Don't split tasks in the modules

[rvhonorato]

Desired feature/enhancement

Refactor code that is splitting tasks in the modules

Motivation

libparallel recieves a set of tasks and handles the split and balancing of them, however this is also being done elsewhere in the code.

haddock3/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py

Line 110 in 01eb9ae

for core in range(ncores):

haddock3/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py

Line 308 in 01eb9ae

for core in range(ncores):

haddock3/src/haddock/modules/analysis/rmsdmatrix/rmsd.py

Line 50 in 01eb9ae

for core in range(ncores):

haddock3/src/haddock/libs/libalign.py

Line 1289 in 01eb9ae

for core in range(ncores):

haddock3/src/haddock/modules/analysis/alascan/__init__.py

Line 63 in 01eb9ae

for core in range(ncores):

haddock3/src/haddock/modules/analysis/rmsdmatrix/__init__.py

Line 88 in 01eb9ae

for core in range(ncores):

haddock3/src/haddock/modules/analysis/rmsdmatrix/__init__.py

Line 141 in 01eb9ae

for core in range(ncores):

Related implementations that generate multiple files relying on the task split to retrieve information;

haddock3/src/haddock/modules/analysis/caprieval/capri.py

Line 615 in 7a9434e

self.make_output()

haddock3/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py

Line 285 in 01eb9ae

rearrange_xyz_files(

Description

For maintanability, consistency and simplicity this should be handled in a single library.

Additional context

Would be good if we could make this clear into some developer manual

[rvhonorato]

I see now that the execution mode is analysis modules is being overwritten (#928 (comment)). This makes this issue much simpler to be resolved, as we can simply set is as local and use the same pattern applied here:

haddock3/src/haddock/modules/analysis/caprieval/capri.py

Line 662 in 844c7ca

return copy.deepcopy(self)

haddock3/src/haddock/modules/analysis/caprieval/capri.py

Lines 915 to 925 in 844c7ca

	def extract_data_from_capri_class(
	capri_objects: list[CAPRI],
	sort_key: str,
	sort_ascending: bool,
	output_fname: Path,
	) -> Union[dict[int, ParamDict], None]:
	"""
	Extracts data attributes from a list of CAPRI objects into a structured dictionary,
	optionally sorts the data based on a specified key, and writes the sorted data to
	a file.