Move all modules into root namespace.

[bdice]

Description

Closes #756, supersedes #862.

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.
• The changes introduced by this pull request are covered by existing or newly introduced tests.
• The package documentation and framework documentation in signac-docs are up to date with these changes.
• I have updated the changelog and added any related issue and pull request numbers for future reference.

[bdice]

@csadorf @vyasr I rebased the changes from #862 into this PR. Feel free to push to this branch directly.

[codecov]

Codecov Report

Merging #868 (de097c8) into master (766c0b7) will decrease coverage by 0.09%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #868      +/-   ##
==========================================
- Coverage   86.63%   86.53%   -0.10%     
==========================================
  Files          48       41       -7     
  Lines        4570     4531      -39     
  Branches      901      901              
==========================================
- Hits         3959     3921      -38     
+ Misses        430      429       -1     
  Partials      181      181              

Impacted Files	Coverage Δ
signac/__main__.py	77.72% <100.00%> (-0.07%)	⬇️
signac/_dict_manager.py	88.37% <100.00%> (ø)
signac/_search_indexer.py	97.72% <100.00%> (ø)
signac/_utility.py	68.00% <100.00%> (ø)
signac/config.py	90.47% <100.00%> (ø)
signac/diff.py	100.00% <100.00%> (ø)
signac/filterparse.py	89.65% <100.00%> (ø)
signac/h5store.py	91.03% <100.00%> (ø)
signac/hashing.py	100.00% <100.00%> (ø)
signac/import_export.py	77.24% <100.00%> (ø)
... and 9 more

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[vyasr]

I've made two changes:

• I modified the pre-commit config to use a single global excludes pattern for _vendor rather than specifying it separately for each hook.
• I implemented the first bullet point from my request on #862, moving search_indexer.py, dict_manager.py, and utility.py into an _internal subpackage. I did not move filterparse.py because I remembered that its functionality is leveraged by signac-dashboard, which means that we probably should be importing parse_filter_args into the top-level signac namespace as well. WDYT?

Assuming those changes look OK I'm happy with the current state of this PR. I would be fine with addressing any additional changes (such as the ones I proposed in #862) in follow-ups.

[bdice]

@vyasr I’m not a huge fan of an _internal subpackage. Nothing ties together the contents of that subpackage except API visibility, which feels odd. I’d rather keep things at the top level and start the module names with _. It doesn’t feel too cluttered to me.

The pre-commit change is good! I forgot that top level excludes were possible.

[vyasr]

@vyasr I’m not a huge fan of an _internal subpackage. Nothing ties together the contents of that subpackage except API visibility, which feels odd. I’d rather keep things at the top level and start the module names with _. It doesn’t feel too cluttered to me.

The pre-commit change is good! I forgot that top level excludes were possible.

Sounds good, I reverted that change and prefixed those modules with underscores.

[bdice]

Thanks @vyasr! I pushed one small tweak to generalize our exclusions. Otherwise I think this PR is ready to go with a reviewer approval.

[b-butler]

LGTM

[vyasr]

For posterity, here's what the project structure looks like now:

signac/
├── __init__.py
├── __main__.py
├── _dict_manager.py
├── _search_indexer.py
├── _utility.py
├── _vendor
│   ├── configobj
│   │   ├── LICENSE
│   │   ├── __init__.py
│   │   ├── _version.py
│   │   └── validate.py
│   └── deprecation
│       ├── LICENSE
│       ├── README
│       └── __init__.py
├── config.py
├── diff.py
├── errors.py
├── filterparse.py
├── h5store.py
├── hashing.py
├── import_export.py
├── job.py
├── linked_view.py
├── migration
│   ├── __init__.py
│   ├── v0_to_v1.py
│   └── v1_to_v2.py
├── project.py
├── schema.py
├── sync.py
├── syncutil.py
└── version.py

In the interest of quicker progress, I'm going to go ahead and merge this now. We can make further changes in subsequent PRs, and merging this now should allow us to make those changes in smaller, more self-contained PRs.

[vyasr]

@bdice the question I had about filterparse still stands. I think since dashboard is using it we should be exposing whatever functionality it needs more publicly than we are now (but that can be done in a subsequent PR).