refactor: core functionality into class and methods

[kdheepak]

This PR abstracts the core functionality into the following:

    sim = Simulation(mTEPES, DirName, CaseName, SolverName, pIndOutputResults, pIndLogConsole)

    sim.input_data()

    sim.define_variables()

    sim.objective_function_and_investment_constraints()

    sim.initialize_pduals_and_na()

    if sim.is_pcm():
        sim.build_and_solve_pcm()
    else:
        sim.build_and_solve_capex()

    sim.output_results()

[kdheepak]

@erikfilias @arght I made two commits in this PR. The first commit retains the exact order of all operations from the master branch, and just refactors the code into individual methods. The second commit moves the check for sim.is_pcm() outside of the for loop, which allows introducing two more methods and rewriting it as:

    if sim.is_pcm():
        sim.build_and_solve_pcm()
    else:
        sim.build_and_solve_capex()

I chose method names based on the comments + what I thought made sense, but that is completely open to change. I noticed that the code in the master branch uses camelCase for the naming convention, but I picked snake_case instead of camelCase just to differentiate between the new methods introduced in this PR and existing functionality. That can be changed too.

[erikfilias]

The set mTEPES.strepresents different stages, typically structured as "st" + number. However, this set is unordered, which means that the initial and final stages may vary with each execution, even when using identical input data.

[kdheepak]

We changed everything to an ordered set in #66. So the sorting of pyomo should handle this correctly here, right?

[erikfilias]

I think we removed both ordered=True and ordered=False. Perhaps, it might be more effective to determine the first and last stages based on the position of each stage's initial time step within the overall collection of time steps considered in the model.

[kdheepak]

To clarify, the default in pyomo is ordered=True, so when we removed the keyword argument we made everything ordered.

[erikfilias]

Thanks for the clarification @kdheepak. If the default in Pyomo is indeed ordered=True, then it should handle the stage ordering as expected. Let me know if you think we should run additional tests to verify this.

[erikfilias]

In addition to my previous comment, the first st should include the initial time step of the year when aggregating all time steps across stages. Similarly, the final st should represent the last time step. @arght, please let me know if there are any corrections needed.

[arght]

When I introduced mTEPES.First_st and mTEPES.Last_st was to allow periods where the first local levels do not correspond to the first hours of the year, which may happen if we assign duration 0 to the starting hours. For this reason I wrote these instructions
# first/last stage
FirstST = 0
for st in mTEPES.st:
if FirstST == 0:
FirstST = 1
mTEPES.First_st = st
mTEPES.Last_st = st
instead of using .first() and .last() constructions from Pyomo. mTEPES.st only have the active stages (duration <>0) from the stage set.
I don't know if this clarifies the question.