haddock3-traceback

[mgiulini]

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Closes #402 by tracking all the PDB files in a HADDOCK3 workflow.

Starting from the end of the workflow, this CLI gathers the information contained in the io.json file to understand name and rank of each model and, more importantly, the name of the parent model (ori_name attribute) that was used to generate the current structure. In order to do this, I added the ori_name attribute to all the modules, with the exception of the rigidbody module, in which the topology attribute is employed to guess the (typically two) ancestors.

Usage:
haddock3-traceback -r run_dir

Doubt: now the modules to be excluded from the traceback are listed here

haddock3/src/haddock/clis/cli_traceback.py

Line 26 in 61773b6

ANA_MODULES = ["caprieval",

: do you think it is better to list the modules on which the traceback must act?

Important: for new modules that generate PDB files (such as Openmm #482 ), the attribute ori_name should be defined for a successful traceback.

Important 2.0: the traceback does not work on old HADDOCK3 runs (the attribute ori_name is not defined for all the modules).

[codecov-commenter]

Codecov Report

Patch coverage: 84.51% and project coverage change: +0.21% 🎉

Comparison is base (27321d5) 74.73% compared to head (aec97bb) 74.94%.
Report is 8 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #668      +/-   ##
==========================================
+ Coverage   74.73%   74.94%   +0.21%     
==========================================
  Files         111      113       +2     
  Lines        7642     7800     +158     
==========================================
+ Hits         5711     5846     +135     
- Misses       1931     1954      +23     

Files Changed	Coverage Δ
...haddock/modules/analysis/seletopclusts/__init__.py	22.22% <0.00%> (-0.42%)	⬇️
src/haddock/modules/refinement/emref/__init__.py	20.00% <0.00%> (-1.22%)	⬇️
src/haddock/modules/refinement/flexref/__init__.py	22.53% <0.00%> (-1.35%)	⬇️
src/haddock/modules/refinement/mdref/__init__.py	20.00% <0.00%> (-1.22%)	⬇️
src/haddock/libs/libworkflow.py	30.48% <50.00%> (+0.48%)	⬆️
src/haddock/clis/cli_traceback.py	91.66% <91.66%> (ø)
tests/test_cli_traceback.py	96.87% <96.87%> (ø)

... and 2 files with indirect coverage changes

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[VGPReys]

'_'.join(st.split("_")[1:])
Just to make sure if any module has an underscore character one day ?

[mgiulini]

I would not worry about it..

[VGPReys]

I have to try it out now.
I am not so familiar with the panda library, hence cannot clearly assess this part.

[rvhonorato]

amazing addition! just a few comments

[mgiulini]

hi @rvhonorato can you check this again and, in case it's Ok, approve it?

[VGPReys]

Nice to put it directly after a Haddock3 run !
Almost wondering if it still has to be a separated client and not embedded in the analysis one

[amjjbonvin]

I will trust on on it