Add constructor and annotate parameters

Author: mohamed-laarej

malariagen_data/anoph/phenotype_params.py

@@ -1,13 +1,19 @@
-"""
-Type aliases for phenotype-related parameters.
-"""
-from typing import TypeAlias, Optional, Union, List
+from typing import TypeAlias, Optional, Union, List, Annotated
 
 # Type alias for insecticide parameter
-insecticide: TypeAlias = Optional[Union[str, List[str]]]
+insecticide: TypeAlias = Annotated[
+    Optional[Union[str, List[str]]],
+    "Insecticide name(s) to filter by. Can be a single insecticide name or a list of names.",
+]
 
 # Type alias for dose parameter
-dose: TypeAlias = Optional[Union[float, List[float]]]
+dose: TypeAlias = Annotated[
+    Optional[Union[float, List[float]]],
+    "Insecticide dose(s) to filter by. Can be a single dose value or a list of dose values.",
+]
 
 # Type alias for phenotype parameter
-phenotype: TypeAlias = Optional[Union[str, List[str]]]
+phenotype: TypeAlias = Annotated[
+    Optional[Union[str, List[str]]],
+    "Phenotype outcome(s) to filter by. Can be a single phenotype value (e.g., 'alive', 'dead') or a list of values.",
+]

malariagen_data/anoph/phenotypes.py

@@ -3,7 +3,7 @@
 from typing import Callable, Optional, List, Any
 import warnings
 import fsspec
-from . import base_params, phenotype_params
+from malariagen_data.anoph import base_params, phenotype_params
 
 
 class AnophelesPhenotypeData:
@@ -21,6 +21,44 @@ class AnophelesPhenotypeData:
     _prep_sample_sets_param: Callable[..., Any]
     haplotypes: Callable[..., Any]
 
+    def __init__(
+        self,
+        url: str,
+        fs: fsspec.AbstractFileSystem,
+        sample_metadata: Callable[..., pd.DataFrame],
+        sample_sets: list[str],
+        snp_calls: Callable[..., Any],
+        prep_sample_sets_param: Callable[..., Any],
+        haplotypes: Callable[..., Any],
+    ):
+        """
+        Initialize the AnophelesPhenotypeData class.
+
+        Parameters
+        ----------
+        url : str
+            Base URL for accessing phenotype data.
+        fs : fsspec.AbstractFileSystem
+            File system interface for accessing remote data.
+        sample_metadata : callable
+            Function to retrieve sample metadata.
+        sample_sets : list of str
+            List of available sample sets.
+        snp_calls : callable
+            Function to retrieve SNP calls.
+        prep_sample_sets_param : callable
+            Function to prepare sample sets parameter.
+        haplotypes : callable
+            Function to retrieve haplotype data.
+        """
+        self._url = url
+        self._fs = fs
+        self.sample_metadata = sample_metadata
+        self.sample_sets = sample_sets
+        self.snp_calls = snp_calls
+        self._prep_sample_sets_param = prep_sample_sets_param
+        self.haplotypes = haplotypes
+
     def _load_phenotype_data(
         self,
         sample_sets: base_params.sample_sets,