Bad version string; slow failure on dependency mismatch

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-6.8.0-57-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.10.dev202504300222 (2025-04-30 02:22:20 UTC)
Description
Trying to get ISOLDE/Clipper up to date with the latest daily builds. I'm reporting from the Ubuntu 22 build which seems fine, but as usual build the wheels themselves using the RHEL8 version in a Singularity container (freshly built using the chimerax-daily.rpm downloaded today from https://www.rbvi.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?commercial=1&file=current/centos-8/chimerax-daily.rpm).

That's failing because the RHEL8 chimerax-daily build is still reporting its version as 1.9.dev202410312003 (checked on a freshly downloaded file by extracting the RPM contents and grepping for the version string). 

Secondary issue: it still makes it all the way through the actual build process despite the requirements mismatch, and only fails on the final install step (traceback below). Given that the dependency on "ChimeraX-Core ~=1.10.0.dev202504300222" is declared in multiple places in the pyproject.toml (attached), I think it should really be failing much earlier. For Clipper, each build takes a few minutes to get through so failing at this end stage is a pain. 

{{{
Executing: toolshed install /home/tcroll/my-gits/chimerax-clipper/dist/ChimeraX_Clipper-0.25.0-cp311-cp311-linux_x86_64.whl
Traceback (most recent call last):
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 528, in _pip_install
    results = run_logged_pip(command, logger)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/chimerax/core/python_utils.py", line 143, in run_logged_pip
    raise RuntimeError(s)
RuntimeError: ERROR: Could not find a version that satisfies the requirement ChimeraX-Core~=1.10.0.dev202504300222 (from chimerax-clipper) (from versions: none)
ERROR: No matching distribution found for ChimeraX-Core~=1.10.0.dev202504300222
}}} 

OpenGL version: 3.3.0 NVIDIA 535.230.02
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        13Gi       2.3Gi       390Mi        15Gi        16Gi
	Swap:          2.0Gi       1.0Gi       1.0Gi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)	
	Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.1
    build: 1.2.2.post1
    certifi: 2025.4.26
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.17
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.6
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202504300222
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.9
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.57.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.6
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.14
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.1.1
    OpenMM: 8.2.0
    openmm-cuda: 8.1.1.11.8
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    pluggy: 1.5.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
File attachment: pyproject.toml

pyproject.toml​

[Tristan Croll]

Added by email2trac

[Tristan Croll]

*Seems* to be just that the version specifier hasn't been updated. If I
manually install the wheel using the Ubuntu ChimeraX, Clipper appears to
work correctly.

On Thu, May 1, 2025 at 2:35 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

[Greg Couch]

With today's RedHat 8 daily build:

$ chimerax-daily --version
UCSF ChimeraX version: 1.10.dev202505010007 (2025-05-01)
© 2016-2025 Regents of the University of California.  All rights reserved.

[Greg Couch]

To test pip's version number matching, use:

from packaging.version import Version
from packaging.specifiers import Specifier
spec = Specifier("~=1.10.0.dev202504300222")
ver = Version("1.10.dev202505010007")
ver in spec
ver19 = Version("1.9")
ver19 in spec

Which outputs True for 1.10.dev202505010007 and False for 1.9.

[Tristan Croll]

Must be a problem with the download server then?

{{{
cd ~/Downloads
ls *.rpm

ls: cannot access '*.rpm': No such file or directory

{use browser to download from the Daily Build section of
https://www.rbvi.ucsf.edu/chimerax/commercial_download.html (
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?commercial=1&file=current/centos-8/chimerax-daily.rpm
)}

mkdir rpm_contents
cd rpm_contents
rpm2cpio ../chimerax-daily.rpm | cpio -idmv
grep -r "1.9.dev"

usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/chimerax/core/buildinfo.py:#
1.9.dev202410312003 2.1
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/chimerax/core/buildinfo.py:version
= "1.9.dev202410312003" # Chimerax core version
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/RECORD:ChimeraX_Core-1.9.dev202410312003.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/RECORD:ChimeraX_Core-1.9.dev202410312003.dist-info/METADATA,sha256=7CTw1n6yVItHUpfkJUNS8unLUEr5F1yavbvKdIvBHlU,1327
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/RECORD:ChimeraX_Core-1.9.dev202410312003.dist-info/RECORD,,
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/RECORD:ChimeraX_Core-1.9.dev202410312003.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/RECORD:ChimeraX_Core-1.9.dev202410312003.dist-info/WHEEL,sha256=BbwEHnplQi27k2WzlwFVqlnQcGtT21PYXfeY1Xqnk8M,104
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/RECORD:ChimeraX_Core-1.9.dev202410312003.dist-info/direct_url.json,sha256=MJXE43beRSGknFcpGiAd9CZYcEjaFZzGNP7MxKEd6UQ,316
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/RECORD:ChimeraX_Core-1.9.dev202410312003.dist-info/top_level.txt,sha256=QjtALFTWLUbNyVu9Tm8rZ90bEJOSd0mgfAJpWWJ_wGw,9
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/METADATA:Version:
1.9.dev202410312003
usr/libexec/UCSF-ChimeraX-daily/lib/python3.11/site-packages/ChimeraX_Core-1.9.dev202410312003.dist-info/direct_url.json:{"archive_info":
{"hash":
"sha256=7f754c85e1156d781b4e3dc5ed6420d420ecde48c6dcb3213941c4ec9386444e",
"hashes": {"sha256":
"7f754c85e1156d781b4e3dc5ed6420d420ecde48c6dcb3213941c4ec9386444e"}},
"url":
"file:///__w/ChimeraX/ChimeraX/src/bundles/core/dist/ChimeraX_Core-1.9.dev202410312003-cp311-cp311-linux_x86_64.whl"}

grep -r "1.10.dev"

{no output}

}}}

On Fri, May 2, 2025 at 12:10 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>

[Zach Pearson]

Thank you for investigating/reporting this. I was looking around Plato and I realized you caught a symbolic link in installers/current/centos-8 pointing at the wrong file. I have fixed it. New downloads should work immediately.