Input to json

[mgiulini]

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---

Closes #704 by adding information about input models in the io.json file of each module. This makes each module self-describing, i.e., all the I/O information is present in the module directory, thus facilitating the information retrieval.

An example application of this will be provided in the implementation of interactive commands (#686) that have to deal with small pieces of a HADDOCK3 run (modules) without having access to the whole run folder.

[codecov]

Codecov Report

Attention: 12 lines in your changes are missing coverage. Please review.

Comparison is base (b93fbe9) 74.92% compared to head (70967e8) 74.97%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #705      +/-   ##
==========================================
+ Coverage   74.92%   74.97%   +0.05%     
==========================================
  Files         113      113              
  Lines        8035     8048      +13     
==========================================
+ Hits         6020     6034      +14     
+ Misses       2015     2014       -1     

Files	Coverage Δ
src/haddock/modules/__init__.py	73.88% <100.00%> (+0.16%)	⬆️
src/haddock/modules/analysis/clustfcc/__init__.py	88.02% <100.00%> (ø)
src/haddock/modules/analysis/clustrmsd/__init__.py	90.99% <100.00%> (ø)
...rc/haddock/modules/analysis/rmsdmatrix/__init__.py	89.33% <100.00%> (ø)
tests/test_module_clustfcc.py	100.00% <100.00%> (ø)
src/haddock/modules/analysis/caprieval/__init__.py	34.28% <0.00%> (ø)
src/haddock/modules/analysis/seletop/__init__.py	52.38% <0.00%> (ø)
...haddock/modules/analysis/seletopclusts/__init__.py	22.22% <0.00%> (ø)
src/haddock/modules/refinement/emref/__init__.py	18.91% <0.00%> (ø)
src/haddock/modules/refinement/flexref/__init__.py	21.33% <0.00%> (ø)
... and 7 more

... and 1 file with indirect coverage changes

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[VGPReys]

Quite dangerous to modify a function name that is used all around the software !
I have double checked that all files containing this functions were modified, and it should run smoothly.

! Just that people may have to modify this function call in unmerged branches too !

Do we want a to temporarly add a deprection warning and a function wrapper ?

def export_output_models(self, *args, **kwargs):
    self.export_io_models(*args, **kwargs)
    print('WARNING: function export_output_models is depecated, use export_io_models instead')

?

[mgiulini]

Quite dangerous to modify a function name that is used all around the software ! I have double checked that all files containing this functions were modified, and it should run smoothly.

! Just that people may have to modify this function call in unmerged branches too !

Do we want a to temporarly add a deprection warning and a function wrapper ?

def export_output_models(self, *args, **kwargs):
    self.export_io_models(*args, **kwargs)
    print('WARNING: function export_output_models is depecated, use export_io_models instead')

?

no need for that: as soon as this PR is accepted and merged into the main branch, any further modification will have to merge the main into itself, possibly highlighting a conflict.

I am adding a test to this function though, to make it pass the patch coverage test.

[mgiulini]

added a new test, but it's not enough for the patch coverage to pass..It does not make sense to create 12 new tests, so I would skip it and merge this as is.