Re: Python 3 release - Wed Feb 10

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Ludtke, Steven J.

Feb 3, 2021, 9:15:03 AMFeb 3
to, Thorsten Wagner, Stabrin, Markus, Stefan Raunser, Dr. Tapu Shaikh, Durmaz, Tunay, Chen, Muyuan
Ok, after discussing the state of the binaries, etc, Tunay is going to make sure the final set of dependencies are in place by Friday, and that all of the binaries, with the possible exception of the native Windows, will be compiling properly. Everyone will then have a few days to do any final testing they want to do. The plan is for the release to occur on Wed Feb 10

As of now, please limit pushes to the release branch to:
- critical issues which cause errors/crashes/bad results
- changes to individual programs (ie - not core libraries) with limited potential impact on the whole system

the master branch is still active for more 'exploratory' changes. In the end all changes in the release branch will wind up on master again, but we will tag the release branch as well. (pardon any lapses in terminology there, my point was that the branch needs to remain in existence so we can always check out the release)

On Feb 2, 2021, at 11:14 AM, Ludtke, Steven J. <> wrote:

No objections to any of these proposals. Are they things that can happen very soon? Once you make such changes we will want to do a quick final round of tests before we do the release. I am running some testing right now, but the main tests can run pretty quickly when you're ready.

On Feb 2, 2021, at 8:15 AM, Durmaz, Tunay <> wrote:

We will merge the release branch to master.

The binary issues, I think, are resolved now. But, I want to change eman-deps and remove eman-deps-cxx, eman-deps-cli and eman-deps-dev. It takes a little time to install. Instead we will have only eman-deps, guy and no-gui versions. I think the release should use this new eman-deps. The installation of eman-deps has been slow and I'm afraid it might get worse. Also, upgrading boost might be a good idea to avoid dependency conflicts in the near future.

On Feb 2, 2021, at 7:10 AM, Ludtke, Steven J. <> wrote:

Hi Thorsten,
great!  We'll do some final testing, and check with Tunay whether he has all of the binary issues solved.

I think it's likely that we will merge back to master, but let's see if Tunay has a different opinion....

On Feb 2, 2021, at 4:39 AM, Thorsten Wagner <> wrote:

Hi Steve,

from our side we are ready. Can you tell us what will happen with the release branch? Will it be merged into master at some point?


From: Ludtke, Steven J. <>
Sent: Friday, January 8, 2021 1:41:56 PM
To: Thorsten Wagner
Cc: Markus Stabrin; Stefan Raunser; Durmaz, Tunay
Subject: Re: Python 3 release
End of January sounds good to me!

On Jan 8, 2021, at 3:01 AM, Thorsten Wagner <> wrote:

***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
Hi Steve,

Happy new year! I hope you had a good start.

From our side we are ready to release.  Do you create the release branch? We would maybe push one or two changes next week, but we can certainly fix the date to end of January?

Please let me know how you want to proceed.


Dr. Thorsten Wagner
Max-Planck-Institute of Molecular Physiology
Structural Biochemistry
Otto-Hahn Strasse 11
D-44227 Dortmund


From: "Ludtke, Steven J." <>
Subject: Python 3 release
Date: 5. January 2021 at 19:57:47 CET
To: Markus Stabrin <>
Cc: Stefan Raunser <>, "Durmaz, Tunay" <>

Happy New Year!  Let's hope this one is better than the last...

So, we're now about 1 full year late on the promised Python 3 release of the Python 3 version of EMAN2/SPHIRE/SPARX. Much of the fault for this was on our end, in continuously delaying for the addition of new features, but I think now that we've hit the new year we really need to pull the trigger on this as soon as we possibly can.  Aside from new feature additions, things have been pretty stable/functional for us for 9+ months now. Our plan would be to call this EMAN 2.39, with the next release being "EMAN3", which will include some major changes to how we do a bunch of things internally for better interoperability.

Can I ask where you guys stand on this issue now? 

Steven Ludtke, Ph.D. <>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (
Academic Director, CryoEM Core                                        (
Co-Director CIBR Center                                    (

Prof. Dr. Stefan Raunser | Director | Dep. Structural Biochemistry | Max Planck Institute of Molecular Physiology | Otto-Hahn-Straße 11, 44227 Dortmund, Germany | +49 231 133 2300

Ludtke, Steven J.

Feb 10, 2021, 12:12:33 PMFeb 10
to, Thorsten Wagner, Stabrin, Markus, Stefan Raunser, Dr. Tapu Shaikh, Durmaz, Tunay, Chen, Muyuan
Ok, as previously discussed, as far as we can tell things are stable. We are getting a couple of last patches into some individual EMAN2 programs (shouldn't be anything library level) and plan on the release a few hours from now.
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