Doc redesign for new website

[benjeffery]

This branch will be used by the new website demo deploy to show how the docs will look. We can merge this PR whenever we are happy with the new docs.

[codecov[bot]]

Codecov Report

Merging #2399 (0b047e8) into main (3692105) will decrease coverage by 0.88%. The diff coverage is n/a.

:exclamation: Current head 0b047e8 differs from pull request most recent head 145e974. Consider uploading reports for the commit 145e974 to get more accurate results

@@            Coverage Diff             @@
##             main    #2399      +/-   ##
==========================================
- Coverage   93.91%   93.02%   -0.89%     
==========================================
  Files          28       28              
  Lines       27213    27545     +332     
  Branches     1261     1298      +37     
==========================================
+ Hits        25556    25624      +68     
- Misses       1623     1885     +262     
- Partials       34       36       +2     

Flag	Coverage Δ
c-tests	92.26% <ø> (+0.02%)	:arrow_up:
lwt-tests	89.05% <ø> (ø)
python-c-tests	71.20% <ø> (-0.49%)	:arrow_down:
python-tests	98.95% <ø> (-0.01%)	:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
python/tskit/trees.py	92.93% <0.00%> (-5.82%)	:arrow_down:
python/_tskitmodule.c	91.01% <0.00%> (-1.89%)	:arrow_down:
python/tskit/genotypes.py	99.02% <0.00%> (ø)
c/tskit/core.c	97.93% <0.00%> (+0.01%)	:arrow_up:
c/tskit/tables.c	90.24% <0.00%> (+0.03%)	:arrow_up:

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[hyanwong]

Report theme issues at https://github.com/benjeffery/tskit-book-theme

[benjeffery]

I've attempted to fix all trees and figures see, e.g. https://benjeffery.github.io/tskit-site/tskit/docs/latest/topological-analysis.html I'm trying a method where they can still be black-on-white for printout. Tables are fixed. Left to fix - code style in jupyter cells and "Click to show" colour, then we'll try the design on the tutorials, which are the most challenging I think.

[hyanwong]

Looks nice. I wonder if the page titles in the forwards and backwards links at the bottom of the page should be all in the light green, rather than a mix of green and blue:

If it proved difficult, we could have the tutorials in black-on-white? Certainly I think workbooks should be the colour that people will see them when they work through the Jupiter notebook on their one machine. Tutorials could go either way.

[benjeffery]

Looks nice. I wonder if the page titles in the forwards and backwards links at the bottom of the page should be all in the light green, rather than a mix of green and blue:

Done!

[benjeffery]

I'm now happy with this, we can merge now, or wait till tskit-book-theme is on PyPI after I've checked it on the other repos.

[jeromekelleher]

Sounds good. Can we try this out on a "beta" build of the website before it all goes fully live?

[benjeffery]

Sounds good. Can we try this out on a "beta" build of the website before it all goes fully live?

It's already part of the demo site at https://benjeffery.github.io/tskit-site/tskit/docs/latest/introduction.html

[benjeffery]

@jeromekelleher Can I get a review here? I'm ready to start merging the doc PRs now that the site is ready and tskit-book-theme has been released on PyPI.

[benjeffery]

@mergifyio rebase

[mergify[bot]]

rebase

✅ Branch has been successfully rebased