EMAN2 and SPARX Development

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This group is for discussion of EMAN2 & SPARX development issues. There is a separate list for users to ask for help. This list is for active discussion of very technical issues and coordinating releases.

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9/20/21

Eman-deps updated to v29

The version of eman-deps has been updated to version 29. The code on master uses this new version for

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Eman-deps updated to v29

The version of eman-deps has been updated to version 29. The code on master uses this new version for

9/20/21

8/10/21

Bsddb3 is deprecated starting with py 3.10

Bsddb3 is not going to be supported after python 3.9. We are currently on python 3.7, but looking to

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Bsddb3 is deprecated starting with py 3.10

Bsddb3 is not going to be supported after python 3.9. We are currently on python 3.7, but looking to

8/10/21

6/8/21

helicon box files

Is the format of the Helicon box files documented somewhere? -Tapu

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helicon box files

Is the format of the Helicon box files documented somewhere? -Tapu

6/8/21

Ludtke, Steven J.

3/5/21

EMAN2 2.91 - bugfix release

In the debugging process we got several additional bug reports, and spent much of the week fixing

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EMAN2 2.91 - bugfix release

In the debugging process we got several additional bug reports, and spent much of the week fixing

3/5/21

2/18/21

Problem with the release

It looks like (as usual) there is a problem with the release. This was totally my fault, with an

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Problem with the release

It looks like (as usual) there is a problem with the release. This was totally my fault, with an

2/18/21

Ludtke, Steven J.2

2/10/21

Re: Python 3 release - Wed Feb 10

Ok, as previously discussed, as far as we can tell things are stable. We are getting a couple of last

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Re: Python 3 release - Wed Feb 10

Ok, as previously discussed, as far as we can tell things are stable. We are getting a couple of last

2/10/21

2/8/21

EMAN2/SPHIRE/SPARX Release Wed

We still consider everything to be on-track for a release version this Wed. If anyone has any issues

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EMAN2/SPHIRE/SPARX Release Wed

We still consider everything to be on-track for a release version this Wed. If anyone has any issues

2/8/21

1/14/21

The branch for the upcoming release is 'release-2.9', the pull request is at https://github.

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The branch for the upcoming release is 'release-2.9', the pull request is at https://github.

1/14/21

Ludtke, Steven J., Thorsten Wagner2

9/1/20

Repository for Jupyter notebook sessions with EMAN2 demos/docs

Hi, when I try to use "Save Box Coord" in the e2spt_boxer.py I get the following exception:

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Repository for Jupyter notebook sessions with EMAN2 demos/docs

Hi, when I try to use "Save Box Coord" in the e2spt_boxer.py I get the following exception:

9/1/20

Tapu Shaikh, Steve Ludtke2

8/19/20

numpy2em problem

Hi Tapu, we did revamp the NumPy interface for Python 3, as the mechanism we were using previously

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numpy2em problem

Hi Tapu, we did revamp the NumPy interface for Python 3, as the mechanism we were using previously

8/19/20

DAVID HERREROS, Steve Ludtke3

6/29/20

MemoryError Template Matching

Good morning Steve, First, I would like to thank you for you answer and I also want to apologize for

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MemoryError Template Matching

Good morning Steve, First, I would like to thank you for you answer and I also want to apologize for

6/29/20

4/15/20

Hi, EMNumPy.numpy2em works very nicely, except it does not set apix attributed. So then certain

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Hi, EMNumPy.numpy2em works very nicely, except it does not set apix attributed. So then certain

4/15/20

Paul Penczek, Steve Ludtke8

4/6/20

Fwd: plot function request

Thank you! Pawel On Apr 6, 2020, at 6:52 PM, Steve Ludtke <slud...@gmail.com> wrote:

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Fwd: plot function request

Thank you! Pawel On Apr 6, 2020, at 6:52 PM, Steve Ludtke <slud...@gmail.com> wrote:

4/6/20

Paul Penczek, Steven Ludtke2

4/6/20

Only used when the interpreter is in non-gui mode. Sent from my iPhone > On Apr 6, 2020, at 2:38

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Only used when the interpreter is in non-gui mode. Sent from my iPhone > On Apr 6, 2020, at 2:38

4/6/20

12/11/19

Strange boost error with cmake

I am getting this error on Linux and on Mac, even for installations that worked as of day before

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Strange boost error with cmake

I am getting this error on Linux and on Mac, even for installations that worked as of day before

12/11/19

12/11/19

Strange failure.

Hi, I noticed that after my changes yesterday build failed. However, the failure was caused by

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Strange failure.

Hi, I noticed that after my changes yesterday build failed. However, the failure was caused by

12/11/19

Ludtke, Steven J.

12/10/19

Hi Pawel, pushing to master is the correct thing to do, as changes made to Python2 are only possible

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Hi Pawel, pushing to master is the correct thing to do, as changes made to Python2 are only possible

12/10/19

12/3/19

Python 3 transition tomorrow (Dec 4, 2019)

Having heard no objections from the various leads, the plan is to officially start the Python 3

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Python 3 transition tomorrow (Dec 4, 2019)

Having heard no objections from the various leads, the plan is to officially start the Python 3

12/3/19

Steve Ludtke, shadow walker11

11/14/19

Python 3 transition

The branch with boost upgrade to 1.66 will be merged into master as soon as the running tests finish.

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Python 3 transition

The branch with boost upgrade to 1.66 will be merged into master as soon as the running tests finish.

11/14/19

9/30/19

2.31 Release this morning!

If you recall, we were supposed to put out a quick 2.31 bugfix release sometime a couple of months

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2.31 Release this morning!

If you recall, we were supposed to put out a quick 2.31 bugfix release sometime a couple of months

9/30/19

Paul Penczek, shadow walker2

6/17/19

The failing test was disabled and a todo item was files under GitHub issues, https://github.com/

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The failing test was disabled and a todo item was files under GitHub issues, https://github.com/

6/17/19

4/26/19

Warning, release branch merged and deleted!

Please note, with the completion of the release yesterday, the release branch, as always, was merged

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Warning, release branch merged and deleted!

Please note, with the completion of the release yesterday, the release branch, as always, was merged

4/26/19

Steve Ludtke, Markus Stabrin3

4/22/19

How do things look for the planned release tomorrow?

Let's try and target Wed then. That is the day people for the UTMB workshop were told they could

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How do things look for the planned release tomorrow?

Let's try and target Wed then. That is the day people for the UTMB workshop were told they could

4/22/19

Steve Ludtke, Paul Penczek3

4/18/19

Release 2.3 branched - release planned for next Tuesday

Hi I just heard from Stefan and we came to an agreement. Therefore, I am fine with the 23d as a date

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Release 2.3 branched - release planned for next Tuesday

Hi I just heard from Stefan and we came to an agreement. Therefore, I am fine with the 23d as a date

4/18/19

Paul Penczek, Steve Ludtke9

3/10/19

Yes, now it works fine. Thank you. ____________________ Pawel A. Penczek, Ph.D. Professor Structural

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Yes, now it works fine. Thank you. ____________________ Pawel A. Penczek, Ph.D. Professor Structural

3/10/19

Steve Ludtke, … Paul Penczek6

3/1/19

Nope, no idea what that one is about... -------------------------------------------------------------

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Nope, no idea what that one is about... -------------------------------------------------------------

3/1/19

Steve Ludtke, Paul Penczek4

3/1/19

Not a problem :^) -----------------------------------------------------------------------------------

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Not a problem :^) -----------------------------------------------------------------------------------

3/1/19

Thorsten Wagner, … shadow walker9

2/27/19

tqdm is, now, part of eman-deps=13.2. On Mon, Feb 25, 2019 at 7:17 AM Steve Ludtke <sludtke42@

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tqdm is, now, part of eman-deps=13.2. On Mon, Feb 25, 2019 at 7:17 AM Steve Ludtke <sludtke42@

2/27/19

luca lusnig, … Paul Penczek5

2/22/19

problem in recognizing libEM libraries

Hi Steve is correct. The way system is set up there is no need for debugging in vast majority of

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problem in recognizing libEM libraries

Hi Steve is correct. The way system is set up there is no need for debugging in vast majority of

2/22/19

2/22/19

Import mpi problem

Hello everybody, I just encountered a problem when I use an installation that is linked against an

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Import mpi problem

Hello everybody, I just encountered a problem when I use an installation that is linked against an

2/22/19

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