Fix inefficient and sometimes inaccurate build process

[rly]

Motivation

Fix #337 and fix NeurodataWithoutBorders/pynwb#1313

This moves the setting of reference builders to the end of the build process, similar to how in h5tools.py, the writing of references is done at the end of the writing process. This ensures that all reference targets are built when they are encountered while traversing the build hierarchy, NOT when they are the target of a reference, which can lead to inefficient and sometimes inaccurate builds, especially with DynamicTables.

Now BuildManager.build(...) which must have the new argument root=True when building the root container in the hierarchy.

This also adds a few missing tests for the setting of datasets of references, compound datasets with references, and untyped datasets with references.

This also handles the rare case when a Container data type does not match the data type described in the spec.

This also fixes a floating point precision issue with TestCase.assertContainerEqual(...)

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
• Is your contribution compliant with our coding style? This can be checked running flake8 from the source directory.
• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov]

Codecov Report

Merging #451 (ae08f81) into dev (f4b8232) will increase coverage by 0.27%.
The diff coverage is 90.00%.

@@            Coverage Diff             @@
##              dev     #451      +/-   ##
==========================================
+ Coverage   81.03%   81.30%   +0.27%     
==========================================
  Files          36       36              
  Lines        7365     7425      +60     
  Branches     1617     1618       +1     
==========================================
+ Hits         5968     6037      +69     
+ Misses       1024     1016       -8     
+ Partials      373      372       -1     

Impacted Files	Coverage Δ
src/hdmf/build/builders.py	87.65% <0.00%> (-0.24%)	⬇️
src/hdmf/build/objectmapper.py	83.78% <88.75%> (+1.79%)	⬆️
src/hdmf/backends/io.py	94.64% <100.00%> (ø)
src/hdmf/build/__init__.py	100.00% <100.00%> (ø)
src/hdmf/build/errors.py	100.00% <100.00%> (ø)
src/hdmf/build/manager.py	78.95% <100.00%> (+0.90%)	⬆️

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[bendichter]

Wow, looks like a lot of work. Much appreciated!

[rly]

There is one related condition that I want to improve:
Container B contains a link to Container A.
Container A is built.
During the build of Container B, Container A is rebuilt (there is no difference in the end result).

[rly]

Done. @oruebel @ajtritt please review. This is a relatively bulky PR. Happy to discuss over video.