Refactor codes

- Categorize constraint definitions based on type (co2, cost, demand, generation, hydro, investment, nondispatchable, storage, transmission) for better organization.
- Split `rule.py` class into serveral smaller, focused classes according to categorized constraint definitions.
- Simplify model by replacing intermediate constraints with direct expressions.
- Extract new modules `solver.py`, `output_data.py`, and `set_up.py` from `run.py` and `utils.py`
- Move `parameters.py` into `set_up.py`

This improves readability and maintainability of the codebase.

prepshot/_model/co2.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+""" This module contains constraints related to carbon emissions. 
+"""
+
+import pyoptinterface as poi
+import numpy as np
+
+class AddCo2EmissionConstraints:
+    """Class for carbon emission constraints and calculations.
+    """
+    def __init__(self, model):
+        """Initialize the class.
+
+        Parameters
+        ----------
+        model : pyoptinterface._src.solver.Model
+            Model index.
+        para : dict
+            Dictionary containing parameters.
+        """
+        self.model = model
+        model.carbon_breakdown = poi.make_tupledict(
+            model.year_zone_tech_tuples,
+            rule=self.carbon_breakdown
+        )
+        model.carbon_capacity = poi.make_tupledict(
+            model.year_zone_tuples,
+            rule=self.emission_calc_by_zone_rule
+        )
+        model.carbon = poi.make_tupledict(
+            model.year,
+            rule=self.emission_calc_rule
+        )
+        model.emission_limit_cons = poi.make_tupledict(
+            model.year,
+            rule=self.emission_limit_rule
+        )
+
+    def emission_limit_rule(self, y):
+        """Annual carbon emission limits across all zones and technologies.
+        
+        Parameters
+        ----------
+        y : int
+            Planned year.
+            
+        Returns
+        -------
+        pyoptinterface._src.core_ext.ConstraintIndex
+            Constraint index of the model.
+        """
+        model = self.model
+        limit = model.para['carbon_emission_limit']
+        if limit[y] == np.Inf:
+            return None
+        lhs = model.carbon[y] - limit[y]
+        return model.add_linear_constraint(lhs, poi.Leq, 0)
+
+    def emission_calc_rule(self, y):
+        """Calculation of annual carbon emission across all zones and
+            technologies.
+
+        Parameters
+        ----------
+        y : int
+            Planned year.
+
+        Returns
+        -------
+        pyoptinterface._src.core_ext.ConstraintIndex
+            Constraint index of the model.
+        """
+        model = self.model
+        return poi.quicksum(
+            model.carbon_capacity[y, z]
+            for z in model.zone
+        )
+
+    def emission_calc_by_zone_rule(self, y, z):
+        """Calculation of annual carbon emissions by zone.
+
+        Parameters
+        ----------
+        y : int
+            Planned year.
+        z : str
+            Zone.
+
+        Returns
+        -------
+        pyoptinterface._src.core_ext.ConstraintIndex
+            Constraint index of the model.
+        """
+        model = self.model
+        return poi.quicksum(
+            model.carbon_breakdown[y, z, te]
+            for te in model.tech
+        )
+
+    def carbon_breakdown(self, y, z, te):
+        """Carbon emission cost breakdown.
+
+        Parameters
+        ----------
+        y : int
+            Year.
+        z : str
+            Zone.
+        te : str
+            Technology.
+
+        Returns
+        -------
+        pyoptinterface._src.core_ext.ExprBuilder
+            index of expression of the model.
+        """
+        model = self.model
+        ef = model.para['emission_factor'][te, y]
+        dt = model.para['dt']
+        return poi.quicksum(
+            ef * model.gen[h, m, y, z, te] * dt
+            for h, m in model.hour_month_tuples
+        )