Ensure that some methods and functions are called with named paramete…

…rs (#48)

CHANGELOG.rst

@@ -1,14 +1,18 @@
 Changelog
 =========
 
-Version 0.11.5
+Version 0.12.0
 --------------
 
-Bug Fixes
-~~~~~~~~~
+Breaking changes
+~~~~~~~~~~~~~~~~
 
-- Skip simulations with empty path in the simulation campaign configuration (fix regression in blueetl 0.8.0).
+- Ensure that some methods and functions are called with named parameters. In particular, the following public methods require named parameters:
 
+  - ``blueetl.analysis.run_from_file()``
+  - ``blueetl.extract.report.ReportExtractor.from_simulations()``
+  - ``blueetl.repository.Repository.__init__()``
+  - ``blueetl.repository.FilteredRepository.__init__()``
 
 Version 0.11.4
 --------------
@@ -17,6 +21,7 @@ Bug Fixes
 ~~~~~~~~~
 
 - Fix tests with libsonata 0.1.28.
+- Skip simulations with empty path in the simulation campaign configuration (fix regression in blueetl 0.8.0).
 
 
 Version 0.11.3

pyproject.toml

@@ -153,7 +153,7 @@ ignored-modules = ["bluepy"]
 # Maximum number of arguments for function / method.
 max-args = 8
 # Maximum number of positional arguments for function / method.
-max-positional-arguments = 10
+max-positional-arguments = 5
 # Maximum number of attributes for a class (see R0902).
 max-attributes = 40
 # Maximum number of boolean expressions in an if statement (see R0916).

src/blueetl/analysis.py

@@ -327,6 +327,7 @@ def show(self):
 
 def run_from_file(
     analysis_config_file: StrOrPath,
+    *,
     seed: Optional[int] = 0,
     extract: bool = True,
     calculate: bool = True,

src/blueetl/apps/run.py

@@ -33,6 +33,7 @@
 @click.option("-i", "--interactive/--no-interactive", help="Start an interactive IPython shell.")
 @click.option("-v", "--verbose", count=True, help="-v for INFO, -vv for DEBUG")
 def run(
+    *,
     analysis_config_file,
     seed,
     extract,

src/blueetl/extract/compartment_report.py

@@ -30,6 +30,7 @@ class CompartmentReport(ReportExtractor):
     @classmethod
     def _load_values(
         cls,
+        *,
         simulation: Simulation,
         population: Optional[str],
         gids,

src/blueetl/extract/neurons.py

@@ -31,6 +31,7 @@ def _get_property_names(neuron_classes: dict[str, NeuronClassConfig]) -> list[st
 
 
 def _load_cells(
+    *,
     circuit: Circuit,
     property_names: list[str],
     cells_cache: CellsCache,

src/blueetl/extract/report.py

@@ -61,6 +61,7 @@ def calculate_window_slice(rec) -> WindowSlice:
     @abstractmethod
     def _load_values(
         cls,
+        *,
         simulation: Simulation,
         population: Optional[str],
         gids,
@@ -83,6 +84,7 @@ def _load_values(
     @classmethod
     def from_simulations(
         cls: type[ReportExtractorT],
+        *,
         simulations: Simulations,
         neurons: Neurons,
         windows: Windows,
@@ -122,6 +124,7 @@ def from_simulations(
 
 
 def _merge_filter_func(
+    *,
     task_index: int,
     key: NamedTuple,
     df_list: list[pd.DataFrame],

src/blueetl/extract/soma_report.py

@@ -21,6 +21,7 @@ class SomaReport(ReportExtractor):
     @classmethod
     def _load_values(
         cls,
+        *,
         simulation: Simulation,
         population: Optional[str],
         gids,

src/blueetl/extract/spikes.py

@@ -31,6 +31,7 @@ def _assign_window(cls, df: pd.DataFrame, rec) -> pd.DataFrame:
     @classmethod
     def _load_values(
         cls,
+        *,
         simulation: Simulation,
         population: Optional[str],
         gids,

src/blueetl/extract/windows.py

@@ -56,6 +56,7 @@ def _load_dynamic_gids(
 
 
 def _load_dynamic_spikes(
+    *,
     simulation: Simulation,
     population: Optional[str],
     gids: np.ndarray,
@@ -145,6 +146,7 @@ def _validate(cls, df: pd.DataFrame) -> None:
     @classmethod
     def _load_records_from_resolver(
         cls,
+        *,
         name: str,
         win: str,
         simulation_id: int,

src/blueetl/features.py

@@ -390,6 +390,7 @@ def _calculate_new(
 
 
 def _user_func_wrapper(
+    *,
     task_index: int,
     key: NamedTuple,
     neurons_df: pd.DataFrame,
@@ -446,6 +447,7 @@ def _user_func_wrapper(
 
 
 def _merge_filter_func(
+    *,
     task_index: int,
     key: NamedTuple,
     df_list: list[pd.DataFrame],

src/blueetl/repository.py

@@ -209,6 +209,7 @@ class Repository:
 
     def __init__(
         self,
+        *,
         simulations_config: SimulationCampaign,
         extraction_config: ExtractionConfig,
         cache_manager: CacheManager,
@@ -391,7 +392,7 @@ def needs_filter(self, name: str) -> bool:
 class FilteredRepository(Repository):
     """FilteredRepository class."""
 
-    def __init__(self, parent: Repository, simulations_filter: dict[str, Any]) -> None:
+    def __init__(self, *, parent: Repository, simulations_filter: dict[str, Any]) -> None:
         """Initialize the object using the given dict of DataFrames.
 
         Filtered dataframes are never written to disk.