#4032 closed defect (fixed)
"toolshed install" not allowing upgrade
| Reported by: | Eric Pettersen | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | normal | Milestone: | 1.2 |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
The bug isn't in fact the traceback (which has already been reported), but the fact that the toolshed wanted to report a "bundle already installed" error. The installed AddH was version 2.1.1. The wheel I was trying to install was 2.1.3.
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help toolshed
> toolshed install browse
browse does not match any bundles
> toolshed install
> /Users/pett/src/chimerax/src/bundles/addh/dist/ChimeraX_AddH-2.1.3-py38-none-
> any.whl
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 298, in toolshed_install
ts.install_bundle(bundles, logger, **kw)
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
AttributeError: 'str' object has no attribute 'name'
AttributeError: 'str' object has no attribute 'name'
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
See log for complete Python traceback.
> help toolshed
> toolshed list
List of installed bundles:
* AddH (2.1.1): Add hydrogens
* AlignmentAlgorithms (2.0): Sequence alignment algorithms
* AlignmentHdrs (3.2): Alignment header support
* AlignmentMatrices (2.0): Sequence alignment similarity matrices
* Alignments (2.1): Sequence alignment support
* Arrays (1.0): C++ library for parsing numpy arrays
* AtomSearch (2.0): 3D atom search
* Atomic (1.6.1): Atomic-structure functionality
* AxesPlanes (2.0): Depict axes or planes
* BILD (1.0): BILD file reader
* BasicActions (1.1): Basic actions for user-defined specifier names
* BlastProtein (1.0.1): Search PDB/NR using BLAST
* BondRot (2.0): Bond rotation support
* BugReporter (1.0): Report bugs when an error occurs
* BuildStructure (2.0): Create/modify structures
* Bumps (1.0): Find protrusions in density maps
* ButtonPanel (1.0): Create custom user interface panels
* CageBuilder (1.0): Build polygonal meshes for oligomeric molecular assemblies
* CellPack (1.0): Fetch cellPACK models from web
* Centroids (1.1): Depict centroid of atoms
* ChemGroup (2.0): Detect chemically functional groups
* Clashes (2.0): Find clashes/contacts in structures
* ColorActions (1.0): Simple interface for coloring objects
* ColorGlobe (1.0): Show directional resolution colored sphere
* CommandLine (1.1.3): Command line support
* ConnectStructure (2.0): Add bonds to structures that lack them
* Contacts (1.0): Display chain contact maps
* Core (1.1): ChimeraX Core Package
* CoreFormats (1.0): ChimeraX session support
* Crosslinks (1.0): Analyze crosslinks
* Crystal (1.0): Crystal symmetries
* DataFormats (1.0): Data format management
* Dicom (1.0): Read medical imaging and segmentations in DICOM format
* DistMonitor (1.1): Interactive distance display
* DistUI (1.0): Distance measurement user interface
* Dssp (2.0): Compute/assign secondary structure
* EMDB-SFF (1.0): EMDB SFF file reader
* ExperimentalCommands (1.0): Experimental commands
* FileHistory (1.0): File History Panel
* FunctionKey (1.0): Assign function keys to run commands
* Geometry (1.1): Vector and coordinate system routines
* Graphics (1.0): OpenGL graphics rendering
* HKCage (1.0): Create icosahedral mesh of hexagons and pentagons
* Hbonds (2.0): Identify hydrogen bonds in and among structures
* Help (1.0): Show ChimeraX Help
* IHM (1.0): Integrative Hybrid Models file reader
* IMOD (1.0): IMOD model file reader
* IO (1.0): Python convenience input/output functions
* ImageFormats (1.0): Support for saving images
* Label (1.0): Add text labels to graphics
* ListInfo (1.0): Report attributes for selected atomic data
* Log (1.1.1): Log support
* LookingGlass (1.1): LookingGlass holographic display
* MDcrds (2.0): Molecular dynamics support
* MLP (1.0): Molecular lipophilicity calculation
* MMTF (2.0): MMTF format read/write
* Map (1.0.1): Density maps
* MapData (2.0): Volume data file formats
* MapEraser (1.0): Map eraser
* MapFilter (2.0): Operations on maps
* MapFit (2.0): Fit molecules into maps
* MapSeries (2.0): Volume series
* Markers (1.0): Place markers on density maps
* Mask (1.0): Mask a volume to a surface
* MatchMaker (1.1): Superimpose structures
* MedicalToolbar (1.0.1): Toolbar for medical image analysis
* Meeting (1.0): Shared interactive VR sessions.
* ModelPanel (1.0): ChimeraX Model Panel
* ModelSeries (1.0): Display sequences of models one by one
* Modeller (1.0): Interface to Modeller
* Mol2 (2.0): Mol2 reader/writer
* Morph (1.0): Morph atomic structures
* MouseModes (1.0): Provide right button mouse mode tool
* Movie (1.0): Commands to record movies
* Neuron (1.0): Read SWC neuron trace files
* Nucleotides (2.0): Create nucleotide-specific displays
* OpenCommand (1.2.1): Manages 'open' command extensibility
* PDB (2.1): PDB format read/write
* PDBBio (1.0): PDB biological assembly fetch
* PickBlobs (1.0): Measure and color blobs
* Positions (1.0): Read and write model position matrices
* PresetMgr (1.0): Preset management
* PubChem (2.0): PubChem fetch
* RNALayout (1.0): Make RNA models
* Read-Pbonds (1.0): Read in pseudobonds from a file
* Registration (1.1): Register ChimeraX
* RemoteControl (1.0): Control ChimeraX from other apps
* ResidueFit (1.0): Display fit of residues to density map
* RestServer (1.0): Starts REST server to execute commands from network requests
* RotamerLibMgr (2.0): Manage rotamer libraries
* RotamerLibsDunbrack (2.0): Dunbrack rotamer library
* RotamerLibsDynameomics (2.0): Dynameomics rotamer library
* RotamerLibsRichardson (2.0): Richardson rotamer libraries
* SDF (2.0): SDF file reader
* STL (1.0): STL file read/write
* SaveCommand (1.2): Manages 'save' command extensibility
* SchemeMgr (1.0): HTTP scheme management
* Segger (1.0): Segment map
* Segment (1.0): Watershed segment calculation
* SeqView (2.2): Sequence viewer
* Shape (1.0.1): Make models for geometric shapes
* Shell (1.0): Interactive Python shell
* Shortcuts (1.0): Button and keyboard shortcuts
* ShowAttr (1.0): Render/select by attribute
* ShowSequences (1.0): Choose/show structure sequences
* SideView (1.0): Side view of scene
* Smiles (2.0): SMILES fetch
* SmoothLines (1.0): Smooth network of lines
* SpaceNavigator (1.0): Space Navigator device support
* StdCommands (1.0.4): Standard commands
* Storm (1.0): STORM file reader
* Struts (1.0): struts for 3D printing
* Surface (1.0): Surface calculations
* SwapAA (2.0): Swap amino acid
* SwapRes (2.0): Swap residue side chains
* TapeMeasure (1.0): Tape measure mouse mode
* Test (1.0): simple regression test
* Toolbar (1.0): Toolbar
* ToolshedUtils (1.0): Toolshed bundle utilities
* Tug (1.0): Tug on atoms with molecular dynamics
* UI (1.2.3): ChimeraX user interface
* VTK (1.0): Legacy VTK file reader and writer
* ViewDockX (1.0): Analyze ligand-receptor docking results
* Vive (1.1): Virtual reality headset support
* VolumeMenu (1.0): Volume menu
* WavefrontOBJ (1.0): Wavefront OBJ file read/write
* WebCam (1.0): Combine camera video with graphics
* WebServices (1.0): Web service and HTTP request support
* Zone (1.0): Mouse mode to show atom and map zones
* coulombic (1.0.1): Compute/show electrostatic potential
* gltf (1.0): Read/write glTF 3d scene files
* mmCIF (2.2): mmCIF format read/write
* uniprot (2.0): UniProt database support
* SEQCROW (0.17): Structure Editing and Quantum Chemical Representation and Organization for Workflows
> help toolshed
> toolshed install
> /Users/pett/src/chimerax/src/bundles/addh/dist/ChimeraX_AddH-2.1.3-py38-none-
> any.whl
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 298, in toolshed_install
ts.install_bundle(bundles, logger, **kw)
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
AttributeError: 'str' object has no attribute 'name'
AttributeError: 'str' object has no attribute 'name'
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 16 GB
Boot ROM Version: 236.0.0.0.0
SMC Version (system): 2.32f21
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H15)
Kernel Version: Darwin 19.6.0
Time since boot: 3:32
Graphics/Displays:
Intel Iris Pro Graphics 6200:
Chipset Model: Intel Iris Pro Graphics 6200
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1622
Revision ID: 0x000a
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
iMac:
Display Type: LCD
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
Send2Trash: 1.5.0
SEQCROW: 0.17
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (8)
comment:1 by , 5 years ago
| Component: | Unassigned → Tool Shed |
|---|---|
| Description: | modified (diff) |
| Milestone: | → 1.2 |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → "toolshed install" not allowing upgrade from wheel file |
comment:2 by , 5 years ago
| Summary: | "toolshed install" not allowing upgrade from wheel file → "toolshed install" not allowing upgrade |
|---|
comment:3 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
The fix is the same as #3996. "toolshed install" used to need the reinstall option when the bundle name is the same. Now, it's only needed if both bundle name and its version are the same. Could make a toolshed release of the bundles (bundle_builder and toolshed_utils), but not sure if all of the changes since the 1.1 release would be okay, but that would fix the traceback too.
comment:4 by , 5 years ago
I don't see how a toolshed release of bundle_builder and toolshed_utils would help. Wouldn't they suffer from the exact same problem (i.e. be "not installable" because the bundle name is the same as an already-installed bundle)?
comment:5 by , 5 years ago
Try installing from the Updates tool. The Updates tool is blindly setting the reinstall option (need to fix), so, if there were no dependency changes, it would work. Looking forward, toolshed_utils has a new dependency, so no point in putting a new version on the toolshed because installing would fail (since, due to how pip works, we turn off installing dependencies when forcing a package to be installed).
comment:6 by , 5 years ago
Running the 1.1 release, AddH does not show up in the Updates tool, despite the fact that all its dependencies are available in 1.1. What gives? It does show up in the daily build's Updates tool.
Also, it would be nice if "toolshed list" was alphabetical, so that it was easy to find dependencies. Right now it's upper-case built-in bundles, then lower-case builtin bundles, then 3rd-party bundles.
Now that the wheel file is corrected on plato, same problem when installing from Toolshed.