Optimize H5Store init.

[bdice]

Description

Optimizes the H5Store initializer to use os.path.abspath instead of os.path.realpath. As mentioned in #442, the cost of realpath is fairly high and it isn't necessary to use a "real" path in this case.

(Note that this optimization would not apply to job.document or anything that must interface with signac's buffering logic, in my understanding. Buffering relies on "real" paths to ensure that data is correctly loaded in the buffer.)

Motivation and Context

Speeds up H5Store initialization.

I noticed this optimization while using a signac-flow project with a condition that checks for a key in job.data. For my simple test case with 157 jobs, the time spent in the condition function went from 2.72 seconds to 2.15 seconds (21% faster).

Note: Another 20-30% of the time could be trimmed by adding lazy state point loading and avoiding the state point validation when accessing the job.data (which never needs to know the state point).

Types of Changes

• Documentation update
• Bug fix
• New feature
• Breaking change¹

¹The change breaks (or has the potential to break) existing functionality.

Checklist:

• I am familiar with the Contributing Guidelines.
• I agree with the terms of the Contributor Agreement.
• My name is on the list of contributors.
• My code follows the code style guideline of this project.
• The changes introduced by this pull request are covered by existing or newly introduced tests.

If necessary:

• I have updated the API documentation as part of the package doc-strings.
• I have created a separate pull request to update the framework documentation on signac-docs and linked it here.
• I have updated the changelog and added all related issue and pull request numbers for future reference (if applicable). See example below.

[codecov]

Codecov Report

Merging #443 (8ec81e1) into master (ffc9116) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master     #443   +/-   ##
=======================================
  Coverage   77.13%   77.13%           
=======================================
  Files          42       42           
  Lines        5738     5738           
  Branches     1119     1119           
=======================================
  Hits         4426     4426           
  Misses       1027     1027           
  Partials      285      285           

Impacted Files	Coverage Δ
signac/core/h5store.py	89.00% <100.00%> (ø)

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[kidrahahjo]

I don't have expertise in the buffering logic currently but, in the interest of this PR, this is a straight forward change, so I am approving this PR.