Please upgrade auditwheel to 1.9

ehashman commented 6 years ago

It looks like auditwheel was pinned a little over a year ago and hasn't been updated. Would you mind bumping the version to 1.9.0 and seeing if that works?

Thanks!

hainm commented 6 years ago

thanks @ehashman. I will test that.

dprada commented 5 years ago

Hi! I tried to overcome the problem with auditwheel installing ambertools 18 with conda. But then I realized that I have to downgrade the environment from Python 3.7 to 3.6. Having a conda package built to be used with Python 3.7 would be great. Thanks in advance for considering this suggestion.

hainm commented 5 years ago

thanks. I will work on that.

slochower commented 5 years ago

Hi @hainm , I'm not sure that I'm being blocked by the same dependency, but I also can't get pytraj to run on a Travis Python 3.7 environment. Do you have a rough estimate of when you think a 3.7-compatible version will be ready?

UnsatisfiableError: The following specifications were found to be in conflict:
  - python=3.7
  - pytraj -> python=3.6
Use "conda search <package> --info" to see the dependencies for each package.

Edit: I am installing ambertools from http://ambermd.org/downloads/ambertools/conda/ channel and pytraj from ambermd. Is there a better way to do this?

hainm commented 5 years ago

hi @slochower, both pytraj and ambertools 18 were released before python 3.7 so there are no 3.7 versions yet

Edit: I am installing ambertools from http://ambermd.org/downloads/ambertools/conda/ channel and pytraj from ambermd. Is there a better way to do this?

pytraj is already included in ambertools (official release hosted in amber server), so you don't need to install pytraj from ambermd channel in anaconda server. Sorry for the confusion.

Do you have a rough estimate of when you think a 3.7-compatible version will be ready? it's pretty easy to get this done on Linux but I got some header file missing issue with new MacOS update. Do you only need 3.7 for Linux?

slochower commented 5 years ago

hi @slochower, both pytraj and ambertools 18 were released before python 3.7 so there are no 3.7 versions yet

Got it.

pytraj is already included in ambertools (official release hosted in amber server), so you don't need to install pytraj from ambermd channel in anaconda server. Sorry for the confusion.

To be clear, are you saying that I should be able to install both ambertools and pytraj from the http://ambermd.org/downloads/ambertools/conda/ channel?

$ conda install pytraj -c http://ambermd.org/downloads/ambertools/conda/
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - pytraj

it's pretty easy to get this done on Linux but I got some header file missing issue with new MacOS update. Do you only need 3.7 for Linux?

I think both would be ideal, but Linux support would definitely be welcome :) I personally am not using any Python 3.7 features, but I'm migrating one of my repositories to the MolSSI cookiecutter that includes MacOS and Linux Python 3.7 builds on Travis.

dprada commented 5 years ago

it's pretty easy to get this done on Linux but I got some header file missing issue with new MacOS update. Do you only need 3.7 for Linux?

Thumbs up.

hainm commented 5 years ago

To be clear, are you saying that I should be able to install both ambertools and pytraj from the http://ambermd.org/downloads/ambertools/conda/ channel?

No. I meant you can just install ambertools from that channel since it already has pytraj. There is no pytraj standalone install in that channel. :D

I personally prefer to install pytraj via pip since it's super quick to do that (it takes time for conda to resolve the conflicting recently).

but I'm migrating one of my repositories to the MolSSI cookiecutter that includes MacOS and Linux Python 3.7 builds on Travis.

I see.

PS: Since there are several request for ambertools 3.7 (e.g: https://github.com/openforcefield/openforcefield/issues/153#issue-394092437), I will try to make it happen asap. cheers.

hainm commented 5 years ago

Dear all, I am sorry for the long delay. I am finally done with few things

Upgrade auditwheel to v2.0 that makes pytraj work with Ubuntu 18.04
Support python 3.7 (only available via pip install or macOS conda); drop support for python 3.4.
- Due to some compiling issues with conda, python 3.5 release for MacOS is only available via pip install.
Release pytraj v2.0.4 (will be soon released in AmberTools 19 too). It should be available in ambermd conda channel or in pypi (pip install).

Please let me know if there's any unresolved issue. Thanks.

root@6696a5051e30:/work# cat /etc/os-release  |grep VERSION
VERSION="18.04.2 LTS (Bionic Beaver)"
VERSION_ID="18.04"
VERSION_CODENAME=bionic

root@6696a5051e30:/work# /root/miniconda3/bin/python 
Python 3.7.1 (default, Dec 14 2018, 19:28:38) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pytraj as pt
p>>> pt.__version__
'2.0.4'
>>> traj = pt.datafiles.load_tz2()
>>> pt.rmsd(traj, mask='@CA', ref=0)
array([1.94667955e-07, 2.54596866e+00, 4.22333034e+00, ...,
       4.97189564e+00, 5.53947712e+00, 4.83201237e+00])

hainm commented 5 years ago

In short, I recommend to install pytraj v2.0.4 via pip install (thanks to the amazing work from auditwheel folks.

dprada commented 5 years ago

Thanks!

Amber-MD / pytraj

Please upgrade auditwheel to 1.9 #1464