Trim equilibration during analysis

[candidechamp]

Description

The main objective behind these changes is to perform the "trimming" of the trajectories during the analysis step, rather than by submitting the parts which were removed for equilibration as a separate set of jobs.

The purpose behind those changes are twofold:

• Remove input parameter for a lot of the submission functions to clarify what they are doing.
• Simplify submission such that the calculations don't need to be broken down into too many sub-jobs.

NOTE: It is impossible to get perfect reproduction of results when comparing the old code (job submitted into 10 sub-jobs, including 1 for equilibration) and the new code (single larger job from which the first 10% is trimmed during analysis). This is because of numerical differences which make the simulation diverge. However average results and general behavior can be compared.

Todos

Notable points that this PR has either accomplished or will accomplish.

• test code

• Completely remove the input parameters separating "equilibration" and "production" runs?

This second bullet point will be done at a later stage if we find it necessary.

[codecov-commenter]

Codecov Report

Merging #90 (b7154d9) into main (33ef630) will not change coverage.
The diff coverage is 28.94%.

@@           Coverage Diff           @@
##             main      #90   +/-   ##
=======================================
  Coverage   15.72%   15.72%           
=======================================
  Files          51       51           
  Lines        5534     5534           
=======================================
  Hits          870      870           
  Misses       4664     4664           

Flag	Coverage Δ
unittests	15.72% <28.94%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
...s/function_libs/analysis/parameter_optimization.py	0.00% <0.00%> (ø)
reeds/function_libs/analysis/replica_exchanges.py	0.00% <0.00%> (ø)
reeds/function_libs/analysis/sampling.py	45.39% <ø> (ø)
reeds/function_libs/pipeline/module_functions.py	0.00% <0.00%> (ø)
...cripts/analysis_workers/RE_EDS_general_analysis.py	0.00% <0.00%> (ø)
...ipts/analysis_workers/RE_EDS_optimization_final.py	0.00% <0.00%> (ø)
reeds/modules/do_RE_EDS_eoffEstimation.py	0.00% <ø> (ø)
reeds/modules/do_RE_EDS_eoffRebalancing.py	0.00% <ø> (ø)
reeds/modules/do_RE_EDS_generateOptimizedStates.py	0.00% <ø> (ø)
reeds/modules/do_RE_EDS_mixedOptimisation.py	0.00% <ø> (ø)
... and 4 more

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