Rename source format

.github/workflows/test_and_deploy.yml

@@ -56,6 +56,23 @@ jobs:
           auto-update-conda: true
           channels: conda-forge,defaults
           activate-environment: movement-env
+      - name: "Ensure D: Drive on Windows"
+        if: matrix.os == 'windows-latest'
+        shell: cmd
+        run: |
+          echo Current directory: %CD%
+          if not "%CD:~0,2%"=="D:" (
+            echo Switching to D: drive
+            D:
+            cd "%GITHUB_WORKSPACE%"
+            if not "%CD:~0,2%"=="D:" (
+              echo ERROR: Failed to switch to D: drive
+              exit 1
+            )
+            echo Now on: %CD%
+          ) else (
+            echo Already on D: drive
+          )
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}

CONTRIBUTING.md

@@ -415,7 +415,7 @@ To add a new file, you will need to:
 ```yaml
 "SLEAP_three-mice_Aeon_proofread.analysis.h5":
   sha256sum: "82ebd281c406a61536092863bc51d1a5c7c10316275119f7daf01c1ff33eac2a"
-  source_software: "SLEAP"
+  source_format: "SLEAP"
   type: "poses"  # "poses" or "bboxes" depending on the type of tracked data
   fps: 50
   species: "mouse"

docs/source/user_guide/input_output.md

@@ -44,7 +44,7 @@ ds = load_poses.from_sleap_file("/path/to/file.analysis.h5", fps=30)
 
 # or equivalently
 ds = load_poses.from_file(
-    "/path/to/file.analysis.h5", source_software="SLEAP", fps=30
+    "/path/to/file.analysis.h5", source_format="SLEAP", fps=30
 )
 ```
 To load [SLEAP analysis files](sleap:tutorials/analysis) in .slp format (experimental, see notes in {func}`movement.io.load_poses.from_sleap_file`):
@@ -62,7 +62,7 @@ ds = load_poses.from_dlc_file("/path/to/file.h5", fps=30)
 
 # or equivalently
 ds = load_poses.from_file(
-    "/path/to/file.h5", source_software="DeepLabCut", fps=30
+    "/path/to/file.h5", source_format="DeepLabCut", fps=30
 )
 ```
 
@@ -80,7 +80,7 @@ ds = load_poses.from_lp_file("/path/to/file.analysis.csv", fps=30)
 
 # or equivalently
 ds = load_poses.from_file(
-    "/path/to/file.analysis.csv", source_software="LightningPose", fps=30
+    "/path/to/file.analysis.csv", source_format="LightningPose", fps=30
 )
 ```
 :::
@@ -95,7 +95,7 @@ ds = load_poses.from_anipose_file(
 
 # or equivalently
 ds = load_poses.from_file(
-    "/path/to/file.analysis.csv", source_software="Anipose", fps=30, individual_name="individual_0"
+    "/path/to/file.analysis.csv", source_format="Anipose", fps=30, individual_name="individual_0"
 )
 
 ```
@@ -149,7 +149,7 @@ ds = load_bboxes.from_via_tracks_file("path/to/file.csv", fps=30)
 # or equivalently
 ds = load_bboxes.from_file(
     "path/to/file.csv",
-    source_software="VIA-tracks",
+    source_format="VIA-tracks",
     fps=30,
 )
 ```

docs/source/user_guide/movement_dataset.md

@@ -55,7 +55,7 @@ Data variables:
 Attributes:
     fps:              50.0
     time_unit:        seconds
-    source_software:  SLEAP
+    source_format:  SLEAP
     source_file:      /home/user/.movement/data/poses/SLEAP_three-mice_Aeon...
     ds_type:          poses
     frame_path:       /home/user/.movement/data/frames/three-mice_Aeon_fram...
@@ -88,7 +88,7 @@ Data variables:
     confidence   (time, individuals) float64 3kB nan nan nan nan ... nan nan nan
 Attributes:
     time_unit:        frames
-    source_software:  VIA-tracks
+    source_format:  VIA-tracks
     source_file:      /home/user/.movement/data/bboxes/VIA_multiple-crabs_5...
     ds_type:          bboxes
 ```
@@ -175,7 +175,7 @@ Both poses and bounding boxes datasets in `movement` have associated metadata. T
 Right after loading a `movement` dataset, the following **attributes** are created:
 - `fps`: the number of frames per second in the video (absent if not provided by the user during loading).
 - `time_unit`: the unit of the `time` **coordinates** (either `frames` or `seconds`).
-- `source_software`: the software that produced the pose or bounding box tracks.
+- `source_format`: the software that produced the pose or bounding box tracks.
 - `source_file`: the path to the file from which the data were loaded (absent if the dataset was not loaded from a file).
 - `ds_type`: the type of dataset loaded (either `poses` or `bboxes`).
 

movement/io/load_bboxes.py

@@ -29,7 +29,7 @@ def from_numpy(
     individual_names: list[str] | None = None,
     frame_array: np.ndarray | None = None,
     fps: float | None = None,
-    source_software: str | None = None,
+    source_format: str | None = None,
 ) -> xr.Dataset:
     """Create a ``movement`` bounding boxes dataset from NumPy arrays.
 
@@ -70,7 +70,7 @@ def from_numpy(
         the ``time`` coordinates are in seconds, they will indicate the
         elapsed time from the capture of the first frame (assumed to be frame
         0).
-    source_software : str, optional
+    source_format : str, optional
         Name of the software that generated the data. Defaults to None.
 
     Returns
@@ -145,14 +145,14 @@ def from_numpy(
         individual_names=individual_names,
         frame_array=frame_array,
         fps=fps,
-        source_software=source_software,
+        source_format=source_format,
     )
     return _ds_from_valid_data(valid_bboxes_data)
 
 
 def from_file(
     file_path: Path | str,
-    source_software: Literal["VIA-tracks"],
+    source_format: Literal["VIA-tracks"],
     fps: float | None = None,
     use_frame_numbers_from_file: bool = False,
     frame_regexp: str = DEFAULT_FRAME_REGEXP,
@@ -166,7 +166,7 @@ def from_file(
     file_path : pathlib.Path or str
         Path to the file containing the tracked bounding boxes. Currently
         only VIA-tracks .csv files are supported.
-    source_software : "VIA-tracks".
+    source_format : "VIA-tracks".
         The source software of the file. Currently only files from the
         VIA 2.0.12 annotator [1]_ ("VIA-tracks") are supported.
         See .
@@ -216,12 +216,12 @@ def from_file(
     >>> from movement.io import load_bboxes
     >>> ds = load_bboxes.from_file(
     >>>     "path/to/file.csv",
-    >>>     source_software="VIA-tracks",
+    >>>     source_format="VIA-tracks",
     >>>     fps=30,
     >>> )
 
     """
-    if source_software == "VIA-tracks":
+    if source_format == "VIA-tracks":
         return from_via_tracks_file(
             file_path,
             fps,
@@ -230,7 +230,7 @@ def from_file(
         )
     else:
         raise log_error(
-            ValueError, f"Unsupported source software: {source_software}"
+            ValueError, f"Unsupported source software: {source_format}"
         )
 
 
@@ -356,11 +356,11 @@ def from_via_tracks_file(
             else None
         ),
         fps=fps,
-        source_software="VIA-tracks",
+        source_format="VIA-tracks",
     )  # it validates the dataset via ValidBboxesDataset
 
     # Add metadata as attributes
-    ds.attrs["source_software"] = "VIA-tracks"
+    ds.attrs["source_format"] = "VIA-tracks"
     ds.attrs["source_file"] = file.path.as_posix()
 
     logger.info(f"Loaded tracks of the bounding boxes from {via_file.path}:")
@@ -666,7 +666,7 @@ def _ds_from_valid_data(data: ValidBboxesDataset) -> xr.Dataset:
     time_unit = "frames"
 
     dataset_attrs: dict[str, str | float | None] = {
-        "source_software": data.source_software,
+        "source_format": data.source_format,
         "ds_type": "bboxes",
     }
     # if fps is provided: