Opened 6 years ago

Closed 6 years ago

#2013 closed defect (fixed)

Trouble pip-installing Pyyaml prereq for bundle

Reported by: andresgineranton@… Owned by: Conrad Huang
Priority: normal Milestone: 0.91
Component: Tool Shed Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.18.0-20-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.9 (2019-04-28)
Description
Hello, we are from Insilichem team at the UAB, Barcelona, Spain; and we are having troubles with the creation of a ChimeraX bundle. We have specified the Pyyaml package as a requeriment of our bundle; however when we install it, the installation fail trying to download the Pyyaml package. We obtain the next log:

Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing ./Downloads/GaudiViewX-0.5-py3-none-any.whl Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in /usr/lib/ucsf-chimerax/lib/python3.7/site-packages (from GaudiViewX==0.5) (1.0) Collecting Pyyaml>=5.0 (from GaudiViewX==0.5) Using cached https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz Files/directories not found in /tmp/pip-install-qwkg5e4n/Pyyaml/pip-egg-info You are using pip version 19.0.3, however version 19.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

OpenGL version: 4.5 (Core Profile) Mesa 18.2.8
OpenGL renderer: Mesa DRI Intel(R) HD Graphics 520 (Skylake GT2) 
OpenGL vendor: Intel Open Source Technology Center
File attachment: bundle_info.xml

bundle_info.xml​

Attachments (1)

bundle_info.xml​ (2.0 KB ) - added by andresgineranton@… 6 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (9)

by andresgineranton@…, 6 years ago

Attachment: bundle_info.xml​ added

Added by email2trac

comment:1 by pett, 6 years ago

Component: Unassigned → Tool Shed
Milestone: → 0.91
Owner: set to Conrad Huang
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Trouble pip-installing Pyyaml prereq for bundle

Reported by Andrés Giner Antón

comment:2 by Conrad Huang, 6 years ago

Status: assigned → feedback

Using the supplied bundle_info.xml, I created an empty bundle and tried to install it using ChimeraX built from the latest source on a Windows 10 machine. The output is attached below and seems to indicate that everything worked as expected. (This is the platform I do most of my development on, so it's not surprising that it worked here.)

Which version of ChimeraX and what platform were you using, and what commands did you use to build/install your bundle?

$ ls -lR
.:
total 4
-rwx------+ 1 conrad None 2083 Jun 19 09:49 bundle_info.xml*
drwxr-xr-x+ 1 conrad None    0 Jun 19 10:19 src/

./src:
total 0
-rw-r--r--+ 1 conrad None 0 Jun 19 10:07 __init__.py
drwxr-xr-x+ 1 conrad None 0 Jun 19 10:07 docs/

./src/docs:
total 0
drwxr-xr-x+ 1 conrad None 0 Jun 19 10:07 user/

./src/docs/user:
total 0
drwxr-xr-x+ 1 conrad None 0 Jun 19 10:08 tools/

./src/docs/user/tools:
total 0
-rw-r--r--+ 1 conrad None 0 Jun 19 10:08 guide.html


$ /d/chimerax/ChimeraX.app/bin/ChimeraX.exe -m pip list
Package                       Version
----------------------------- -----------
alabaster                     0.7.12
appdirs                       1.4.3
[...]
ChimeraX-FileHistory          1.0
ChimeraX-gltf                 1.0
ChimeraX-Hbonds               1.0
ChimeraX-Help                 0.9a1
[...]
pycollada                     0.6
pydicom                       1.2.2
Pygments                      2.4.2
PyOpenGL                      3.1.3b2
PyOpenGL-accelerate           3.1.3b2
pyparsing                     2.4.0
PyQt5-commercial              5.12.2
PyQt5-sip                     4.19.17
PyQtWebEngine-commercial      5.12.1
python-dateutil               2.8.0
pytz                          2019.1
pyzmq                         18.0.1
[...]
webcolors                     1.9.1
wheel                         0.33.4


$ /d/chimerax/ChimeraX.app/bin/ChimeraX.exe --nogui --safemode --exit --cmd "devel install ."
INFO:
Executing: devel install .
running build
running build_py
creating build
creating build\lib
creating build\lib\chimerax
creating build\lib\chimerax\gaudiviewx
copying src\__init__.py -> build\lib\chimerax\gaudiviewx
creating build\lib\chimerax\gaudiviewx\docs
creating build\lib\chimerax\gaudiviewx\docs\user
creating build\lib\chimerax\gaudiviewx\docs\user\tools
copying src\docs\user\tools\guide.html -> build\lib\chimerax\gaudiviewx\docs\user\tools
running test
Searching for Pyyaml>=5.0
Best match: pyyaml 5.1.1
Processing pyyaml-5.1.1-py3.7-win-amd64.egg

Using d:\home\conrad\tmp\tbundle\.eggs\pyyaml-5.1.1-py3.7-win-amd64.egg
running egg_info
creating ChimeraX_GaudiViewX.egg-info
writing ChimeraX_GaudiViewX.egg-info\PKG-INFO
writing dependency_links to ChimeraX_GaudiViewX.egg-info\dependency_links.txt
writing requirements to ChimeraX_GaudiViewX.egg-info\requires.txt
writing top-level names to ChimeraX_GaudiViewX.egg-info\top_level.txt
writing manifest file 'ChimeraX_GaudiViewX.egg-info\SOURCES.txt'
reading manifest file 'ChimeraX_GaudiViewX.egg-info\SOURCES.txt'
writing manifest file 'ChimeraX_GaudiViewX.egg-info\SOURCES.txt'
running build_ext
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\gaudiviewx
creating build\bdist.win-amd64\wheel\chimerax\gaudiviewx\docs
creating build\bdist.win-amd64\wheel\chimerax\gaudiviewx\docs\user
creating build\bdist.win-amd64\wheel\chimerax\gaudiviewx\docs\user\tools
copying build\lib\chimerax\gaudiviewx\docs\user\tools\guide.html -> build\bdist.win-amd64\wheel\.\chimerax\gaudiviewx\docs\user\tools
copying build\lib\chimerax\gaudiviewx\__init__.py -> build\bdist.win-amd64\wheel\.\chimerax\gaudiviewx
running install_egg_info
Copying ChimeraX_GaudiViewX.egg-info to build\bdist.win-amd64\wheel\.\ChimeraX_GaudiViewX-0.5-py3.7.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\ChimeraX_GaudiViewX-0.5.dist-info\WHEEL
creating 'dist\ChimeraX_GaudiViewX-0.5-py3-none-any.whl' and adding 'build\bdist.win-amd64\wheel' to it
adding 'chimerax/gaudiviewx/__init__.py'
adding 'chimerax/gaudiviewx/docs/user/tools/guide.html'
adding 'ChimeraX_GaudiViewX-0.5.dist-info/METADATA'
adding 'ChimeraX_GaudiViewX-0.5.dist-info/WHEEL'
adding 'ChimeraX_GaudiViewX-0.5.dist-info/top_level.txt'
adding 'ChimeraX_GaudiViewX-0.5.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Distribution is in .\dist\ChimeraX_GaudiViewX-0.5-py3-none-any.whl
INFO:
Executing: toolshed install ".\\dist\\ChimeraX_GaudiViewX-0.5-py3-none-any.whl"
Successfully installed ChimeraX-GaudiViewX-0.5 Pyyaml-5.1.1
Installed ChimeraX-GaudiViewX (0.5)

INFO:
UCSF ChimeraX version: 0.91 (2019-06-19)
INFO:
© 2016-2019 Regents of the University of California.  All rights reserved.
0.00% done: Initializing core
50.00% done: Initializing bundles

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK
100.00% done: Finished initialization


$ /d/chimerax/ChimeraX.app/bin/ChimeraX.exe -m pip list
Package                       Version
----------------------------- -----------
alabaster                     0.7.12
appdirs                       1.4.3
[...]
ChimeraX-FileHistory          1.0
ChimeraX-GaudiViewX           0.5
ChimeraX-gltf                 1.0
ChimeraX-Hbonds               1.0
ChimeraX-Help                 0.9a1
[...]
pycollada                     0.6
pydicom                       1.2.2
Pygments                      2.4.2
PyOpenGL                      3.1.3b2
PyOpenGL-accelerate           3.1.3b2
pyparsing                     2.4.0
PyQt5-commercial              5.12.2
PyQt5-sip                     4.19.17
PyQtWebEngine-commercial      5.12.1
python-dateutil               2.8.0
pytz                          2019.1
PyYAML                        5.1.1
pyzmq                         18.0.1
[...]
webcolors                     1.9.1
wheel                         0.33.4

in reply to:  4 comment:3 by andresgineranton@…, 6 years ago 

We used two machines: one for the creation of the bundle and other for testing. Both have the platform Ubuntu 18.04 and ChimeraX 0.9. The bundle was build with the command "devel build" and we tried to install it in the other machine with the command "toolshed install".

In the machine used for the creation of the bundle there was no problem because we installed manually the Pyyaml package, so we didn't any tests with it.
Last edited 6 years ago by Conrad Huang (previous) (diff)

comment:4 by Conrad Huang, 6 years ago

I just reread the description and found something I missed the first time around:

Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing ./Downloads/GaudiViewX-0.5-py3-none-any.whl Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in /usr/lib/ucsf-chimerax/lib/python3.7/site-packages (from GaudiViewX==0.5) (1.0) Collecting Pyyaml>=5.0 (from GaudiViewX==0.5) Using cached https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz Files/directories not found in /tmp/pip-install-qwkg5e4n/Pyyaml/pip-egg-info

It looks like pip is trying to install PyYAML and thinks it has a cached file, but then finds that it does not. I don't think ChimeraX passes in any cache-related flags to pip, so it should just be using its defaults. Can you check whether the directory /tmp/pip-install-qwkg5e4n exists on the two machines?

I infer from ​https://stackoverflow.com/questions/34578168/where-is-pip-cache-folder that there may actually be two cache directories in play: one for pip and one for wheel. Can you run the following code in the ChimeraX Shell tool and see what is the output?

from pip._internal.utils.appdirs import user_cache_dir
import os.path
pip_cache = user_cache_dir("pip")
print("pip cache exists:", pip_cache, os.path.exists(pip_cache))
wheel_cache = user_cache_dir("wheel")
print("wheel cache exists:", wheel_cache, os.path.exists(wheel_cache))

in reply to:  6 comment:5 by andresgineranton@…, 6 years ago 

The directories /tmp/pip-install-(random_numbers_letters)/ is found in both machines during the installation process. Then, after a successfully installation or a failed installation the directories is removed.

Running the code in the ChimeraX Shell tool returns in both machine:

      pip cache exists: /home/.cache/pip True
      wheel cache exists: /home/.cache/wheel False

Additional information: when we remove the directories /home/andres/.local/share/ChimeraX/0.9/site-packages/PyYAML-5.1.dist-info and /home/andres/.local/share/ChimeraX/0.9/site-packages/yaml in the first machine, we receive the error in the installation. And with the command devel install we obtain the next log:

"""

devel install /home/andres/practicas/chimerax/gaudiviewx

running build
running build_py
running test
running egg_info
writing ChimeraX_GaudiViewX.egg-info/PKG-INFO
writing dependency_links to ChimeraX_GaudiViewX.egg-info/dependency_links.txt
writing requirements to ChimeraX_GaudiViewX.egg-info/requires.txt
writing top-level names to ChimeraX_GaudiViewX.egg-info/top_level.txt
reading manifest file 'ChimeraX_GaudiViewX.egg-info/SOURCES.txt'
writing manifest file 'ChimeraX_GaudiViewX.egg-info/SOURCES.txt'
running build_ext

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK
running bdist_wheel
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/chimerax
creating build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx
creating build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/docs
creating build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/docs/user
creating build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/docs/user/tools
copying build/lib/chimerax/gaudiviewx/docs/user/tools/guide.html -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/docs/user/tools
copying build/lib/chimerax/gaudiviewx/docs/user/tools/tutorial.html -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/docs/user/tools
copying build/lib/chimerax/gaudiviewx/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx
copying build/lib/chimerax/gaudiviewx/gui.py -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx
copying build/lib/chimerax/gaudiviewx/tool.py -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx
copying build/lib/chimerax/gaudiviewx/browser.py -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx
creating build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/icons
copying build/lib/chimerax/gaudiviewx/icons/insilichem.png -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/icons
copying build/lib/chimerax/gaudiviewx/icons/icon_save.png -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/icons
copying build/lib/chimerax/gaudiviewx/icons/icon_folder.png -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx/icons
copying build/lib/chimerax/gaudiviewx/example.py -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx
copying build/lib/chimerax/gaudiviewx/gaudireader.py -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx
copying build/lib/chimerax/gaudiviewx/toolbar.py -> build/bdist.linux-x86_64/wheel/chimerax/gaudiviewx
running install_egg_info
Copying ChimeraX_GaudiViewX.egg-info to build/bdist.linux-x86_64/wheel/ChimeraX_GaudiViewX-0.9-py3.7.egg-info
running install_scripts
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
creating build/bdist.linux-x86_64/wheel/ChimeraX_GaudiViewX-0.9.dist-info/WHEEL
creating 'dist/ChimeraX_GaudiViewX-0.9-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'chimerax/gaudiviewx/__init__.py'
adding 'chimerax/gaudiviewx/browser.py'
adding 'chimerax/gaudiviewx/example.py'
adding 'chimerax/gaudiviewx/gaudireader.py'
adding 'chimerax/gaudiviewx/gui.py'
adding 'chimerax/gaudiviewx/tool.py'
adding 'chimerax/gaudiviewx/toolbar.py'
adding 'chimerax/gaudiviewx/docs/user/tools/guide.html'
adding 'chimerax/gaudiviewx/docs/user/tools/tutorial.html'
adding 'chimerax/gaudiviewx/icons/icon_folder.png'
adding 'chimerax/gaudiviewx/icons/icon_save.png'
adding 'chimerax/gaudiviewx/icons/insilichem.png'
adding 'ChimeraX_GaudiViewX-0.9.dist-info/LICENSE'
adding 'ChimeraX_GaudiViewX-0.9.dist-info/METADATA'
adding 'ChimeraX_GaudiViewX-0.9.dist-info/WHEEL'
adding 'ChimeraX_GaudiViewX-0.9.dist-info/top_level.txt'
adding 'ChimeraX_GaudiViewX-0.9.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Distribution is in /home/andres/practicas/chimerax/gaudiviewx/dist/ChimeraX_GaudiViewX-0.9-py3-none-any.whl
toolshed install
/home/andres/practicas/chimerax/gaudiviewx/dist/ChimeraX_GaudiViewX-0.9-py3-none-
any.whl

[toolshed install
/home/andres/practicas/chimerax/gaudiviewx/dist/ChimeraX_GaudiViewX-0.9-py3-none-
any.whl](cxcmd:toolshed install
/home/andres/practicas/chimerax/gaudiviewx/dist/ChimeraX_GaudiViewX-0.9-py3-none-
any.whl)

unloading module chimerax.gaudiviewx
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/toolshed/__init__.py", line 988, in _pip_install
results = self._run_pip(command)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/toolshed/__init__.py", line 1018, in _run_pip
raise RuntimeError(s)
RuntimeError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./practicas/chimerax/gaudiviewx/dist/ChimeraX_GaudiViewX-0.9-py3-none-any.whl
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages (from ChimeraX-GaudiViewX==0.9) (1.0)
Collecting Pyyaml>=5.0 (from ChimeraX-GaudiViewX==0.9)
Using cached https://files.pythonhosted.org/packages/a3/65/837fefac7475963d1eccf4aa684c23b95aa6c1d033a2c5965ccb11e22623/PyYAML-5.1.1.tar.gz
ERROR: Files/directories not found in /tmp/pip-install-md2mwq3p/Pyyaml/pip-egg-info


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/devel.py", line 151, in _run
unbound_method(bb, *args, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/bundle_builder/bundle_builder.py", line 93, in make_install
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2631, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/toolshed.py", line 230, in toolshed_install
ts.install_bundle(bi, logger, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/toolshed/__init__.py", line 612, in install_bundle
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/toolshed/__init__.py", line 991, in _pip_install
raise UserError(str(e))
chimerax.core.errors.UserError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./practicas/chimerax/gaudiviewx/dist/ChimeraX_GaudiViewX-0.9-py3-none-any.whl
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages (from ChimeraX-GaudiViewX==0.9) (1.0)
Collecting Pyyaml>=5.0 (from ChimeraX-GaudiViewX==0.9)
Using cached https://files.pythonhosted.org/packages/a3/65/837fefac7475963d1eccf4aa684c23b95aa6c1d033a2c5965ccb11e22623/PyYAML-5.1.1.tar.gz
ERROR: Files/directories not found in /tmp/pip-install-md2mwq3p/Pyyaml/pip-egg-info

"""
If we restore both directories in the .local/share/ChimeraX/0.9/site-packages, the installation is successful.

​Andrés Giner Antón
________________________________
De: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Enviado: miércoles, 19 de junio de 2019 20:56
Cc: andresgineranton@outlook.com; conrad@cgl.ucsf.edu
Asunto: Re: [ChimeraX] #2013: Trouble pip-installing Pyyaml prereq for bundle

#2013: Trouble pip-installing Pyyaml prereq for bundle
-----------------------------------------+----------------------
          Reporter:  andresgineranton@…  |      Owner:  conrad
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:  0.91
         Component:  Tool Shed           |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------

Comment (by conrad):

 I just reread the description and found something I missed the first time
 around:

 {{{
 Looking in indexes: https://pypi.org/simple,
 https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing
 ./Downloads/GaudiViewX-0.5-py3-none-any.whl Requirement already satisfied,
 skipping upgrade: ChimeraX-UI>=1.0 in /usr/lib/ucsf-chimerax/lib/python3.7
 /site-packages (from GaudiViewX==0.5) (1.0) Collecting Pyyaml>=5.0 (from
 GaudiViewX==0.5) Using cached
 https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz
 Files/directories not found in /tmp/pip-install-qwkg5e4n/Pyyaml/pip-egg-
 info
 }}}

 It looks like pip is ''trying'' to install PyYAML and thinks it has a
 cached file, but then finds that it does not.  I don't think ChimeraX
 passes in any cache-related flags to pip, so it should just be using its
 defaults.  Can you check whether the directory '''/tmp/pip-install-
 qwkg5e4n''' exists on the two machines?

 I infer from https://stackoverflow.com/questions/34578168/where-is-pip-
 cache-folder that there may actually be two cache directories in play: one
 for pip and one for wheel.  Can you run the following code in the ChimeraX
 Shell tool and see what is the output?

 {{{
 from pip._internal.utils.appdirs import user_cache_dir
 import os.path
 pip_cache = user_cache_dir("pip")
 print("pip cache exists:", pip_cache, os.path.exists(pip_cache))
 wheel_cache = user_cache_dir("wheel")
 print("wheel cache exists:", wheel_cache, os.path.exists(wheel_cache))
 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2013#comment:4>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:6 by Conrad Huang, 6 years ago

This should be fixed (09f53d30d) in tomorrow's build (dated June 21 or later).

ChimeraX was not setting the name of the main module when running "-c" code from the command line. pip uses this mechanism, and PyYAML has one of the few setup.py files that actually checks the main module name.

Can you please confirm? Thanks.

in reply to:  8 comment:7 by andresgineranton@…, 6 years ago 

Yes, the problem was resolved with the new version!

Thank you very much.
________________________________
De: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Enviado: viernes, 21 de junio de 2019 2:45
Cc: andresgineranton@outlook.com; conrad@cgl.ucsf.edu
Asunto: Re: [ChimeraX] #2013: Trouble pip-installing Pyyaml prereq for bundle

#2013: Trouble pip-installing Pyyaml prereq for bundle
-----------------------------------------+----------------------
          Reporter:  andresgineranton@…  |      Owner:  conrad
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:  0.91
         Component:  Tool Shed           |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
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           Project:  ChimeraX            |
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Comment (by conrad):

 This should be fixed ([changeset:09f53d30d]) in tomorrow's build (dated
 June 21 or later).

 ChimeraX was not setting the name of the main module when running "-c"
 code from the command line.  {{{pip}}} uses this mechanism, and PyYAML has
 one of the few {{{setup.py}}} files that actually checks the main module
 name.

 Can you please confirm?  Thanks.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2013#comment:6>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:8 by Conrad Huang, 6 years ago

Resolution: → fixed
Status: feedback → closed
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