Better parameters handling

src/lussac/core/__init__.py

@@ -1,4 +1,5 @@
 from .lussac_data import LussacData, MonoSortingData, MultiSortingsData
+from .lussac_params import LussacParams
 from .module import LussacModule, MonoSortingModule, MultiSortingsModule
 from .module_factory import ModuleFactory
 from .pipeline import LussacPipeline

src/lussac/core/lussac_params.py

@@ -0,0 +1,79 @@
+import json
+import pathlib
+import platform
+
+import jsmin
+
+import lussac
+
+
+class LussacParams:
+
+	@staticmethod
+	def load_from_string(params: str, params_folder: pathlib.Path | str | None = None):
+		"""
+		Loads the parameters from a string and returns them as a dict.
+
+		@param params: str
+			Lussac's parameters.
+		@param params_folder: str
+			Path to replace the "$PARAMS_FOLDER".
+		"""
+
+		if params_folder is not None:
+			params_folder = str(pathlib.Path(params_folder).absolute())
+			params = params.replace("$PARAMS_FOLDER", params_folder)
+		if platform.system() == "Windows":  # pragma: no cover (OS specific).
+			params = params.replace("\\", "\\\\")
+
+		return json.loads(params)
+
+	@staticmethod
+	def load_from_json_file(filename: str, params_folder: pathlib.Path | str | None = None) -> dict:
+		"""
+		Loads the JSON parameters file and returns its content as a dict.
+
+		@param filename: str
+			Path to the file containing Lussac's parameters.
+		@param params_folder: Path | str | None
+			Path to replace the "$PARAMS_FOLDER".
+			If None (default), will use the parent folder of the filename.
+		@return params: dict
+			Lussac's parameters.
+		"""
+
+		if params_folder is None:
+			params_folder = str(pathlib.Path(filename).parent.absolute())
+		else:
+			params_folder = str(pathlib.Path(params_folder).absolute())
+
+		with open(filename) as json_file:
+			minified = jsmin.jsmin(json_file.read())  # Parses out comments.
+			return LussacParams.load_from_string(minified, params_folder)
+
+	@staticmethod
+	def load_default_params(name: str, folder: pathlib.Path | str) -> dict:
+		"""
+		Loads the default parameters from the "params_example" folder.
+
+		@param name: str
+			The name of the default params file to load.
+		@param folder: str
+			Path to the folder where to create the "lussac" folder.
+		@return params: dict
+			The default parameters.
+		"""
+
+		if not name.startswith("params_"):
+			name = f"params_{name}"
+		if not name.endswith(".json"):
+			name = f"{name}.json"
+
+		params_folder = pathlib.Path(lussac.__file__).parent.parent.parent / "params_examples"
+		file = params_folder / name
+
+		return LussacParams.load_from_json_file(str(file), folder)
+
+
+
+

src/lussac/main.py

@@ -1,11 +1,7 @@
 import logging
-import pathlib
-import platform
 import sys
 import argparse
-import json
-import jsmin
-from lussac.core import LussacData, LussacPipeline, LussacSpikeSorter
+from lussac.core import LussacData, LussacParams, LussacPipeline, LussacSpikeSorter
 
 
 def parse_arguments(args: list | None) -> str:
@@ -25,34 +21,14 @@ def parse_arguments(args: list | None) -> str:
 	return args.params_file
 
 
-def load_json(filename: str) -> dict:
-	"""
-	Loads the JSON parameters file and returns its content.
-
-	@param filename: str
-		Path to the file containing Lussac's parameters.
-	@return params: dict
-		Lussac's parameters.
-	"""
-
-	folder = pathlib.Path(filename).parent
-	with open(filename) as json_file:
-		minified = jsmin.jsmin(json_file.read())  # Parses out comments.
-		minified = minified.replace("$PARAMS_FOLDER", str(folder.absolute()))
-		if platform.system() == "Windows":  # pragma: no cover (OS specific).
-			minified = minified.replace("\\", "\\\\")
-
-		return json.loads(minified)
-
-
 def main() -> None:  # pragma: no cover
 	"""
 	The main function to execute Lussac.
 	"""
 
 	# STEP 0: Loading the parameters into the LussacData object.
 	params_file = parse_arguments(sys.argv[1:])
-	params = load_json(params_file)
+	params = LussacParams.load_from_json_file(params_file)
 	data = LussacData.create_from_params(params)
 
 	# STEP 1: Running the spike sorting.

tests/conftest.py

@@ -3,8 +3,7 @@
 import shutil
 import sys
 import pytest
-from lussac.core import LussacData, LussacPipeline, MonoSortingData, MultiSortingsData
-import lussac.main
+from lussac.core import LussacData, LussacParams, LussacPipeline, MonoSortingData, MultiSortingsData
 
 
 sys.path.append(str(pathlib.Path(__file__).parent.parent.absolute()))  # Otherwise the tests are not found properly with 'pytest'.
@@ -13,7 +12,7 @@
 
 @pytest.fixture(scope="session")
 def params() -> dict:
-	return lussac.main.load_json(str(params_path.resolve()))
+	return LussacParams.load_from_json_file(str(params_path.resolve()))
 
 
 @pytest.fixture(scope="session")

tests/core/test_lussac_params.py

@@ -0,0 +1,7 @@
+from lussac.core import LussacParams
+
+
+def test_load_default_params() -> None:
+	params = LussacParams.load_default_params('params_synthetic', '/aze/')
+	print(params)
+	assert params['lussac']['tmp_folder'] == "/aze/lussac/tmp"