RFC: public/private separation

[ttung]

Some basic rules of thumb:

1. starfish_impl code should never reference starfish.
2. tests in starfish_impl should generally reference starfish whenever possible. exception: imports in tests for package X should use relative imports to its enclosing package whenever possible. for example, importing ImageStack from ImageStack tests should be done as from ..imagestack import ImageStack. Rationale: it's easy to move code around without breaking references.
3. notebook/vignette code should never use starfish_impl.

I also created some public APIs where they did not previously exist. Basically, go check out what was added in starfish/

[ttung]

Contents of starfish:

In [2]: dir(starfish)                                                                                                                                                                                                                                                     
Out[2]: 
['Codebook',
 'Experiment',
 'ExpressionMatrix',
 'FieldOfView',
 'ImageStack',
 'IntensityTable',
 '__builtins__',
 '__cached__',
 '__doc__',
 '__file__',
 '__is_release_tag__',
 '__loader__',
 '__name__',
 '__package__',
 '__path__',
 '__spec__',
 '__version__',
 'config',
 'display',
 'image',
 'spots',
 'starfish']

In [3]:

[ttung]

starfish autocomplete:

In [2]: starfish. 
                  Codebook           display()          ExpressionMatrix   image              IntensityTable     starfish           starfish.wdl      
                  config             Experiment         FieldOfView        ImageStack         spots              starfish.egg-info/                                                                                                                                  

[ambrosejcarr]

I see that I dropped it too, but I think starfish.data would be good to drop into the main namespace.

Otherwise this LGTM from the end-user perspective.

[codecov-io]

Codecov Report

Merging #1244 into master will decrease coverage by 2.38%.
The diff coverage is 97.2%.

@@            Coverage Diff             @@
##           master    #1244      +/-   ##
==========================================
- Coverage   88.86%   86.47%   -2.39%     
==========================================
  Files         140      146       +6     
  Lines        5244     5524     +280     
==========================================
+ Hits         4660     4777     +117     
- Misses        584      747     +163

Impacted Files	Coverage Δ
starfish/core/spacetx_format/test_field_of_view.py	100% <ø> (ø)
starfish/core/spacetx_format/test_coordinates.py	100% <ø> (ø)
starfish/core/types/_constants.py	100% <ø> (ø)
starfish/core/spots/__init__.py	100% <ø> (ø)
starfish/core/_version.py	41.36% <ø> (ø)
starfish/core/util/try_import.py	50% <ø> (ø)
starfish/core/errors.py	100% <ø> (ø)
starfish/core/spacetx_format/test_fov_manifest.py	100% <ø> (ø)
starfish/core/recipe/__init__.py	100% <ø> (ø)
starfish/core/recipe/errors.py	100% <ø> (ø)
... and 138 more

---

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[ttung]

I see that I dropped it too, but I think starfish.data would be good to drop into the main namespace.

I didn't move starfish.data...?

[ambrosejcarr]

I mean: it should be imported by default.

[ttung]

Was it done so previously?

[neuromusic]

I want to let @ambrosejcarr or @shanaxel42 do the actual PR review, but I really dig the API changes here

[ttung]

By the way, this is passing all notebooks now.

[shanaxel42]

fiiiiiiine