Improving documentation

[lrouhier]

This PR aims at improving the documentation as a few section needs to be modified.

fix #473.
fix #475

to visualize: https://ivadomed.org/en/lr-fixing_documentation/

[jcohenadad]

you could use this PR to also fix #475

[coveralls]

Pull Request Test Coverage Report for Build 311305440

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 90.721%

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Totals
Change from base Build 310721790:	0.0%
Covered Lines:	5524
Relevant Lines:	6089

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💛 - Coveralls

[lrouhier]

I'll do that !

[lrouhier]

I guess something like this would work.
Could we build this doc @jcohenadad ?

[jcohenadad]

referring to #477 (comment):

• could you find a green check not enclosed in a box? i vaguely remember seeing an ivadomed-like JMLR paper doing the same table, with nicer-looking checks/crosses
• could you center the checks/cross
• under uncertainty: could you split the two sub-columns?

[lrouhier]

are these the checkmarks you were thinking about ?

[jcohenadad]

are these the checkmarks you were thinking about ?

yup! these are nice. Do you have a red cross that is a bit less aggressive? (same style as the green check)

[lrouhier]

like this one ?

[lrouhier]

Just to be clear, this is actually HTML Unicode. I created two commands ( |yes| and |no|) that refer to HTML Unicode in purpose.rst. So the table needs to be filled with |yes| and |no| see here. It is a copy of the original table, because it ia WIP, it will replace the original one after approval.

[lrouhier]

Do we have anything else to fix in the doc? otherwise I think it is fairly ready.

[jcohenadad]

• @lrouhier pls update wiht master
• could you pls build this branch on RTD and add the link in your PR body so we can all review the rendered doc
  thx!

[lrouhier]

@jcohenadad I think that you need to trigger the first build (or I need access code)

[jcohenadad]

@jcohenadad I think that you need to trigger the first build (or I need access code)

i just triggered it-- @alexfoias can you add Lucas on the RTD so he can select the build in the future

[jcohenadad]

hum, looks like there is a windows/macOS difference in the red cross:

Build #12118292
lr-fixing_documentation (c8ca60683cd5f0f3c8e51546a865c4a10da3d500)

[lrouhier]

Check now! I forgot to push yesterday evening, I just built it again.

[jcohenadad]

neat!
minor fixes:

• ANTSPYNET: Kears --> Keras
• ANTSPYNET: segmentation,clustering --> segmentation, clustering
• column "Data dimension" --> be consistent with space after comma, and replace the "/" with comma

I'll also make suggestions for the "data" section

[jcohenadad]

the file should be renamed architectures.rst

[lrouhier]

done in
9eb7885

[jcohenadad]

links to example config files are broken-- i'm fixing it

[jcohenadad]

@lrouhier about 9eb7885: i've noticed this renaming broke the hard-coded path to models.rst in ivadomed's code.

also: index.rst needs to be updated

[lrouhier]

It broke something in the code? I know it broke something in the pupose.rst (which I changed)
I have just changed what was needed in index.rst.

[jcohenadad]

It broke something in the code? I know it broke something in the pupose.rst (which I changed)

my bad, looking good 👍

[jcohenadad]

purpose table: niftytorch: Classificication --> Classification

also: use comma for consistency

[jcohenadad]

purpose table: DL base library
what is the difference between "Keras (backend TF)" and "Tensorflow/Keras"?

[jcohenadad]

purpose: table: https://github.com/neuropoly/ivado-medical-imaging --> https://github.com/ivadomed/ivadomed

[lrouhier]

purpose table: DL base library
what is the difference between "Keras (backend TF)" and "Tensorflow/Keras"?

I don't think there is one. I think it just depends on who filled the row.

[jcohenadad]

purpose table: DL base library
what is the difference between "Keras (backend TF)" and "Tensorflow/Keras"?

I don't think there is one. I think it just depends on who filled the row.

so it should be changed to be consistent across cells

[lrouhier]

I modified the table so it is consistent. I will check for typo and/or similar cases after compilation.