Gsoc blog 2021 #475

SunTzunami · 2021-07-27T14:23:23Z

Weekly Check-in #1 (community bonding period)

…jag.rst

codecov · 2021-07-27T14:28:47Z

Codecov Report

Merging #475 (f88430c) into master (5ddd888) will increase coverage by 0.21%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #475      +/-   ##
==========================================
+ Coverage   88.31%   88.53%   +0.21%     
==========================================
  Files          31       31              
  Lines        6446     6575     +129     
  Branches      770      787      +17     
==========================================
+ Hits         5693     5821     +128     
- Misses        534      535       +1     
  Partials      219      219

Impacted Files	Coverage Δ
fury/ui/tests/test_core.py	`96.51% <0.00%> (-3.49%)`	⬇️
fury/ui/elements.py	`88.54% <0.00%> (-0.81%)`	⬇️
fury/ui/tests/test_elements.py	`83.23% <0.00%> (-0.14%)`	⬇️
fury/ui/tests/test_helpers.py	`100.00% <0.00%> (ø)`
fury/ui/core.py	`93.38% <0.00%> (+1.33%)`	⬆️
fury/ui/containers.py	`83.81% <0.00%> (+1.56%)`	⬆️
fury/ui/helpers.py	`98.21% <0.00%> (+5.35%)`	⬆️

skoudoro

Hi @SunTzunami,

Thank you for this. See below for some comments. Please, render locally to see the result of your rst. There are several issues.

Please, can you review this PR @devmessias and @antrikshmisri?

Thank you

docs/source/posts/2021/2021-06-08-week-1-sajag.rst

skoudoro · 2021-07-28T12:46:21Z

docs/source/posts/2021/2021-06-08-week-1-sajag.rst

+I had weekly meetings with my mentors and other core team members. In the first meeting I got acquainted with the team members and learnt about the organisation and its goal/vision.
+In the later meetings we discussed about various representations of proteins and how to go about implementing them in FURY.
+We discussed about various libraries which can be used to parse PDB and PDBx files.
+I made a `document <https://docs.google.com/document/d/1mSoAWyXlLNrCa3hN-hiP35Lj7rURYMk5jFnWZbZp70s>`_ for the same to list pros and cons of using each library. 


We might need to put this google document in rst and somewhere else.

Any suggestions as to where should I put it?

docs/source/posts/2021/2021-06-08-week-1-sajag.rst

docs/source/posts/2021/2021-06-14-week-2-sajag.rst

docs/source/posts/2021/2021-07-05-week-5-sajag.rst

docs/source/posts/2021/2021-07-12-week-6-sajag.rst

docs/source/posts/2021/2021-07-19-week-7-sajag.rst

docs/source/posts/2021/2021-07-26-week-8-sajag.rst

SunTzunami · 2021-07-28T19:14:21Z

Hi @skoudoro ! Thank you very much for the feedback! I made changes as per your feedback and tested it locally by generating html via the following code -

import docutils.core
docutils.core.publish_file(
    source_path ="restructured.rst",
    destination_path ="Output.html",
    writer_name ="html")

The output html files were all fine.
About the documents, should I make separate rst files or create gists?

skoudoro · 2021-07-29T10:30:39Z

Hi @skoudoro ! Thank you very much for the feedback! I made changes as per your feedback and tested it locally by generating html via the following code -

Please, use the standard of the project to generate your HTML files and to check them. Your command does not take into consideration style sheet design, API standard, etc.....

Currently, there are still some issues.

if you have an issue with the examples/tutorials during the generation, use the following command:

$ make -C . clean && make -C . html-no-examples

more info here

skoudoro · 2021-07-29T10:31:55Z

Also @devmessias and @antrikshmisri, Can you review this PR please? Thank you

antrikshmisri

Hey @SunTzunami, just a few comments rest everything looks good to me.

antrikshmisri · 2021-07-29T10:34:33Z

docs/source/posts/2021/2021-06-08-week-1-sajag.rst

+I worked upon my `previous PR <https://github.com/fury-gl/fury/pull/404>`_ too during the community bonding period and fixed its docstring syntax.
+
+As my college ended early courtesy covid, I had extra time during which I experimented and learnt more about PDB and PDBx files - the details they contain and how to parse them. 
+A small backbone visualisation  of 1mb0 protein made on FURY by extracting coordinate data of its alpha carbons - 


Suggested change

A small backbone visualisation of 1mb0 protein made on FURY by extracting coordinate data of its alpha carbons -

A small backbone visualisation of 1mb0 protein made on FURY by extracting coordinate data of its alpha carbons

It's better with a hyphen as I'm displaying a graphic below it.

+1 with @antrikshmisri, it does not look good, I recommend removing this hyphen too.

Furthermore, it would be better if the image is centered.

docs/source/posts/2021/2021-06-21-week-3-sajag.rst

docs/source/posts/2021/2021-06-28-week-4-sajag.rst

docs/source/posts/2021/2021-07-12-week-6-sajag.rst

antrikshmisri · 2021-07-29T10:42:24Z

docs/source/posts/2021/2021-07-26-week-8-sajag.rst

+----------------------------
+
+#. Work more on molecular module, meeting with mentors and core team on
+   thursday to optimize the module and merge `PR #452`_.


typo: Thursday

Co-authored-by: Antriksh Misri <54466356+antrikshmisri@users.noreply.github.com>

SunTzunami · 2021-07-29T11:57:47Z

Thanks for the feedback @skoudoro , @antrikshmisri ! I made the changes as requested and generated the docs locally (to take into consideration style sheet design, API standard etc..). The docs looked fine to me.

skoudoro · 2021-07-29T12:07:07Z

Thank you for the update! we are looking for the feedback of @devmessias and then we can go ahead! Thanks @antrikshmisri for the review also.

devmessias

Thank you for the update! we are looking for the feedback of @devmessias and then we can go ahead! Thanks @antrikshmisri for the review also.

Hi @SunTzunami and @skoudoro . I don't know if you already seen that but I've made this comment,

devmessias · 2021-07-28T13:41:03Z

docs/source/posts/2021/2021-06-08-week-1-sajag.rst

+
+Hi all! 
+I'm Sajag Swami, a sophomore at Indian Institute of Technology, Roorkee. This summer, I will be working on adding a new functionality to **FURY** which shall enable users to 
+visualise various types of proteins via different representations like Richardson aka Ribbon diagrams and molecular surface diagrams. 


Nice. Everything looks good for me. How about putting some references about molecular representations?

Hi @devmessias ! Thanks for review! No paper/blog was used as such yet in the project so I've used no references.

Ah ok, but I was talking about this 1mb0 protein. For anyone which doesn't work with this topic, this can sound cryptic

skoudoro · 2021-07-30T13:50:01Z

Thank you @SunTzunami, merging!

SunTzunami added 18 commits July 27, 2021 12:27

Create 2021-06-07-week-1-sajag.rst

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Weekly Check-in #1 (community bonding period)

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…jag.rst

Create 2021-06-14-week-2-sajag.rst

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skoudoro reviewed Jul 28, 2021

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SunTzunami added 10 commits July 28, 2021 22:56

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skoudoro requested review from antrikshmisri and devmessias July 29, 2021 10:31

antrikshmisri reviewed Jul 29, 2021

View reviewed changes

SunTzunami and others added 4 commits July 29, 2021 16:35

Update docs/source/posts/2021/2021-06-28-week-4-sajag.rst

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Co-authored-by: Antriksh Misri <54466356+antrikshmisri@users.noreply.github.com>

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devmessias reviewed Jul 29, 2021

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skoudoro merged commit 0f97a6d into fury-gl:master Jul 30, 2021

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Gsoc blog 2021 #475

Gsoc blog 2021 #475

SunTzunami commented Jul 27, 2021

codecov bot commented Jul 27, 2021 •

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skoudoro commented Jul 30, 2021

	A small backbone visualisation of 1mb0 protein made on FURY by extracting coordinate data of its alpha carbons -
	A small backbone visualisation of 1mb0 protein made on FURY by extracting coordinate data of its alpha carbons

Gsoc blog 2021 #475

Gsoc blog 2021 #475

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SunTzunami commented Jul 27, 2021

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