Final GSoC blog post and call for mentors

[jennaswa]

It would be great to share all of the great work @xhgchen and @marinegor did during this year's GSoC program. Would you both be comfortable sharing .md files of your final project reports to be posted on the MDAnalysis blog and linked in this post? If so, it'd be great if you could please add your reports as blog posts as indicated in the README for this repo: https://github.com/MDAnalysis/MDAnalysis.github.io#blog-mdanalysisorgblog and add the appropriate links to the skeleton provided here. Thanks!

[jennaswa]

I have added 2023 mentors/org admins as reviewers to this PR once @xhgchen and @marinegor have had the chance to add their final project reports.

[marinegor]

hi @jennaswa , sorry for the huge delay in this.
If I understood you correctly, this file should be enough: https://github.com/marinegor/marinegor.github.io/blob/master/_posts/2023-07-30-GSOC-6.md

I could add that as a separate PR, if needed.

[jennaswa]

Thank you, @marinegor and @xhgchen for sending me your final submission files! To match our blog formatting, I've edited the formatting of your files slightly and signed with your GH handles at the bottom. Please review and approve if everything looks okay. I'd love to try to merge this tomorrow! :)

[marinegor]

hi @jennaswa , it looks fine -- the only thing is that I think it makes sense to add link to the page with previous posts on "previous posts" in the first paragraph, since the reader isn't on my blog page now (I added a comment).

[orbeckst]

@xhgchen could you please review the installation instructions for transport analysis — it currently says "no release" and "install from source" but there's actually a 0.1.0 available that is pip-installable. Could we please also add some links to MDAKit things? We worked hard on MDAKits and would like to show that the infrastructure is being used.

@marinegor could you please look at one comment about the commented out select line in the RMSD calculation?

Otherwise I have various comments/suggestions — please implement as you see fit @jennaswa .

Thanks a lot for pulling it finally together!!

[xhgchen]

@xhgchen could you please review the installation instructions for transport analysis — it currently says "no release" and "install from source" but there's actually a 0.1.0 available that is pip-installable. Could we please also add some links to MDAKit things? We worked hard on MDAKits and would like to show that the infrastructure is being used.

@marinegor could you please look at one comment about the commented out select line in the RMSD calculation?

Otherwise I have various comments/suggestions — please implement as you see fit @jennaswa .

Thanks a lot for pulling it finally together!!

I see the new mention of MDAKits at the beginning and I think it is a nice edit - feel free to add any more MDAKit mentions/links as you feel is appropriate.

[orbeckst]

Thank you all for addressing my comments so I am giving it a ✅ from my end.

@RMeli is raising some excellent points but I let him make a blocking review if necessary.

[jennaswa]

I believe all requested changes have now been addressed (please confirm @RMeli). Thank you for your help with this, everyone!

[RMeli]

Thanks @jennaswa

[orbeckst]

Thanks for completing this big triple-post! But looking at https://www.mdanalysis.org/2024/01/11/gsoc2023_xhgchen/ , there seem to be plots not showing:

• https://www.mdanalysis.org/2024/01/11/gsoc2023_xhgchen/#vacf-plot
• https://www.mdanalysis.org/2024/01/11/gsoc2023_xhgchen/#running-integral-plot

I think the actual PNG files were not committed. Can you please fix this @xhgchen ?

[jennaswa]

I tried making direct commits to the master branch (bad practice, I know, but figured it was easier with small fixes). For some reason the checks are failing and it’s not building correctly for the website. Maybe someone who knows better than I can check out those commits and see what’s going on? Thanks!

…

On Thu 18. Jan 2024 at 19:50, Oliver Beckstein ***@***.***> wrote: Thanks for completing this big triple-post! But looking at https://www.mdanalysis.org/2024/01/11/gsoc2023_xhgchen/ , there seem to be plots not showing: - https://www.mdanalysis.org/2024/01/11/gsoc2023_xhgchen/#vacf-plot - https://www.mdanalysis.org/2024/01/11/gsoc2023_xhgchen/#running-integral-plot I think the actual PNG files were not committed. Can you please fix this @xhgchen <https://github.com/xhgchen> ? — Reply to this email directly, view it on GitHub <#341 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJEDTQKUTJ5PLGBXGQP76OLYPFVH3AVCNFSM6AAAAAA77XBVE2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJZGAZTCMRQGA> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[orbeckst]

Looking in the actions workflow https://github.com/MDAnalysis/MDAnalysis.github.io/actions/runs/7573031005/job/20624240225 under "Build with Jekyll" shows the error:

  Liquid Exception: Could not find post "2024-01-11-gsoc2023_marinegor" in tag 'post_url'. Make sure the post exists and the name is correct. in /github/workspace/_posts/2024-01-18-gsoc2023-final.md
             ERROR: YOUR SITE COULD NOT BE BUILT:
                    ------------------------------------
                    Could not find post "2024-01-11-gsoc2023_marinegor" in tag 'post_url'. Make sure the post exists and the name is correct. 

Let me fix this ....

[orbeckst]

I checked my fix locally and it looked fine so I just pushed to the master branch in 73356f8. Hopefully all good now 🤞

[jennaswa]

Aha - I see where I forgot to update the dates to the individual posts now. Thanks for fixing this, @orbeckst !

[jennaswa]

@marinegor - I just noticed that dask.distributed is still mentioned here and L130, although it was removed from other places. Should it remain here? If not, please tell me exactly what needs to be removed/replaced, or open a PR to make the necessary change. Thanks!