pip install girder issue


#1

Hi

I am just trying to install Girder with virtualenv. Have you seen this error message?

(girder_env) sulsj@ssul-dm ~$ pip install girder
Collecting girder
Using cached https://files.pythonhosted.org/packages/1e/47/0ccb4923851fe66c106a114af4033a9cc4b81f10ea5df15169b0e24df256/girder-2.5.0.tar.gz
Complete output from command python setup.py egg_info:
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: ‘python_requires’
warnings.warn(msg)
error in girder setup command: ‘install_requires’ must be a string or list of strings containing valid project/version requirement specifiers; Expected version spec in funcsigs ; python_version < ‘3’ at ; python_version < ‘3’

----------------------------------------

Command “python setup.py egg_info” failed with error code 1 in /private/var/folders/8b/khv7605j59s7cdm9_xfm_jf00000gp/T/pip-install-6_CNhk/girder/

Thanks,
Seung


#2

This is caused by an old version of setuptools in your python environment. Running the following should fix it:

pip install -U pip setuptools

#3

Dear Jonathan

I’ve tried a few solutions including yours but it did not work. I am using macOS High Sierra. Any idea?

(girder_env) sulsj@ssul-dm ~/work/git-repos/girder$ pip install -U pip setuptools
Requirement already up-to-date: pip in /Library/Python/2.7/site-packages (18.0)
Collecting setuptools
Using cached https://files.pythonhosted.org/packages/66/e8/570bb5ca88a8bcd2a1db9c6246bb66615750663ffaaeada95b04ffe74e12/setuptools-40.2.0-py2.py3-none-any.whl
Installing collected packages: setuptools
Found existing installation: setuptools 18.5
Not uninstalling setuptools at /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python, outside environment /Users/sulsj/girder_env
Can’t uninstall ‘setuptools’. No files were found to uninstall.
Successfully installed setuptools-40.2.0

Thanks,
Seung


#4

Hmmm… maybe try pip install --user -U setuptools.


#5

Afraid not. It seems like being affected by the system’s setuptools. I am wondering if there is other way to install and setup Girder.


#6

It’s possible --ignore-installed would force it to install setuptools in the virtualenv.

It’s probably best to avoid using the system python. On a Mac, I usually install an external python using homebrew (brew install python). That should install the latest version of setuptools in an isolated python environment for you.


#7

Thank you for your help.

I am using conda env mostly for my dev environment. So I’ve never had a problem with system’s installation.

Anyway, I’ve tried the flag to ignore the system’s setuptools, but “pip install girder” still does not work.

girder_env) sulsj@ssul-dm ~$ pip install -U pip setuptools --ignore-installed
Collecting pip
Using cached https://files.pythonhosted.org/packages/5f/25/e52d3f31441505a5f3af41213346e5b6c221c9e086a166f3703d2ddaf940/pip-18.0-py2.py3-none-any.whl
Collecting setuptools
Using cached https://files.pythonhosted.org/packages/66/e8/570bb5ca88a8bcd2a1db9c6246bb66615750663ffaaeada95b04ffe74e12/setuptools-40.2.0-py2.py3-none-any.whl
Installing collected packages: pip, setuptools
Successfully installed pip-18.0 setuptools-40.2.0

(girder_env) sulsj@ssul-dm ~$ pip install girder
Collecting girder
Using cached https://files.pythonhosted.org/packages/1e/47/0ccb4923851fe66c106a114af4033a9cc4b81f10ea5df15169b0e24df256/girder-2.5.0.tar.gz
Complete output from command python setup.py egg_info:
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: ‘python_requires’
warnings.warn(msg)
error in girder setup command: ‘install_requires’ must be a string or list of strings containing valid project/version requirement specifiers; Expected version spec in funcsigs ; python_version < ‘3’ at ; python_version < ‘3’

----------------------------------------

Command “python setup.py egg_info” failed with error code 1 in /private/var/folders/8b/khv7605j59s7cdm9_xfm_jf00000gp/T/pip-install-mi0ggQ/girder/

Thanks,
Seung


#8

Using a conda env should work fine here. You just have to make sure that you are using pip from conda rather than the system.


#9

It’s installed using “pip install girder” under my conda env. Thank you!


#10

Well… After running “pip install girder” under a conda env, I can see the below files under “bin”.

girder-install
girder-server
girder-sftpd
girder-shell

However, “girder” cannot be found for testing “girder serve”.


#11

Is it possible you have an older version of Girder already installed? girder-server does the same thing as the newer girder serve command.


#12

There is no older version of Girder installed. Again I am using conda and executed “pip install girder” to install it.

And I’ve tested with “girder-server” and found this.

(qaqc2) sulsj@ssul-dm ~/work/git-repos/girder$ girder-server serve
Traceback (most recent call last):
File “/Users/sulsj/miniconda2/envs/qaqc2/bin/girder-server”, line 7, in
from girder.main import main
ImportError: cannot import name main

Thanks,
Seung


#13

It definitely looks like you have scripts left over from girder 2.4. I just tried installing with miniconda3, and it worked fine. I wonder if you might have an installation of girder from conda-forge. Could you try looking at conda list to see if girder 2.4 is listed? You might also need to make an new virtualenv if the old version cannot be cleaned up successfully.


#14

With a clean env, it works like a charm. Thanks for the help.

One more question. Is there any use case to use Girder for bridging geographically remote file systems or HPSSs? Have you seen any 3rd party plugin related with that?

Thanks,
Seung


#15

One more question. Is there any use case to use Girder for bridging geographically remote file systems or HPSSs? Have you seen any 3rd party plugin related with that?

I think we’ve done some experimenting with Globus integration, but I don’t know what the status is. @Zach_Mullen can probably tell you more.


#16

Thanks for the info. @Zach_Mullen, Is there any way I can access the related info on the Globus integration?


#17

Hi @sulsj,

As of right now, we don’t have anything concrete to point to regarding Globus integration, other than using Globus’s OAuth provider for identity provision here: https://github.com/girder/girder/blob/master/plugins/oauth/server/providers/globus.py

A few of us on the Girder team are talking with some Globus developers tomorrow to try and see what further integrations we can do between the technologies. If we decide on anything to do then, I will update this thread.

Thanks,

-Zach


#18

Hi Zach,

Thank you for the info. I will be looking forward to hear an update.

Thanks,
Seung