.5.3.tar.gz

works

[Zach Pearson]

Thanks to Greg finding a bug in the Python option parsing and fixing it, I was able to install umap-learn as a wiggle dependency on my mac and on Windows. I think we can tell this developer his bundle can go on the toolshed. :) The developer should use bundle_info.xml for now. I haven't yet started the conversation about evaluating whether toolshed can handle TOML based bundles, and we shouldn't rush that for the 1.5 release.

[Tom Goddard]

Good work fixing this toolshed install problem. I've tried installing all the wiggle dependencies and now there is a different toolshed install error reported as bug #7824.