Opened 18 months ago
Closed 18 months ago
#15004 closed defect (limitation)
ArtiaX dependency not installed
Reported by: | Owned by: | Greg Couch | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Tool Shed | Version: | |
Keywords: | Cc: | Utz Ermel | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-14.2-arm64-arm-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Installed latest ArtiaX using toolshed. Error recieved when launching ArtiaX. Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Traceback (most recent call last): File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/__init__.py", line 120, in run_provider from .toolbar import run_provider File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/toolbar/__init__.py", line 3, in <module> from .toolbar import * File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/toolbar/toolbar.py", line 4, in <module> from ..particle.ParticleList import delete_selected_particles, invert_selection File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/particle/__init__.py", line 2, in <module> from .ParticleList import ParticleList File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/particle/ParticleList.py", line 19, in <module> from ..io.ParticleData import ParticleData File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/io/__init__.py", line 7, in <module> from .Copick import CopickParticleData File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/io/Copick/__init__.py", line 3, in <module> from .CopickParticleData import COPICK_FORMAT File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/io/Copick/CopickParticleData.py", line 6, in <module> import pydantic ModuleNotFoundError: No module named 'pydantic' ModuleNotFoundError: No module named 'pydantic' File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/io/Copick/CopickParticleData.py", line 6, in import pydantic See log for complete Python traceback. > artiax start Traceback (most recent call last): File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/__init__.py", line 121, in run_provider run_provider(session, name) File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/toolbar/toolbar.py", line 71, in run_provider run(session, what) File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/cmd/cmd.py", line 36, in artiax_start get_singleton(session) File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/cmd/cmd.py", line 24, in get_singleton from ..tool import ArtiaXUI File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/tool.py", line 29, in <module> from .ArtiaX import ( File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/ArtiaX.py", line 14, in <module> from .io import open_particle_list, save_particle_list, get_fmt_aliases File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/io/__init__.py", line 7, in <module> from .Copick import CopickParticleData File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/io/Copick/__init__.py", line 3, in <module> from .CopickParticleData import COPICK_FORMAT File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/io/Copick/CopickParticleData.py", line 6, in <module> import pydantic ModuleNotFoundError: No module named 'pydantic' ModuleNotFoundError: No module named 'pydantic' File "/Users/joshuahutchings/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/artiax/io/Copick/CopickParticleData.py", line 6, in import pydantic See log for complete Python traceback. OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,3 Model Number: Z1C80001JLL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2 (23C64) Kernel Version: Darwin 23.2.0 Time since boot: 25 days, 5 hours, 20 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.4.5 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 geomdl: 5.3.1 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 pandas: 2.1.4 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 starfile: 0.5.4 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9
Change History (6)
comment:1 by , 18 months ago
Cc: | added |
---|---|
Component: | Unassigned → Tool Shed |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → ArtiaX dependency not installed |
comment:3 by , 18 months ago
Hi Greg and Josh, I had encountered the same thing when I initially added the pydantic requirement, but wasn\u2019t able to reproduce it anymore later on, so thought it was a fluke. This should do the trick for a fix: 1. toolshed uninstall artiax 2. Restart ChimeraX 3. toolshed reload available 4. toolshed install artiax Completely reinstalling seems to add the additional requirements. This may be a bug during bundle installation? Best, Utz
comment:4 by , 18 months ago
If you add a dependency to a bundle, then you need to increase the version number for the new dependency to be picked up. Or, as you appear to have discovered, if the version number doesn't change, uninstall the existing version first.
Does that scenario match what you experienced?
comment:5 by , 18 months ago
I believe I did increase the version from 0.4.2 to 0.4.3 when I added the pydantic requirement (see https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FrangakisLab_ArtiaX_compare_v0.4.2...v0.4.3&d=DwIFaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=CKzZmwKi9_YVvHng-0ezdJFE-0MROfpdFWLsI4CZgtQ&m=3XVJPF1pP0vkMWgJNgCutuW5Z4eLLOKEyq82SMG0V35J78G6vZ2ZCyeHInIVuRrf&s=SKZve1BsLMpZtHOdCO5560KaRAPOT3lB0nbSmGAVgrw&e= ). Do I need to do a minor (or even major) version increase when I add requirements? That would be an easy fix.
comment:6 by , 18 months ago
Resolution: | → limitation |
---|---|
Status: | assigned → closed |
Any version number change should work. ChimeraX uses pip to install dependencies, and there is no option to only update the dependencies of the bundle/wheel that is being forcibly reinstalled.
It is easy to forget to change the version number while developing a bundle. Especially if you have already changed the version number for the next release, installed that, and then decide to add a dependency, but don't change the version number again.
pydantic is listed in the ArtiaX dependencies, but seemingly wasn't installed. Maybe the ArtiaX wheel was directly pip installed?
Reported by Josh Hutchings