+ finalize conda build

Author: André Böni

.gitignore

@@ -89,3 +89,4 @@ docs/_build
 /out/
 /output/bld/rattler-build_gaitalytics_1721919576/work/build_env.bat
 /output/bld/rattler-build_gaitalytics_1721919576/work/conda_build.bat
+/conda-build/

conda.recipe/meta.yaml

@@ -15,6 +15,11 @@ build:
   number: 0
 
 requirements:
+  build:
+    - pip
+    - python >=3.11
+    - setuptools
+    - setuptools_scm
   host:
     - python >=3.11
     - pip

gaitalytics/_version.py

@@ -3,6 +3,7 @@
 TYPE_CHECKING = False
 if TYPE_CHECKING:
     from typing import Tuple, Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +13,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.0'
-__version_tuple__ = version_tuple = (0, 2, 0)
+__version__ = version = "0.2.1.dev0+g524461a.d20240729"
+__version_tuple__ = version_tuple = (0, 2, 1, "dev0", "g524461a.d20240729")

gaitalytics/api.py

@@ -64,7 +64,7 @@ def load_config(config_path: Path | str) -> mapping.MappingConfigs:
 
 @_PathConverter
 def load_c3d_trial(
-        c3d_file: Path | str, configs: mapping.MappingConfigs
+    c3d_file: Path | str, configs: mapping.MappingConfigs
 ) -> model.Trial:
     """Loads a Trial from a c3d file.
 
@@ -93,8 +93,7 @@ def load_c3d_trial(
 
 
 def detect_events(
-        trial: model.Trial, config: mapping.MappingConfigs, method: str = "Marker",
-        **kwargs
+    trial: model.Trial, config: mapping.MappingConfigs, method: str = "Marker", **kwargs
 ) -> pd.DataFrame:
     """Detects the events in the trial.
 
@@ -144,9 +143,9 @@ def check_events(event_table: pd.DataFrame, method: str = "sequence"):
 
 @_PathConverter
 def write_events_to_c3d(
-        c3d_path: Path | str,
-        event_table: pd.DataFrame,
-        output_path: Path | str | None = None,
+    c3d_path: Path | str,
+    event_table: pd.DataFrame,
+    output_path: Path | str | None = None,
 ):
     """Writes the events to the c3d file.
 
@@ -156,8 +155,7 @@ def write_events_to_c3d(
         output_path: The path to write the c3d file with the events.
         If None, the original file will be overwritten.
     """
-    io.C3dEventFileWriter(c3d_path).write_events(event_table,
-                                                 output_path)  # type: ignore
+    io.C3dEventFileWriter(c3d_path).write_events(event_table, output_path)  # type: ignore
 
 
 def segment_trial(trial: model.Trial, method: str = "HS") -> model.TrialCycles:
@@ -185,7 +183,7 @@ def segment_trial(trial: model.Trial, method: str = "HS") -> model.TrialCycles:
 
 
 def time_normalise_trial(
-        trial: model.Trial | model.TrialCycles, method: str = "linear", **kwargs
+    trial: model.Trial | model.TrialCycles, method: str = "linear", **kwargs
 ) -> model.Trial | model.TrialCycles:
     """Normalises the time in the trial.
 
@@ -208,15 +206,15 @@ def time_normalise_trial(
 
 
 def calculate_features(
-        trial: model.TrialCycles,
-        config: mapping.MappingConfigs,
-        methods: list | tuple = (
-                features.TimeSeriesFeatures,
-                features.PhaseTimeSeriesFeatures,
-                features.TemporalFeatures,
-                features.SpatialFeatures,
-        ),
-        **kwargs,
+    trial: model.TrialCycles,
+    config: mapping.MappingConfigs,
+    methods: list | tuple = (
+        features.TimeSeriesFeatures,
+        features.PhaseTimeSeriesFeatures,
+        features.TemporalFeatures,
+        features.SpatialFeatures,
+    ),
+    **kwargs,
 ) -> xr.DataArray:
     """Calculates the features of the trial.
 
@@ -237,7 +235,7 @@ def calculate_features(
 
 
 def _create_feature_methods(
-        methods: list[type] | tuple[type], config: mapping.MappingConfigs, **kwargs
+    methods: list[type] | tuple[type], config: mapping.MappingConfigs, **kwargs
 ) -> list[features.FeatureCalculation]:
     """Checks the feature calculation methods.
 
@@ -258,8 +256,11 @@ def _create_feature_methods(
 
 
 @_PathConverter
-def export_trial(trial: model.Trial | model.TrialCycles, output_path: Path | str,
-                 method: str ="netcdf"):
+def export_trial(
+    trial: model.Trial | model.TrialCycles,
+    output_path: Path | str,
+    method: str = "netcdf",
+):
     """Exports the trial to a c3d file.
 
     This function will create a folder and save the trial as NetCDF files.
@@ -281,7 +282,6 @@ def export_trial(trial: model.Trial | model.TrialCycles, output_path: Path | str
     """
     match method:
         case "netcdf":
-            io.NetCDFTrialExporter(output_path).export_trial(trial)
+            io.NetCDFTrialExporter(output_path).export_trial(trial)  # type: ignore
         case _:
             raise ValueError(f"Unsupported method: {method}")
-    io.NetCDFTrialExporter(output_path).export_trial(trial)

gaitalytics/features.py

@@ -361,7 +361,7 @@ def _calculate(self, trial: model.Trial) -> xr.DataArray:
 
         context = analysis_data.attrs["context"]
 
-        event_ipsi = event_table.loc[
+        event_ipsi = event_table.loc[  # type: ignore
             event_table[io.C3dEventInputFileReader.COLUMN_CONTEXT] == context  # type: ignore
         ]
         event_ipsi_fo = event_ipsi.loc[

gaitalytics/io.py

@@ -254,8 +254,7 @@ class _PyomecaInputFileReader(_BaseFileHandler, ABC):
     """
 
     def __init__(
-            self, file_path: Path,
-            pyomeca_class: type[pyomeca.Markers | pyomeca.Analogs]
+        self, file_path: Path, pyomeca_class: type[pyomeca.Markers | pyomeca.Analogs]
     ):
         """Initializes a new instance of the MarkersInputFileReader class.
 
@@ -270,7 +269,7 @@ def __init__(
         """
         file_ext = file_path.suffix
         if file_ext == ".c3d" and (
-                pyomeca_class == pyomeca.Analogs or pyomeca_class == pyomeca.Markers
+            pyomeca_class == pyomeca.Analogs or pyomeca_class == pyomeca.Markers
         ):
             data = pyomeca_class.from_c3d(file_path)
         elif file_ext == ".trc" and pyomeca_class == pyomeca.Markers:
@@ -296,7 +295,7 @@ def __init__(
 
     @staticmethod
     def _to_absolute_time(
-            data: xr.DataArray, first_frame: int, rate: float
+        data: xr.DataArray, first_frame: int, rate: float
     ) -> xr.DataArray:
         """Converts the time to absolute time.
 
@@ -455,7 +454,6 @@ def get_analysis(self) -> xr.DataArray:
 
 
 class _TrialExporter(_BaseFileHandler):
-
     @abstractmethod
     def export_trial(self, trial: model.Trial | model.TrialCycles):
         """Export the trial to the output folder.
@@ -530,4 +528,3 @@ def _export_trial_cycles(trial: model.TrialCycles, folder_path: Path):
                 file_path = folder_path / f"{category.value}.nc"
                 full_data = xr.Dataset(context_structs).to_dataarray("context")
                 full_data.to_netcdf(file_path, mode="w", engine="h5netcdf")
-

pixi.lock

@@ -71,7 +71,6 @@ python = ">=3.11,<3.12"
 [tool.pixi.feature.py312.dependencies]
 python = ">=3.12.0,<3.13.0"
 
-
 [tool.pixi.feature.docs.tasks]
 clean-docs = "cleanpy --include-builds --exclude .pixi ."
 docs = "sphinx-build -M html ./docs ./docs/_build -W --keep-going"
@@ -84,8 +83,7 @@ test-api = "pytest -vv --capture=sys tests/test_api.py"
 [tool.pixi.feature.dev.tasks]
 ruff-format = "ruff format gaitalytics"
 ruff-check = { cmd = "ruff check gaitalytics --fix", depends-on = ["ruff-format"] }
-load-stubs = { cmd = "mypy --install-types", depends-on = ["ruff-check"] }
-check-code = { cmd = "mypy gaitalytics --check-untyped-defs", depends-on = ["load-stubs"] }
+check-code = { cmd = "mypy gaitalytics --check-untyped-defs", depends-on = ["ruff-check"] }
 
 [tool.pixi.feature.build.tasks]
 build = "python -m build -n"