Sb/refactor process

[basaks]

This PR brings the option to specify process steps in an arbitrary order. This is a massive refactor on how we manage process steps inside process. The function calls are also simplified.

There is a default process sequence that's exactly the same as the steps existing in master/develop now. Full functionality (changed sequences) is not tested. However, the default sequence has been proven to reprouce results from develop.

A lot more work needs to be done for process refactor final state. However, merging will help us avoid merge conflicts with your dev branch (develop forks).

I have attached 2 text files as proof that I have not changed any output.

develop.txt: Generated using the current develop branch. branch.txt: Generated using this branch.

Both used the same command with only edit in the config being coh_mask=1:

mpirun -n 4 pyrate workflow -f tests/test_data/small_test/conf/pyrate_gamma_test.conf

[codecov-commenter]

Codecov Report

Merging #275 into develop will decrease coverage by 0.43%. The diff coverage is 98.21%.

@@             Coverage Diff             @@
##           develop     #275      +/-   ##
===========================================
- Coverage    93.27%   92.83%   -0.44%     
===========================================
  Files           26       26              
  Lines         3198     3239      +41     
  Branches       492      505      +13     
===========================================
+ Hits          2983     3007      +24     
- Misses         133      147      +14     
- Partials        82       85       +3     

Impacted Files	Coverage Δ
pyrate/default_parameters.py	100.00% <ø> (ø)
pyrate/configuration.py	97.72% <75.00%> (-2.28%)	:arrow_down:
pyrate/core/aps.py	85.71% <100.00%> (+0.45%)	:arrow_up:
pyrate/core/config.py	93.71% <100.00%> (+0.27%)	:arrow_up:
pyrate/core/shared.py	95.25% <100.00%> (+<0.01%)	:arrow_up:
pyrate/prepifg.py	97.58% <100.00%> (-0.04%)	:arrow_down:
pyrate/process.py	91.25% <100.00%> (-0.50%)	:arrow_down:
pyrate/core/ref_phs_est.py	90.10% <0.00%> (-5.50%)	:arrow_down:
pyrate/core/refpixel.py	87.71% <0.00%> (-4.10%)	:arrow_down:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 930de93...57cd582. Read the comment docs.