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#4413 assigned defect

Make --force-reinstall the default when building from source

Reported by:	Tristan Croll	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Build System	Version:
Keywords:		Cc:	chimera-programmers
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202103230345 (2021-03-23 03:45:30 UTC)
Description
Finally getting some time to catch ISOLDE up to the daily builds :). Actually quite painless so far! Just noticed this message in the log after rebuilding:

ChimeraX-ISOLDE is already installed with the same version as the provided wheel. Use --force-reinstall to force an installation of the wheel.

I think --force-reinstall should be the default when a bundle has been rebuilt from source (i.e. via `make app-install`).

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.2.dev202103230345 (2021-03-23)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed
'ChimeraX_ISOLDE-1.1.0-cp38-cp38-manylinux_2_17_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
./.cache/ChimeraX/1.2/installers/ChimeraX_ISOLDE-1.1.0-cp38-cp38-manylinux_2_17_x86_64.whl  
Requirement already satisfied: ChimeraX-Clipper~=0.15.0 in
./.local/share/ChimeraX/1.2/site-packages (from ChimeraX-ISOLDE==1.1.0)
(0.15.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ISOLDE==1.1.0) (1.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.12.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ISOLDE==1.1.0) (1.12)  
Requirement already satisfied: ChimeraX-Core~=1.2.dev202103230345 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ISOLDE==1.1.0) (1.2.dev202103230345)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=2.1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ISOLDE==1.1.0) (2.1)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (2.0)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (1.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (1.0)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (2.3)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (2.3)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.1.0) (1.0)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0)
(1.5)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0)
(1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0)
(1.1)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0)
(1.4)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (1.0.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.1.0) (1.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.1.0) (1.7)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (1.3)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (1.0.2)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (2.0)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (2.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (1.1)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (2.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.1.0) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.1.0) (2.0)  
ChimeraX-ISOLDE is already installed with the same version as the provided
wheel. Use --force-reinstall to force an installation of the wheel.  
  

> isolde demo crystal_intro

> set selectionWidth 4

/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/ramaplot.py:347:
MatplotlibDeprecationWarning: shading='flat' when X and Y have the same
dimensions as C is deprecated since 3.3. Either specify the corners of the
quadrilaterals with X and Y, or pass shading='auto', 'nearest' or 'gouraud',
or set rcParams['pcolor.shading']. This will become an error two minor
releases later.  
pcolor_plot = self.axes.pcolormesh(*grid, logvalues, cmap = 'Greys')  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  
Done loading forcefield  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
1.2/A | predicted microcompartment protein  
  

WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at
level 0.303, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at
level -0.0574,0.0574, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723,
shown at level 0.603, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723,
shown at level 0.365, step 1, values float32  
Loaded crystallographic demo: PDB ID 3io0  




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        7.2G         39G        334M         15G         54G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    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: 1.12
    ChimeraX-AtomicLibrary: 2.1
    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
    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-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103230345
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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-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-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    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: 1.1
    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
    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
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.3
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    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
    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-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7
    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: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    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: 0.17
    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: 1.1.1
    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
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    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
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    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: 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: 2020.9.3
    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: 1.2.0

Change History (6)

comment:1 by pett, 5 years ago

Cc:	chimera-programmers added
Component:	Unassigned → Build System
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Make --force-reinstall the default when building from source

comment:2 by pett, 5 years ago

Yes, the current behavior is bad. I made a debugging change to atomic_lib that required several other bundles to be recompiled. Well, I went up into "bundles" and did "make clean; make install" and nothing got reinstalled because e.g. "ChimeraX-Atomic is already installed with the same version as the provided wheel. Use --force-reinstall to force an installation of the wheel." Is there even a target in "bundles" to force reinstall?

--Eric

in reply to: 3 ; follow-up: 3 comment:3 by goddard@…, 5 years ago

I too have been burned by this too many times.  If I say "make install" it means install so I think  force reinstall should be the default.

comment:4 by pett, 5 years ago

To actually get the "install" target in "bundles" to install anything, I had to change the pip install to:

pip install --force-reinstall --no-dependencies */*.whl

comment:5 by pett, 5 years ago

I have pushed the change I mentioned. Unless I hear some reason I shouldn't, I'm going to do the same for the "install" target in core and nuke its "reinstall" target on Monday.

--Eric

comment:6 by pett, 5 years ago

The discussion from today's develop meeting is this:

1) Tristan should try adding the --safe-mode flag

2) Greg will experiment with changing "make install" to do a pip uninstall followed by a pip install

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