id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
5157	"PyPi dependency not installed by ""devel install"""	i.m.lagerwaard@…	Greg Couch	"{{{
The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I’m currently developing a bundle with a dependency on pandas. Even though I included this dependency in my bundle_info.xml file, I get “ModuleNotFoundError: No module named 'pandas'”. 

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> devel install
> C:\Users\ilsel\Documents\MCLS\Bioinformatics_profile\crosslink_mapper

running build  
running build_py  
creating build  
creating build\lib  
creating build\lib\chimerax  
creating build\lib\chimerax\crosslink_mapper  
copying src\tool.py -> build\lib\chimerax\crosslink_mapper  
copying src\\__init__.py -> build\lib\chimerax\crosslink_mapper  
running bdist_wheel  
installing to build\bdist.win-amd64\wheel  
running install  
running install_lib  
creating build\bdist.win-amd64  
creating build\bdist.win-amd64\wheel  
creating build\bdist.win-amd64\wheel\chimerax  
creating build\bdist.win-amd64\wheel\chimerax\crosslink_mapper  
copying build\lib\chimerax\crosslink_mapper\tool.py -> build\bdist.win-
amd64\wheel\\.\chimerax\crosslink_mapper  
copying build\lib\chimerax\crosslink_mapper\\__init__.py -> build\bdist.win-
amd64\wheel\\.\chimerax\crosslink_mapper  
running install_egg_info  
running egg_info  
creating ChimeraX_CrosslinkMapper.egg-info  
writing ChimeraX_CrosslinkMapper.egg-info\PKG-INFO  
writing dependency_links to ChimeraX_CrosslinkMapper.egg-
info\dependency_links.txt  
writing requirements to ChimeraX_CrosslinkMapper.egg-info\requires.txt  
writing top-level names to ChimeraX_CrosslinkMapper.egg-info\top_level.txt  
writing manifest file 'ChimeraX_CrosslinkMapper.egg-info\SOURCES.txt'  
reading manifest file 'ChimeraX_CrosslinkMapper.egg-info\SOURCES.txt'  
writing manifest file 'ChimeraX_CrosslinkMapper.egg-info\SOURCES.txt'  
Copying ChimeraX_CrosslinkMapper.egg-info to build\bdist.win-
amd64\wheel\\.\ChimeraX_CrosslinkMapper-0.1-py3.8.egg-info  
running install_scripts  
creating build\bdist.win-amd64\wheel\ChimeraX_CrosslinkMapper-0.1.dist-
info\WHEEL  
creating 'dist\ChimeraX_CrosslinkMapper-0.1-py3-none-any.whl' and adding
'build\bdist.win-amd64\wheel' to it  
adding 'chimerax/crosslink_mapper/__init__.py'  
adding 'chimerax/crosslink_mapper/tool.py'  
adding 'ChimeraX_CrosslinkMapper-0.1.dist-info/METADATA'  
adding 'ChimeraX_CrosslinkMapper-0.1.dist-info/WHEEL'  
adding 'ChimeraX_CrosslinkMapper-0.1.dist-info/top_level.txt'  
adding 'ChimeraX_CrosslinkMapper-0.1.dist-info/RECORD'  
removing build\bdist.win-amd64\wheel  
Distribution is in
C:\Users\ilsel\Documents\MCLS\Bioinformatics_profile\crosslink_mapper\dist\ChimeraX_CrosslinkMapper-0.1-py3-none-
any.whl  
[toolshed install](help:user/commands/toolshed.html#install)  
C:\Users\ilsel\Documents\MCLS\Bioinformatics_profile\crosslink_mapper\dist\ChimeraX_CrosslinkMapper-0.1-py3-none-  
any.whl reinstall true  
  
[toolshed install  
C:\Users\ilsel\Documents\MCLS\Bioinformatics_profile\crosslink_mapper\dist\ChimeraX_CrosslinkMapper-0.1-py3-none-  
any.whl reinstall true](cxcmd:toolshed install  
C:\\\Users\\\ilsel\\\Documents\\\MCLS\\\Bioinformatics_profile\\\crosslink_mapper\\\dist\\\ChimeraX_CrosslinkMapper-0.1-py3-none-  
any.whl reinstall true)  
  
Successfully installed ChimeraX-CrosslinkMapper-0.1  
Installed ChimeraX-CrosslinkMapper (0.1)  
  

> ui tool show ""Crosslink Mapper""

Traceback (most recent call last):  
File ""C:\Users\ilsel\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\crosslink_mapper\tool.py"", line 189, in map_button_clicked  
import pandas as pd  
ModuleNotFoundError: No module named 'pandas'  
  
ModuleNotFoundError: No module named 'pandas'  
  
File ""C:\Users\ilsel\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\crosslink_mapper\tool.py"", line 189, in map_button_clicked  
import pandas as pd  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13476 Core Profile Forward-Compatible Context 22.19.180.513
OpenGL renderer: AMD Radeon(TM) R4 Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: HP
Model: HP Laptop 15-bw0xx
OS: Microsoft Windows 10 Home (Build 18363)
Memory: 8,017,076,224
MaxProcessMemory: 137,438,953,344
CPU: 2 AMD A6-9220 RADEON R4, 5 COMPUTE CORES 2C+3G   
OSLanguage: nl-NL
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    bio: 0.5.0
    biopython: 1.79
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-CrosslinkMapper: 0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-HelloWorld: 0.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestBundle: 0.1
    ChimeraX-TestBundle2: 0.1
    ChimeraX-TestBundle3: 0.1
    ChimeraX-TestBundle4: 0.1
    ChimeraX-TestBundle5: 0.1
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-TutorialCommand: 0.1
    ChimeraX-TutorialReadFormat: 0.1
    ChimeraX-TutorialToolQt: 0.1
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    et-xmlfile: 1.1.0
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openpyxl: 3.0.7
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.2.4
    pkginfo: 1.5.0.1
    plac: 1.3.3
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    seaborn: 0.11.2
    Send2Trash: 1.5.0
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1
    xlrd: 2.0.1
File attachment: bundle_info.xml

}}}

[attachment:""bundle_info.xml""]
"	defect	closed	normal	1.6	Tool Shed		limitation		chimera-programmers				all	ChimeraX