DOC: Fix cut passages from README in documentation index file

[jhlegarreta]

Fix cut passages from README in documentation index file: add comments around the flowchart image in the README file and change the start-line and end-line directive pair for the end-before and start-after pair to skip the flowchart image only.

The start-line and end-line directives were making such that relevant passages of the README file providing context for the tool were not being included. Thus the text shown in the documentation index file had some missing parts, and was not making sense.

[jhlegarreta]

@effigies tagging you here, as I've seen this commit:
f312b43#diff-8d068e8797e88947c320f79e856c3e16a72b730124a8f9d7031e2c4680dfa534

I see that it was intended to avoid showing the picture in the README and locate it through a relative path in the index.rst file. The current version does show both pictures, and Sphinx does not seem to complain:
https://github.com/nipreps/eddymotion/actions/runs/12032435652/job/33544268816

Are you OK including the entire README as-is?

Edit: This is what the current documentation index looks like and what this patch set intends to fix:

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 66.24%. Comparing base (f10fc12) to head (e26943b).
Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #258   +/-   ##
=======================================
  Coverage   66.24%   66.24%           
=======================================
  Files          19       19           
  Lines         942      942           
  Branches      119      119           
=======================================
  Hits          624      624           
  Misses        274      274           
  Partials       44       44           

☔ View full report in Codecov by Sentry.
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[jhlegarreta]

@effigies sorry to ping you again here. Can you please review this?

[effigies]

How about for README.rst:

eddymotion/README.rst

Lines 46 to 54 in f10fc12

	*Eddymotion* is an open implementation of eddy-current and head-motion correction that builds upon
	the work of ``eddy`` and *SHORELine*, while generalizing these methods to multiple acquisition schemes
	(single-shell, multi-shell, and diffusion spectrum imaging) using diffusion models available with DIPY [#r5]_.
	.. image:: https://raw.githubusercontent.com/nipreps/eddymotion/507fc9bab86696d5330fd6a86c3870968243aea8/docs/_static/eddymotion-flowchart.svg
	:alt: The eddymotion flowchart
	.. [#r1] S. Ben-Amitay et al., Motion correction and registration of high b-value diffusion weighted images, Magnetic
	Resonance in Medicine 67:1694–1702 (2012)

We add comments:

 (single-shell, multi-shell, and diffusion spectrum imaging) using diffusion models available with DIPY [#r5]_.
 
+.. BEGIN FLOWCHART
 
 .. image:: https://raw.githubusercontent.com/nipreps/eddymotion/507fc9bab86696d5330fd6a86c3870968243aea8/docs/_static/eddymotion-flowchart.svg
    :alt: The eddymotion flowchart
 
+.. END FLOWCHART
 
 .. [#r1] S. Ben-Amitay et al., Motion correction and registration of high b-value diffusion weighted images, Magnetic

Then we could instead do:

 .. include:: ../README.rst
-   :end-line: 29
+   :end-before: BEGIN FLOWCHART
 .. include:: ../README.rst
-   :start-line: 34
+   :start-after: END FLOWCHART

See https://docutils.sourceforge.io/docs/ref/rst/directives.html#miscellaneous

[jhlegarreta]

Thanks @effigies. Done in 39faa0b.

[effigies]

I haven't rendered this. Could you share an updated screenshot?

[jhlegarreta]

BTW, sorry for having lost your authorship when squashing commits 😔.