Author order: I agree with Jakob’s feelings expressed in the comment quoted below. But Jakob’s comment is about a file in the repo as far as I can see. Alphabetical there would be ok (potentially with a list of contributions). Here we’re talking about an author list for a software DOI reference.

-          Mister AAA who added 1 commit shouldn’t appear as first author.

-          Github automatic ordering won’t be perfect, and we can discuss about how to value contributions for ages, but I’m impressed that it did a reasonable job. And as Casper said, we can then edit once on zenodo.

-          The software is quite different from the paper. The latter clearly should acknowledge all contributions, including testing, design etc. In addition, we should have a file in the repo that acknowledges all contributions https://github.com/CCPPETMR/SIRF/issues/389. However, software copyright is originally owned by people who actually wrote something  (although of course usually that copyright is then transferred to the employer by contract). It feels therefore correct to me to have a software DOI follow the same principle.

-          Adding all “general” contributors will soon become very unwieldy (arguably it is already)

Every system will be imperfect.  The question is which one reflects reality the best.

 

Foobar2016: Casper, if you could ask, that’d be great.

 

Zenodo upload of the SuperBuild releases? No, I don’t think so.

 

CCPPETMR community: this is a Zenodo community created by Ben.

 

Adding VM on github: yes, but we cannot due to the file size limit. As soon as we could, there’s not much point in putting it on zenodo as well as far as I can see (but I wouldn’t mind). But this is for later anyway.

 

Finally, given that we can change the author list after upload according to Casper, let’s not delay the upload… it’s already far too long. Therefore, Edo please use my suggested list below. Happy to continue the discussion in the mean time.

 

Kris

 

From: CCP-PETMR Developers list [mailto:[log in to unmask]] On Behalf Of Edoardo Pasca - UKRI STFC
Sent: 22 May 2019 15:38
To: [log in to unmask]
Subject: Re: VM 2.0.0 on zenodo

 

 

 

• Side note: if we want to add VM ova files to Zenodo in future, as mentioned before I'd recommend adding the files to CCPPETMR/SIRF github releases via the web interface.

Does this mean we have to upload to GitHub?

• Second side note: maybe we should also add a link to installation instructions/superbuild/wiki with each release note so that people landing on Zenodo/github releases immediately see a helpful link rather than attempt to download reasonably useless (ahem I mean nearly impossible to compile :P) code.

I quite agree

On author ordering, it seems a pretty impossible task. Last discussion on the paper is a prime example. You can follow a similar thread in this CCPi issue https://github.com/vais-ral/CCPi-Framework/pull/279#issuecomment-490984999 There we ended up choosing alphabetical.

 

Edo

 

 

On Wed, 22 May 2019 at 14:29, Thielemans, Kris <[log in to unmask]> wrote:

Dear all

 

A question arises on order of authors of the software, as we need to give this when uploading our VM to zenodo. Ben makes the point that this will count as a “citation”. The question then becomes who to include and what order to use.

 

I strongly suggest that the software upload should contain all contributors (in terms of actual lines of code and or documentation) to SIRF, the SuperBuild and the VM, but not anyone else. This is of course different from a paper (which is why we need our paper out…).

 

Alphabetical order is an easy solution, but I feel somewhat weird for a project that has such disparity between level of contribution (as all open source software really). I think it would make most sense to do this in order of “contributions”. On the other hand, thinking very hard about order for every release isn’t possible either.

 

I had a look at the automatic record created by our github release (set-up by Casper), see e.g. for 2.0.0

https://zenodo.org/record/2816414#.XOVKBaR7nb0

This has a list of authors, presumably done automatically by github/zenodo. It is

evgueni-ovtchinnikov; Richard Brown; Kris Thielemans; Casper da Costa-Luis; David Atkinson; Johannes Mayer; Edoardo Pasca; Ashley Gillman; ckolbPTB; foobar2016; Ben Thomas; Matthias J. Ehrhardt; Alexander Whitehead

This order in fact looks quite reasonable to me for SIRF (but Edo and Ben should definitely be moved up if we include the SuperBuild and VM). Does anyone know why foobar2016 appears here? (This github user has no commits to anything, see https://github.com/foobar2016?tab=overview&from=2016-12-01&to=2016-12-31).

 

I would therefore suggest to use for the 2.0.0 VM

evgueni-ovtchinnikov; Richard Brown; Kris Thielemans; Edoardo Pasca; Casper da Costa-Luis; Ben Thomas; David Atkinson; Johannes Mayer; Ashley Gillman; ckolbPTB; Matthias J. Ehrhardt; Alexander Whitehead

Any objections?

 

Aside from this:

• Does this VM become an attachment to the above link? (If so, author list might be irrelevant, so probably not a good idea)
• The github-created releases do not seem to be part of the CCPPETMR community (although I couldn’t find a link for it).

 

Kris

 

From: Edoardo Pasca - UKRI STFC <[log in to unmask]>
Sent: 22 May 2019 12:45
To: Thomas, Ben <[log in to unmask]>; Thielemans, Kris <[log in to unmask]>
Subject: RE: VM 2.0.0 and zenodo

 

Fine for me but you tell me how to order it.

 

After some thought in CCPi we decided to list the authors of the software alphabetically.

 

Edo

 

From: Thomas, Ben <[log in to unmask]>
Sent: 22 May 2019 11:48
To: Thielemans, Kris <[log in to unmask]>; Pasca, Edoardo (STFC,RAL,SC) <[log in to unmask]>
Subject: Re: VM 2.0.0 and zenodo

 

Might want to consider ordering as the reference will behave like a paper.

Ben

Get Outlook for Android

 

---

From: Edoardo Pasca - UKRI STFC <[log in to unmask]>
Sent: Wednesday, May 22, 2019 11:41:10 AM
To: Thomas, Ben; Thielemans, Kris
Subject: RE: VM 2.0.0 and zenodo

 

Ok,

 

It’s asking me to write the authors, which I will take from

https://github.com/CCPPETMR/SIRF/blob/master/NOTICE.txt

 

OK?

 

Edo

 

From: Thomas, Ben <[log in to unmask]>
Sent: 22 May 2019 10:47
To: Thielemans, Kris <[log in to unmask]>; Pasca, Edoardo (STFC,RAL,SC) <[log in to unmask]>
Subject: Re: VM 2.0.0 and zenodo

 

Hi,

 

Well you don’t have to upload it using your name per se, you add all authors to the record, so it need not (probably shouldn’t) be just Edo on it. You add the ‘community’ that you want the upload to belong to when you create the entry. I will then receive a request for CCPPETMR. An entry can reside in multiple communities if you wish e.g CCPPETMR and CoSeC.

 

Unfortunately, communities are currently limited to administration by a single user (me in this instance) although I believe this will likely change in the future.

 

Kind regards,

Ben

 

From: "Thielemans, Kris" <[log in to unmask]>
Date: Wednesday, 22 May 2019 at 10:39
To: "Pasca, Edoardo (STFC,RAL,SC)" <[log in to unmask]>, "Thomas, Ben" <[log in to unmask]>
Subject: RE: VM 2.0.0 and zenodo

 

Hi

 

How do we get the VM on zenodo? For data, our strategy was to let people upload it using their own name, and then add it to do the CCPPETMR group (via a PR type of thing I guess). It could work for the VM as well. Possibly CoSeC has a zenodo group, and they might be happy to have the VM there. Doing it as “do Pasca” is maybe a bit weird. Alternatively, Ben, can you add Edo and Evgueni to the CCPPETMR group for direct uploading?

 

From: Edoardo Pasca - UKRI STFC [mailto:[log in to unmask]]
Sent: 21 May 2019 16:25
To: Thielemans, Kris; [log in to unmask]
Subject: RE: VM 2.0.0

 

I am currently rebuilding the VM. Tomorrow I will be uploading it for your testing.

 

Edo

 

From: CCP-PETMR Developers list <[log in to unmask]> On Behalf Of Thielemans, Kris
Sent: 21 May 2019 15:24
To: [log in to unmask]
Subject: Re: VM 2.0.0

 

Hi

 

So… we should never point to personal forks. If we ever need to point to a fork, it’ll need to be on CCPPETMR.

 

This is

https://github.com/CCPPETMR/SIRF-SuperBuild/pull/248

(just merged).

 

We have a question now if that PR is an important enough change to tag the SB with 2.0.1. I wouldn’t harm the VM, but then we have the fun if desyncing the SB and SIRF. My feeling therefore is to leave the tagging of the SB for a bit longer. Especially as presumably this is dragging in other NiftyReg changes which we haven’t tested properly either.

 

Kris

 

PS: By the way, I had suggested to NOT tag the CPPPETMR_VM either, but too much noise on the list I guess :-;

 

From: CCP-PETMR Developers list [mailto:[log in to unmask]] On Behalf Of Brown, Richard
Sent: 21 May 2019 15:14
To: [log in to unmask]
Subject: Re: VM 2.0.0

 

Apologies, it was pointing to my fork and since my PR got accepted, I deleted the branch.

 

I’ve restored the branch, so could you give it another go? Hopefully that should have sorted it. 

 

Since my NiftyReg PR has been accepted, from current master onwards the KCL fork will be used (I’ve updated version_config.cmake), but I’ll make sure not to delete the branch on my fork that was used for SIRF 2.0.0.

 

Rich

 

On 21 May 2019, at 14:49, Edoardo Pasca - UKRI STFC <[log in to unmask]> wrote:

 

Hi guys, 

I tested the PR 137 in the VM. I added a commit. Merged to master and tagged. 

Update_VM fails ... 

[  1%] Creating directories for 'NIFTYREG'
[  2%] Performing download step (git clone) for 'NIFTYREG'
Cloning into 'NIFTYREG'...
warning: remote HEAD refers to nonexistent ref, unable to checkout.

fatal: reference is not a tree: 22f24db1113973507689aeabbc3f17ddeca1d7f6
CMake Error at /home/sirfuser/devel/buildVM/builds/NIFTYREG/tmp/NIFTYREG-gitclone.cmake:75 (message):
 Failed to checkout tag: '22f24db1113973507689aeabbc3f17ddeca1d7f6'

Checking the SuperBuild tag is v2.0.0 and SIRF_TAG is v2.0.0
Apparently NIFTYREG_TAG is wrong?

Edo

-----Original Message-----
From: CCP-PETMR Developers list <[log in to unmask]> On Behalf Of Edoardo Pasca - UKRI STFC
Sent: 17 May 2019 22:02
To: [log in to unmask]
Subject: Re: VM 2.0.0

sure.


The only thing I don't have access to is Zenodo.


Edo

________________________________
From: CCP-PETMR Developers list <[log in to unmask]> on behalf of Thielemans, Kris <[log in to unmask]>
Sent: Friday, May 17, 2019 4:47:42 PM
To: [log in to unmask]
Subject: Re: VM 2.0.0

Hi

I think the best thing to do is now that Edo run this on his VM, re-zeroes and re-exports, and then upload later. Amazingly, zenodo is down, so we cannot upload there anyway...

So, release on Monday. Edo, can you take care of this then? (website, email with suitably enthusing message to all lists, rest of the checklist anyway). I can help if need be.

Kris

-----Original Message-----
From: CCP-PETMR Developers list <[log in to unmask]> On 
Behalf Of Brown, Richard
Sent: 17 May 2019 16:41
To: [log in to unmask]
Subject: Re: VM 2.0.0

we fixed Evgueni's error with "sudo pip uninstall pyder-kernels".

We're not overly sure what the problem was about, nor why this fixed 
it...

I'll update the VM script.

Rich

On 17 May 2019, at 16:17, Evgueni Ovtchinnikov - UKRI STFC

<[log in to unmask]> wrote:

sorry it appears i replied to edoardo only...


________________________________
From: Ovtchinnikov, Evgueni (STFC,RAL,SC)
Sent: Friday, May 17, 2019 3:36 PM
To: Pasca, Edoardo (STFC,RAL,SC)
Subject: Re: VM 2.0.0


Everything seems ok save for this error message when starting Spyder 
(which

seems to work fine regardless):

File 
"/usr/local/lib/python2.7/dist-packages/spyder/otherplugins.py", 
line 79,

in _import_plugin

  module = _import_module_from_path(module_name, plugin_path)  File 
"/usr/local/lib/python2.7/dist-packages/spyder/otherplugins.py", 
line 101, in

_import_module_from_path

  info = imp.find_module(module_name, [plugin_path])
ImportError: No module named spyder_kernels-0.4.2.dist-info

By the way, when I open a file in Spyder, 'Open file' window looks 
different

from previous VM (which I got from your OneDrive link) - have you 
installed different  version of Spyder lately?

________________________________
From: CCP-PETMR Developers list <[log in to unmask]> on 
behalf of Edoardo Pasca - UKRI STFC <[log in to unmask]>
Sent: Friday, May 17, 2019 12:20:29 PM
To: [log in to unmask]
Subject: VM 2.0.0


Hi there,



If someone wants to try and comment on the VM with SIRF 2.0.0 it can 
be downloaded from

https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fedo
si

l.net%2Fstfc%2Fsirf%2FSIRF_2.0.0.ova&amp;data=02%7C01%7Ck.thielemans%4

 

0UCL.AC.UK%7C46b37bcde41c4d71a35c08d6dade2f7d%7C1faf88fea9984c5b93
c921

 

0a11d9a5c2%7C0%7C0%7C636937045151742495&amp;sdata=pze2eLd6%2BX
ML4qqjN8

oosDCC0MYS8T5GDtmlDFYRdN0%3D&amp;reserved=0



Edo



--
Edoardo Pasca, PhD
Senior Visualisation Scientist
Scientific Computing Department, STFC Rutherford Appleton Laboratory 
Fermi Avenue Chilton Didcot OX11 0QX
0044 (0)1235 44 5660, R89 F16
:wq



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