Rename type alias

kymata/datasets/data_root.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 from typing import Optional
 
-from kymata.io.file import path_type
+from kymata.io.file import PathType
 
 
 _DATA_PATH_ENVIRONMENT_VAR_NAME = "KYMATA_DATA_ROOT"
@@ -17,13 +17,13 @@
 ]
 
 
-def data_root_path(data_root: Optional[path_type] = None) -> Path:
+def data_root_path(data_root: Optional[PathType] = None) -> Path:
 
     # Check if the data root has been specified
 
     # Might be in an environmental variable
     if data_root is None:
-        data_root: path_type | None = getenv(_DATA_PATH_ENVIRONMENT_VAR_NAME, default=None)
+        data_root: PathType | None = getenv(_DATA_PATH_ENVIRONMENT_VAR_NAME, default=None)
 
     # Might have been supplied as an argument
     if data_root is not None:

kymata/datasets/sample.py

@@ -6,7 +6,7 @@
 
 from kymata.datasets.data_root import data_root_path
 from kymata.entities.expression import HexelExpressionSet, SensorExpressionSet
-from kymata.io.file import path_type
+from kymata.io.file import PathType
 from kymata.io.nkg import load_expression_set
 
 _SAMPLE_DATA_DIR_NAME = "tutorial_nkg_data"
@@ -62,7 +62,7 @@ def to_expressionset(self) -> HexelExpressionSet:
 
 
 class KymataMirror2023Q3Dataset(SampleDataset):
-    def __init__(self, data_root: Optional[path_type] = None, download: bool = True):
+    def __init__(self, data_root: Optional[PathType] = None, download: bool = True):
         name = "kymata_mirror_Q3_2023"
         super().__init__(
             name=name,
@@ -81,7 +81,7 @@ def to_expressionset(self) -> HexelExpressionSet:
 
 
 class TVLInsLoudnessOnlyDataset(SampleDataset):
-    def __init__(self, data_root: Optional[path_type] = None, download: bool = True):
+    def __init__(self, data_root: Optional[PathType] = None, download: bool = True):
         name = "TVL_2020_ins_loudness_only"
         super().__init__(
             name=name,
@@ -100,7 +100,7 @@ def to_expressionset(self) -> HexelExpressionSet:
 
 
 class TVLDeltaInsTC1LoudnessOnlyDataset(SampleDataset):
-    def __init__(self, data_root: Optional[path_type] = None, download: bool = True):
+    def __init__(self, data_root: Optional[PathType] = None, download: bool = True):
         name = "TVL_2020_delta_ins_tontop_chan1_loudness_only"
         super().__init__(
             name=name,
@@ -119,7 +119,7 @@ def to_expressionset(self) -> HexelExpressionSet:
 
 
 class TVLDeltaInsTC1LoudnessOnlySensorsDataset(SampleDataset):
-    def __init__(self, data_root: Optional[path_type] = None, download: bool = True):
+    def __init__(self, data_root: Optional[PathType] = None, download: bool = True):
         name = "TVL_2020_delta_ins_tontop_chan1_loudness_only_sensors"
         super().__init__(
             name=name,

kymata/io/config.py

@@ -3,10 +3,10 @@
 import yaml
 
 from kymata.datasets.data_root import data_root_path
-from kymata.io.file import path_type, file_type, open_or_use
+from kymata.io.file import PathType, FileType, open_or_use
 
 
-def load_config(config_location: path_type | file_type):
+def load_config(config_location: PathType | FileType):
     """Load config parameters"""
     with open_or_use(config_location) as stream:
         return yaml.safe_load(stream)

kymata/io/file.py

@@ -2,12 +2,12 @@
 from pathlib import Path
 from typing import TextIO, BinaryIO, Union
 
-file_type = Union[TextIO, BinaryIO]
-path_type = Union[str, Path]
+FileType = Union[TextIO, BinaryIO]
+PathType = Union[str, Path]
 
 
 @contextmanager
-def open_or_use(path_or_file: path_type | file_type, mode: str = "r") -> file_type:
+def open_or_use(path_or_file: PathType | FileType, mode: str = "r") -> FileType:
     """
     If passed a path, will open it and return the file handle, and close when done.
     if passed a file handle, will keep it open, and return it when done.

kymata/io/functions.py

@@ -5,10 +5,10 @@
 from scipy.io import loadmat
 
 from kymata.entities.functions import Function
-from kymata.io.file import path_type
+from kymata.io.file import PathType
 
 
-def load_function(function_path_without_suffix: path_type, func_name: str, n_derivatives: int = 0, bruce_neurons: tuple = (0, 10)) -> Function:
+def load_function(function_path_without_suffix: PathType, func_name: str, n_derivatives: int = 0, bruce_neurons: tuple = (0, 10)) -> Function:
     function_path_without_suffix = Path(function_path_without_suffix)
     func: NDArray
     if 'neurogram' in func_name:

kymata/io/nkg.py

@@ -16,7 +16,7 @@
     SensorExpressionSet
 from kymata.math.p_values import p_to_logp
 from kymata.entities.sparse_data import expand_dims
-from kymata.io.file import path_type, file_type, open_or_use
+from kymata.io.file import PathType, FileType, open_or_use
 
 
 class _Keys(StrEnum):
@@ -64,13 +64,13 @@ def block_names(self) -> list[str]:
 CURRENT_VERSION = "0.4"
 
 
-def file_version(from_path_or_file: path_type | file_type) -> version.Version:
+def file_version(from_path_or_file: PathType | FileType) -> version.Version:
     with open_or_use(from_path_or_file, mode="rb") as archive, ZipFile(archive, "r") as zf:
         with TextIOWrapper(zf.open("_metadata/format-version.txt"), encoding="utf-8") as f:
             return version.parse(str(f.read()).strip())
 
 
-def load_expression_set(from_path_or_file: path_type | file_type) -> ExpressionSet:
+def load_expression_set(from_path_or_file: PathType | FileType) -> ExpressionSet:
     _v, data_dict = _load_data(from_path_or_file)
 
     type_identifier = data_dict[_Keys.expressionset_type]
@@ -97,7 +97,7 @@ def load_expression_set(from_path_or_file: path_type | file_type) -> ExpressionS
 
 
 def save_expression_set(expression_set: ExpressionSet,
-                        to_path_or_file: path_type | file_type,
+                        to_path_or_file: PathType | FileType,
                         compression=ZIP_LZMA,
                         overwrite: bool = False):
     """
@@ -128,7 +128,7 @@ def save_expression_set(expression_set: ExpressionSet,
             zf.writestr(f"/{block_name}/coo-shape.txt", "\n".join(str(x) for x in expression_set._data[block_name].data.shape))
 
 
-def _load_data(from_path_or_file: path_type | file_type) -> tuple[version.Version, dict[str, Any]]:
+def _load_data(from_path_or_file: PathType | FileType) -> tuple[version.Version, dict[str, Any]]:
     """
     Load an ExpressionSet from an open file, or the file at the specified path.
 
@@ -252,7 +252,7 @@ def _load_data(from_path_or_file: path_type | file_type) -> tuple[version.Versio
 
 
 # noinspection DuplicatedCode
-def _load_data_current(from_path_or_file: path_type | file_type) -> dict[str, Any]:
+def _load_data_current(from_path_or_file: PathType | FileType) -> dict[str, Any]:
     """
     Load data from current version
     """

kymata/io/nkg_compatibility.py

@@ -17,11 +17,11 @@
 from numpy.typing import NDArray
 
 from kymata.entities.datatypes import LatencyDType, FunctionNameDType, HexelDType
-from kymata.io.file import path_type, file_type, open_or_use
+from kymata.io.file import PathType, FileType, open_or_use
 
 
 # noinspection DuplicatedCode
-def _load_data_0_3(from_path_or_file: path_type | file_type) -> dict[str, Any]:
+def _load_data_0_3(from_path_or_file: PathType | FileType) -> dict[str, Any]:
     """
     This is a function which loads data format 0.3.
 
@@ -60,7 +60,7 @@ def _load_data_0_3(from_path_or_file: path_type | file_type) -> dict[str, Any]:
 
 
 # noinspection DuplicatedCode
-def _load_data_0_2(from_path_or_file: path_type | file_type) -> dict[str, Any]:
+def _load_data_0_2(from_path_or_file: PathType | FileType) -> dict[str, Any]:
     """
     This is a function which loads data format 0.2.
 
@@ -99,7 +99,7 @@ def _load_data_0_2(from_path_or_file: path_type | file_type) -> dict[str, Any]:
 
 
 # noinspection DuplicatedCode
-def _load_data_0_1(from_path_or_file: path_type | file_type) -> dict[str, Any]:
+def _load_data_0_1(from_path_or_file: PathType | FileType) -> dict[str, Any]:
     """
     This is a function which loads data format 0.1.