Implement typing

Fixes #12

Add type hinting to various functions across multiple files for consistency with Firecrown.

* **`CosmoAPI/two_point_functions/generate_theory.py`**
  - Add type hints to `generate_ell_theta_array_from_yaml`, `load_systematics_factory`, `process_probes_load_2pt`, `generate_two_point_metadata`, and `prepare_2pt_functions`.

* **`CosmoAPI/two_point_functions/nz_loader.py`**
  - Add type hints to `_load_nz`, `load_all_nz`, and `_load_nz_from_module`.

* **`CosmoAPI/__main__.py`**
  - Add type hints to `gen_datavec`, `gen_covariance`, `forecast`, and `main`.

* **`CosmoAPI/api_io.py`**
  - Add type hints to `load_yaml_file` and `load_metadata_function_class`.

Important: Change the placeholder `Any` for the actual firecrown types.

CosmoAPI/__main__.py

@@ -1,23 +1,24 @@
 import argparse
+from typing import Dict, Any
 
 from .api_io import load_yaml_file
 from .not_implemented import not_implemented_message
 
-def gen_datavec(config, verbose=False):
+def gen_datavec(config: Dict[str, Any], verbose: bool = False) -> None:
     # Functionality for generating data vector
     if verbose:
         print("Verbose mode enabled.")
     print("Generating data vector with config:", config)
 
-def gen_covariance(config):
+def gen_covariance(config: Dict[str, Any]) -> None:
     # Functionality for generating covariance
     print(not_implemented_message)
 
-def forecast(config):
+def forecast(config: Dict[str, Any]) -> None:
     # Functionality for forecast
     print(not_implemented_message)
 
-def main():
+def main() -> None:
     parser = argparse.ArgumentParser(
         prog="CosmoAPI",
         description="CosmoAPI: Cosmology Analysis Pipeline Interface"
@@ -83,4 +84,4 @@ def main():
         forecast(config)
 
 if __name__ == "__main__":
-    main()
+    main()

CosmoAPI/api_io.py

@@ -1,12 +1,13 @@
 import yaml
 import importlib
+from typing import Any, Dict
 
-def load_yaml_file(file_path):
+def load_yaml_file(file_path: str) -> Dict[str, Any]:
     """Helper function to load a YAML file"""
     with open(file_path, 'r') as file:
         return yaml.safe_load(file)
 
-def load_metadata_function_class(function_name):
+def load_metadata_function_class(function_name: str) -> Any:
     """
     Dynamically load a class based on the 'function' name specified in the YAML file.
     FIXME: Change the docstrings

CosmoAPI/two_point_functions/generate_theory.py

@@ -6,15 +6,15 @@
 from firecrown.metadata_functions import make_all_photoz_bin_combinations
 import firecrown.likelihood.two_point as tp
 from firecrown.utils import base_model_from_yaml
-
+from typing import Dict, Any, List, Tuple
 
 from .nz_loader import load_all_nz
 sys.path.append("..")
 from not_implemented import not_implemented_message
 from api_io import load_metadata_function_class
 
 
-def generate_ell_theta_array_from_yaml(yaml_data, type_key, dtype=float):
+def generate_ell_theta_array_from_yaml(yaml_data: Dict[str, Any], type_key: str, dtype: type = float) -> np.ndarray:
     """
     Generate a linear or logarithmic array based on the  configuration in the YAML data.
     
@@ -39,7 +39,7 @@ def generate_ell_theta_array_from_yaml(yaml_data, type_key, dtype=float):
     else:
         raise ValueError(f"Unknown array type: {array_type}")
 
-def load_systematics_factory(probe_systematics):
+def load_systematics_factory(probe_systematics: Dict[str, Any]) -> Any:
     """
     Dynamically load a class based on the systematics 'type' specified in the YAML file.
 
@@ -87,7 +87,7 @@ def load_systematics_factory(probe_systematics):
     except AttributeError as e:
         raise AttributeError(f"Class '{systematics_type}' not found in module {module_path}: {e}")
 
-def process_probes_load_2pt(yaml_data):
+def process_probes_load_2pt(yaml_data: Dict[str, Any]) -> Tuple[Any, List[str]]:
     """
     Process the probes from the YAML data, check if 'function' 
     is the same across probes with 'nz_type',
@@ -138,8 +138,8 @@ def process_probes_load_2pt(yaml_data):
 
     return loaded_function, nz_type_probes
 
-def generate_two_point_metadata(yaml_data, two_point_function, two_pt_probes, 
-                                two_point_bins):
+def generate_two_point_metadata(yaml_data: Dict[str, Any], two_point_function: Any, two_pt_probes: List[str], 
+                                two_point_bins: List[Any]) -> List[Any]:
     """
     Generate the metadata for the two-point functions based on the YAML data.
 
@@ -181,7 +181,7 @@ def generate_two_point_metadata(yaml_data, two_point_function, two_pt_probes,
         raise ValueError("Unknown TwoPointFunction type")
     return all_two_point_metadata
 
-def prepare_2pt_functions(yaml_data):
+def prepare_2pt_functions(yaml_data: Dict[str, Any]) -> Tuple[Any, List[Any]]:
     # here we call this X because we do not know if it is ell_bins or theta_bins
     two_point_function, two_pt_probes = process_probes_load_2pt(yaml_data)
 

CosmoAPI/two_point_functions/nz_loader.py

@@ -1,12 +1,13 @@
 import importlib
 import sys
+from typing import Dict, List, Any, Type
 sys.path.append("..")
 from not_implemented import not_implemented_message
 
 _DESC_SCENARIOS = {"LSST_Y10_SOURCE_BIN_COLLECTION", "LSST_Y10_LENS_BIN_COLLECTION",
                    "LSST_Y1_LENS_BIN_COLLECTION", "LSST_Y1_SOURCE_BIN_COLLECTION",}
 
-def _load_nz(yaml_data):
+def _load_nz(yaml_data: Dict[str, Any]) -> List[Any]:
     try: 
         nz_type = yaml_data["nz_type"]
     except KeyError:
@@ -17,15 +18,15 @@ def _load_nz(yaml_data):
     else:
         raise NotImplementedError(not_implemented_message)
 
-def load_all_nz(yaml_data):
+def load_all_nz(yaml_data: Dict[str, Any]) -> List[Any]:
     nzs = []
     for probe, propr in yaml_data['probes'].items():
         if 'nz_type' in propr:
             #print(propr['nz_type'])
             nzs += _load_nz(propr)
     return nzs
 
-def _load_nz_from_module(nz_type):
+def _load_nz_from_module(nz_type: str) -> Type:
     # Define the module path
     module_path = "firecrown.generators.inferred_galaxy_zdist"
 
@@ -37,4 +38,4 @@ def _load_nz_from_module(nz_type):
     except ImportError as e:
         raise ImportError(f"Failed to import module {module_path}: {e}")
     except AttributeError as e:
-        raise AttributeError(f"'{nz_type}' not found in module {module_path}: {e}")
+        raise AttributeError(f"'{nz_type}' not found in module {module_path}: {e}")