pip not python3 compatible

[wharvey31]

It seems that the pip file for toil-vg still relies on execfile() which is python2 specific. Can you change to use exec()? Or am I doing something wrong.

$ pip install toil-vg

Collecting toil-vg
Downloading toil-vg-1.4.1.tar.gz (139 kB)
|████████████████████████████████| 139 kB 13.3 MB/s
ERROR: Command errored out with exit status 1:
command: /net/eichler/vol26/7200/software/modules-sw/toil-vg/202004/Linux/RHEL6/x86_64/toilvenv/bin/python3 -c 'import sys, set
uptools, tokenize; sys.argv[0] = '"'"'/data/nobackup/tmp/pip-install-w5kk3sba/toil-vg/setup.py'"'"'; file='"'"'/data/nobackup/tm
p/pip-install-w5kk3sba/toil-vg/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"
', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /data/nobackup/tmp/pip-install-w5kk3sb
a/toil-vg/pip-egg-info
cwd: /data/nobackup/tmp/pip-install-w5kk3sba/toil-vg/
Complete output (5 lines):
Traceback (most recent call last):
File "", line 1, in
File "/data/nobackup/tmp/pip-install-w5kk3sba/toil-vg/setup.py", line 7, in
execfile(os.path.join(os.path.dirname(os.path.realpath(file)), "version.py"))
NameError: name 'execfile' is not defined
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

[adamnovak]

I think we just haven't done a PyPI release in a while. The version in the repo is 1.6.0a1 and you're getting 1.4.1.

@glennhickey You control the toil-vg PyPI project right?

[glennhickey]

Gitlab doesn't have the pypi credentials either

 Submitting dist/toil-vg-1.6.0.tar.gz to https://upload.pypi.org/legacy/
Upload failed (403): Invalid or non-existent authentication information. See https://pypi.org/help/#invalid-auth for details
error: Upload failed (403): Invalid or non-existent authentication information. See https://pypi.org/help/#invalid-auth for details
make: *** [pypi] Error 1
Makefile:86: recipe for target 'pypi' failed

@cmarkello You are listed as a maintainer here: https://pypi.org/project/toil-vg/#description. I'm not sure what the process is, but could you please log in there and add me and @adamnovak as maintainers, or otherwise share the login credentials? Thanks .

[adamnovak]

I don't think I actually have a pypi account for this; I can go ahead and make one.

…

On 4/28/20, Glenn Hickey ***@***.***> wrote: [Gitlab doesn't have the pypi credentials either](https://ucsc-ci.com/vgteam/toil-vg/-/jobs/50196) ``` Submitting dist/toil-vg-1.6.0.tar.gz to https://upload.pypi.org/legacy/ Upload failed (403): Invalid or non-existent authentication information. See https://pypi.org/help/#invalid-auth for details error: Upload failed (403): Invalid or non-existent authentication information. See https://pypi.org/help/#invalid-auth for details make: *** [pypi] Error 1 Makefile:86: recipe for target 'pypi' failed ``` @cmarkello You are listed as a maintainer here: https://pypi.org/project/toil-vg/#description. I'm not sure what the process is, but could you please log in there and add me and @adamnovak as maintainers, or otherwise share the login credentials? Thanks . -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #804 (comment)

[glennhickey]

An alternative would be to get access to this account: https://pypi.org/user/cgcloud_jenkins/ which is also a toil-vg maintainer.

[adamnovak]

OK, I'm "adamnovak" now. I'm not sure who has the credentials to cgcloud_jenkins. Maybe cluster-admin has a credentials management process we should be using for these sorts of things?

…

On 4/28/20, Glenn Hickey ***@***.***> wrote: An alternative would be to get access to this account: https://pypi.org/user/cgcloud_jenkins/ which is also a toil-vg maintainer. -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #804 (comment)

[cmarkello]

@glennhickey I've added @adamnovak as maintainer for the project. I don't know what your pypi username is.