Input/Output refactor

[kbwestfall]

From CHANGES.md:

• Major overhaul of how paths and output files are defined, needed to complete abstraction and move away from MaNGA-specific code.
  • Input paths and file names now defined as part of the DataCube subclass. For MaNGA, this is done by subclassing the MaNGADataCube from the mangadap.config.manga.MaNGAConfig class. For user-defined DataCube subclasses, these paths can be defined directly.
  • Output paths for primary output files now defined by the AnalysisPlanSet object or a relevant subclass. For MaNGA, a subclass is necessary to put all the files in a subdirectory using the plate and ifu, but likely most other implementations can use AnalysisPlanSet directly. Reference file names adjusted and defined by each main analysis class.
  • Remove all instances of numpy.float, numpy.int, numpy.bool, given impending numpy deprecation of these types.

[codecov[bot]]

Codecov Report

Merging #100 (2fe96ad) into develop (740b345) will decrease coverage by 0.28%. The diff coverage is 30.47%.

@@             Coverage Diff             @@
##           develop     #100      +/-   ##
===========================================
- Coverage    36.20%   35.92%   -0.29%     
===========================================
  Files           82       83       +1     
  Lines        18292    18459     +167     
===========================================
+ Hits          6623     6631       +8     
- Misses       11669    11828     +159     

Impacted Files	Coverage Δ
mangadap/contrib/LambdaR_2D_forMaNGA.py	0.00% <ø> (ø)
mangadap/par/spectralfeaturedb.py	84.44% <ø> (ø)
mangadap/proc/elric.py	11.11% <0.00%> (ø)
mangadap/proc/sasuke.py	59.00% <0.00%> (ø)
mangadap/scripts/calculate_covariance.py	16.66% <0.00%> (ø)
mangadap/scripts/construct_dapall.py	66.66% <ø> (ø)
mangadap/scripts/manga_dap.py	23.25% <0.00%> (-62.17%)	:arrow_down:
mangadap/spectra/rowstackedspectra.py	10.72% <0.00%> (ø)
mangadap/survey/dapall.py	0.00% <0.00%> (ø)
mangadap/survey/manga_dap.py	0.00% <0.00%> (-18.94%)	:arrow_down:
... and 55 more

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