json+struct: padding bytes and no C code

[petrelharp]

This differs from #3437 in that:

• it removes all C code from tskit
• it adds some documentation for the json+struct codec

My intention is that we deal with the python and C code separately, so this supercedes #3437. My proposal for the C side of things is in #3439.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.90%. Comparing base (2f26dc6) to head (dee7859).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3440      +/-   ##
==========================================
- Coverage   91.92%   91.90%   -0.02%     
==========================================
  Files          37       37              
  Lines       32153    32095      -58     
  Branches     5143     5135       -8     
==========================================
- Hits        29556    29498      -58     
  Misses       2264     2264              
  Partials      333      333              

Flag	Coverage Δ
C	82.64% <ø> (-0.07%)	⬇️
c-python	77.54% <ø> (+0.19%)	⬆️
python-tests	96.40% <100.00%> (+<0.01%)	⬆️
python-tests-no-jit	33.21% <0.00%> (-0.01%)	⬇️

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

Components	Coverage Δ
Python API	98.69% <100.00%> (+<0.01%)	⬆️
Python C interface	91.23% <ø> (ø)
C library	88.82% <ø> (-0.04%)	⬇️

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[bhaller]

stopping for now since I suspect I'm somehow looking at the wrong diffs

[bhaller]

next review

[petrelharp]

elsewhere @bhaller points out that

OK; but since you're adding 4-byte ints, you’re not really testing the different padding byte counts very effectively.  You’re only testing the 0 and 4 alignment cases well, which seems vulnerable to bugs since it’s just “none” and “half”.

I don't think having the length of the binary bit be divisible by 4 is a problem, since the number of padding bytes is determined by the length of the JSON (which comes first). I'll add a few more string lengths to make sure we hit everything.

[bhaller]

LGTM, thanks for the revisions. Note the two comments that maybe you missed, but they are trivial so there's no need to hold things up for them. :->