<div dir="auto">A good place to start would be to submit your code to gerrit and link it to the redmine. Instead of comment on redmine, you can then put the comments directly in the parts of the code you have concerns about. This will make it much easier to contextualize what your proposed feature does. It looks like some issues that you are concerned about on the redmine are physics based while others are code based. It would be helpful to separate these to the extent possible.</div><div class="gmail_extra"><br><div class="gmail_quote">On Jul 23, 2018 9:30 PM, "Mirabzadeh, Christopher (<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>)" <<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space">
Thank you for your responses. I did create a CR back in 2015, feature #1849, <a href="http://redmine.gromacs.org/issues/1849#change-12019" target="_blank">
http://redmine.gromacs.org/<wbr>issues/1849#change-12019</a>. There wasn’t any feedback so I’m not sure if there is interest in it’s implementation. My code was working in late 2015 but I had a major set back, possibly due to bug #2264. I have completed and tested
the project and could share my test cases through Jupiter Notebooks on Github. Publication is the next step. I have heard that there may be a change to expanded ensemble. My code works with the current version of expanded ensemble so I don’t know if there
would need to be a revision in the near future. Your comments about sustainability/maintenance are understandable and I’m sure I would be able to triage and troubleshoot any related bugs as they come up. I would become more of an active member in the developer
community as I’ve spent many hours understanding the code base but graduating is my current priority.
<div><br>
</div>
<div>If I could get some feedback on feature #1849, then I will know whether or not it will be worthwhile for me push to get the code into the next code release.</div>
<div><br>
</div>
<div>Again, thank you for your responses.</div>
<div><br>
</div>
<div>-ChrisM<br>
<div><br>
<blockquote type="cite">
<div>On Jul 18, 2018, at 11:40 PM, Erik Lindahl <<a href="mailto:erik.lindahl@gmail.com" target="_blank">erik.lindahl@gmail.com</a>> wrote:</div>
<br class="m_4673335634874736474Apple-interchange-newline">
<div>
<div dir="auto">And one more comment:
<div><br>
</div>
<div>While we usually love improvements, fixes or a new algorithm, one important concern for all new code is how (and by whom) it will be maintained and bug-fixed a few years from now. A new analysis tool that doesn't change much other code can be
quite straightforward, but a complex new algorithm that influences load balancing and the nonbonded kernels would need broad consensus from many developers that it's so useful we will support it together.</div>
<div><br>
</div>
<div>Since it can take a bit of effort to get documentation and unit tests ready, a good strategy is often to start a redmine feature thread about the algorithm and suggested contribution to get feedback earlier than after Gerrit submission!</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Erik</div>
<div><br>
<br>
<div>Erik Lindahl <<a href="mailto:erik.lindahl@scilifelab.se" target="_blank">erik.lindahl@scilifelab.se</a>>
<div>Professor of Biophysics</div>
<div>Science for Life Laboratory</div>
<div>Stockholm University & KTH</div>
<div>Office (SciLifeLab): +46 8 524 81567</div>
<div>Cell (Sweden): +46 73 4618050</div>
<div>Cell (US): +1 267 3078746</div>
<div><br>
</div>
</div>
<div><br>
On 19 Jul 2018, at 06:24, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">Hi Chris,<br>
<br>
<div class="gmail_quote"></div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div dir="ltr">On Tue, Jul 17, 2018 at 10:08 PM Mirabzadeh, Christopher (<a href="mailto:mira2978@vandals.uidaho.edu" target="_blank">mira2978@vandals.uidaho.edu</a>) <<a href="mailto:mira2978@vandals.uidaho.edu" target="_blank">mira2978@vandals.uidaho.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I have a completed project that was tested and has been working since GROMACS 5.1.4. I cloned the newest repo from gerrit and would like to try an include my code in the next code release. I understand that my code will have to fit the changes since 5.1.4.<br>
</blockquote>
<div><br>
</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div>Great. We love getting contributions of useful and well written code :-) Don't hesitate to drop into our fortnightly developer roundtable telcos. I'd offer to set up a specific chat with you, but I'm shortly going on my summer holidays! So perhaps
others can carry on the discussion.</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Question 1: Is it too late to include my code in the upcoming release? I remember getting an email from the group about the next release but got distracted by work and home and I may have missed the deadline.<br>
</blockquote>
<div><br>
</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div>No, it's not too late, but it very soon will be. Reviewable, tested code will need to be in gerrit by early September if we're to integrate it along with all the others things for GROMACS 2019. Do check out the advice in the latest version of
the developer guide at <a href="http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/dev-manual/contribute.html" target="_blank">http://jenkins.gromacs.org/<wbr>job/Documentation_Nightly_<wbr>master/javadoc/dev-manual/<wbr>contribute.html</a>. We
definitely need to hear some more details from you about what you propose so we can see if it's feasible.</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Question 2: I have no idea how to use gerrit. I’m familiar with git, but gerrit looks foreign to me. In the write-up on
<a href="http://gromacs.org/" rel="noreferrer" target="_blank">gromacs.org</a>, there is no mention of creating a local working branch and creating pull requests which is the workflow that I’m familiar with. Is that still the process with gerrit? Is
there a workflow to follow that I missed? Further guidance would be appreciated.<br>
</blockquote>
<div><br>
</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div>We don't use a pull-request workflow. We haven't made a how-to for the mechanics of contributing, but all proposed patches (even from regular developers) are structured as a patch series based on the current HEAD of the master branch, and after
testing and review get rebased on the new HEAD and get submitted. The history ends up linear. Working out how to organize the code so it isn't an unmanageable lump of 20k lines can be a bit of work. But we'd need to know more to have specific suggestions.</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Question 3: If I have completed code for review, that incorporates a new algorithm, does a publication have to be included? The context being, what is the process for explaining the algorithm to a reviewer?<br>
</blockquote>
<div><br>
</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div>That will go a fair way to helping the code review process go smoothly, but do be aware that there will need to be other documentation for both users and developers, plus tests so that we can continue to keep the code working as we modernize the
code base for future needs.</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div><br>
</div>
<div>Mark</div>
</div>
</div>
<div dir="ltr">
<div class="gmail_quote">
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Cheers,<br>
<br>
-ChrisM<br>
<br>
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