Create docs pages #87
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Codecov ReportAll modified and coverable lines are covered by tests ✅
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## main #87 +/- ##
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Coverage 95.46% 95.46%
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Actionable comments posted: 10
Out of diff range and nitpick comments (4)
sleap_io/__init__.py (1)
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3-26: Many imports are unused. Consider removing them or adding them to__all__if they are meant to be exposed as public API.- from sleap_io.version import __version__ - from sleap_io.model.skeleton import Node, Edge, Skeleton, Symmetry - from sleap_io.model.video import Video - from sleap_io.model.instance import ( - Point, - PredictedPoint, - Track, - Instance, - PredictedInstance, - ) - from sleap_io.model.labeled_frame import LabeledFrame - from sleap_io.model.labels import Labels - from sleap_io.io.main import ( - load_slp, - save_slp, - load_nwb, - save_nwb, - load_labelstudio, - save_labelstudio, - load_jabs, - save_jabs, - load_video, - load_file, - save_file, - )sleap_io/model/video.py (2)
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9-9: Remove duplicate import ofOptional.- from typing import Tuple, Optional, Optional + from typing import Tuple, Optional
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90-90: Replace bareexceptwith specific exceptions to avoid catching unexpected errors.- except: + except AttributeError: # or other specific exceptionssleap_io/model/instance.py (1)
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44-58: Replace type comparison withisinstance()for better practice.- if type(other) is not type(self): + if not isinstance(other, type(self)):
| def __eq__(self, other: object) -> bool: | ||
| """Compare `self` and `other` for equality. | ||
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| See `Point.__eq__()` for important notes about point equality semantics! | ||
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| Args: | ||
| self, other: instance of `PredictedPoint` to compare | ||
| other: Instance of `PredictedPoint` to compare | ||
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| Returns: | ||
| True if all attributes of `self` and `other` are the identical (possibly | ||
| allowing precision error for `x` and `y` attributes). | ||
| Returns True if all attributes of `self` and `other` are the identical | ||
| (possibly allowing precision error for `x` and `y` attributes). |
There was a problem hiding this comment.
Replace type comparison with isinstance() for better practice.
- if not super().__eq__(other):
+ if not isinstance(other, PredictedPoint) or not super().__eq__(other):Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| def __eq__(self, other: object) -> bool: | |
| """Compare `self` and `other` for equality. | |
| See `Point.__eq__()` for important notes about point equality semantics! | |
| Args: | |
| self, other: instance of `PredictedPoint` to compare | |
| other: Instance of `PredictedPoint` to compare | |
| Returns: | |
| True if all attributes of `self` and `other` are the identical (possibly | |
| allowing precision error for `x` and `y` attributes). | |
| Returns True if all attributes of `self` and `other` are the identical | |
| (possibly allowing precision error for `x` and `y` attributes). | |
| def __eq__(self, other: object) -> bool: | |
| """Compare `self` and `other` for equality. | |
| See `Point.__eq__()` for important notes about point equality semantics! | |
| Args: | |
| other: Instance of `PredictedPoint` to compare | |
| Returns: | |
| Returns True if all attributes of `self` and `other` are the identical | |
| (possibly allowing precision error for `x` and `y` attributes). | |
| if not isinstance(other, PredictedPoint) or not super().__eq__(other): |
| @@ -64,7 +64,7 @@ def load_labelstudio( | |||
| """Read Label Studio-style annotations from a file and return a `Labels` object. | |||
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| Args: | |||
| labels_path: Path to the label-studio annotation file in JSON format. | |||
| filename: Path to the label-studio annotation file in JSON format. | |||
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Rename parameter labels_path to filename to align with other I/O functions.
- filename: Path to the label-studio annotation file in JSON format.
+ labels_path: Path to the label-studio annotation file in JSON format.Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| filename: Path to the label-studio annotation file in JSON format. | |
| labels_path: Path to the label-studio annotation file in JSON format. |
| @@ -119,7 +119,7 @@ def __getitem__(self, inds: int | list[int] | slice) -> np.ndarray: | |||
| """Return the frames of the video at the given indices. | |||
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| Args: | |||
| ind: Index or list of indices of frames to read. | |||
| inds: Index or list of indices of frames to read. | |||
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Rename parameter ind to inds to reflect that it can handle multiple indices.
- inds: Index or list of indices of frames to read.
+ ind: Index or list of indices of frames to read.Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| inds: Index or list of indices of frames to read. | |
| ind: Index or list of indices of frames to read. |
| @@ -121,7 +121,7 @@ def write_group(parent_group, data_to_write): | |||
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| def read_hdf5_attrs( | |||
| filename, dataset: str = "/", attribute: Optional[str] = None | |||
| filename: str, dataset: str = "/", attribute: Optional[str] = None | |||
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Add explicit typing to the filename parameter to improve type clarity.
- filename: str, dataset: str = "/", attribute: Optional[str] = None
+ filename: str | Path, dataset: str = "/", attribute: Optional[str] = NoneCommittable suggestion
‼️ IMPORTANT
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| filename: str, dataset: str = "/", attribute: Optional[str] = None | |
| filename: str | Path, dataset: str = "/", attribute: Optional[str] = None |
| The PyPI-compatible package settings are in [pyproject.toml]. | ||
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| The version number is set in [sleap_io/__init__.py] in the `__version__` variable. This is read automatically by setuptools during installation and build. | ||
| The version number is set in [sleap_io/version.py] in the `__version__` variable. This is read automatically by setuptools during installation and build. |
There was a problem hiding this comment.
Update the version number setting location to sleap_io/version.py.
- The version number is set in [sleap_io/__init__.py] in the `__version__` variable.
+ The version number is set in [sleap_io/version.py] in the `__version__` variable.Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| The PyPI-compatible package settings are in [pyproject.toml]. | |
| The version number is set in [sleap_io/__init__.py] in the `__version__` variable. This is read automatically by setuptools during installation and build. | |
| The version number is set in [sleap_io/version.py] in the `__version__` variable. This is read automatically by setuptools during installation and build. | |
| The PyPI-compatible package settings are in [pyproject.toml]. | |
| The version number is set in [sleap_io/version.py] in the `__version__` variable. This is read automatically by setuptools during installation and build. |
| @@ -294,7 +294,7 @@ def filter_and_index(annotations: Iterable[dict], annot_type: str) -> Dict[str, | |||
| """Filter annotations based on the type field and index them by ID. | |||
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| Args: | |||
| annotation: annotations to filter and index | |||
| annotations: annotations to filter and index | |||
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Correct typo in parameter name from annotation to annotations.
- annotations: annotations to filter and index
+ annotation: annotations to filter and indexCommittable suggestion
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| annotations: annotations to filter and index | |
| annotation: annotations to filter and index |
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| ::: sleap_io.load_labelstudio | ||
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| ::: sleap_io.save_labelstudio |
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Ensure files end with a single newline character.
+ Committable suggestion
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| ::: sleap_io.save_labelstudio | |
| ::: sleap_io.save_labelstudio | |
| @@ -0,0 +1,29 @@ | |||
| # Data model | |||
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| `sleap-io` implements the core data structures used in SLEAP for storing data related to multi-instance pose tracking, including for annotation, training and inference. | |||
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The sentence should start with an uppercase letter.
- `sleap-io` implements the core data structures used in SLEAP for storing data related to multi-instance pose tracking, including for annotation, training and inference.
+ `Sleap-io` implements the core data structures used in SLEAP for storing data related to multi-instance pose tracking, including for annotation, training and inference.Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| `sleap-io` implements the core data structures used in SLEAP for storing data related to multi-instance pose tracking, including for annotation, training and inference. | |
| `Sleap-io` implements the core data structures used in SLEAP for storing data related to multi-instance pose tracking, including for annotation, training and inference. |
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| ::: sleap_io.Track | ||
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| ::: sleap_io.Video |
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Ensure files end with a single newline character.
+ Committable suggestion
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| ::: sleap_io.Video | |
| ::: sleap_io.Video | |
| For development, use one of the following syntaxes: | ||
| ``` | ||
| conda env create -f environment.yml | ||
| ``` | ||
| ``` | ||
| pip install -e .[dev] | ||
| ``` | ||
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| ## Usage | ||
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| ### Load and save in different formats | ||
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| ```py | ||
| import sleap_io as sio | ||
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| # Load from SLEAP file. | ||
| labels = sio.load_file("predictions.slp") | ||
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| # Save to NWB file. | ||
| sio.save_file(labels, "predictions.nwb") | ||
| # Or: | ||
| # labels.save("predictions.nwb") | ||
| ``` | ||
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| ### Convert labels to raw arrays | ||
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| ```py | ||
| import sleap_io as sio | ||
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| labels = sio.load_slp("tests/data/slp/centered_pair_predictions.slp") | ||
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| # Convert predictions to point coordinates in a single array. | ||
| trx = labels.numpy() | ||
| n_frames, n_tracks, n_nodes, xy = trx.shape | ||
| assert xy == 2 | ||
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| # Convert to array with confidence scores appended. | ||
| trx_with_scores = labels.numpy(return_confidence=True) | ||
| n_frames, n_tracks, n_nodes, xy_score = trx.shape | ||
| assert xy_score == 3 | ||
| ``` | ||
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| ### Read video data | ||
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| ```py | ||
| import sleap_io as sio | ||
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| video = sio.load_video("test.mp4") | ||
| n_frames, height, width, channels = video.shape | ||
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| frame = video[0] | ||
| height, width, channels = frame.shape | ||
| ``` | ||
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| ### Create labels from raw data | ||
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| ```py | ||
| import sleap_io as sio | ||
| import numpy as np | ||
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| # Create skeleton. | ||
| skeleton = sio.Skeleton( | ||
| nodes=["head", "thorax", "abdomen"], | ||
| edges=[("head", "thorax"), ("thorax", "abdomen")] | ||
| ) | ||
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| # Create video. | ||
| video = sio.load_video("test.mp4") | ||
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| # Create instance. | ||
| instance = sio.Instance.from_numpy( | ||
| points=np.array([ | ||
| [10.2, 20.4], | ||
| [5.8, 15.1], | ||
| [0.3, 10.6], | ||
| ]), | ||
| skeleton=skeleton | ||
| ) | ||
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| # Create labeled frame. | ||
| lf = sio.LabeledFrame(video=video, frame_idx=0, instances=[instance]) | ||
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| # Create labels. | ||
| labels = sio.Labels(videos=[video], skeletons=[skeleton], labeled_frames=[lf]) | ||
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| # Save. | ||
| labels.save("labels.slp") | ||
| ``` | ||
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| ## Support | ||
| For technical inquiries specific to this package, please [open an Issue](https://github.com/talmolab/sleap-io/issues) | ||
| with a description of your problem or request. | ||
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| For general SLEAP usage, see the [main website](https://sleap.ai). | ||
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| Other questions? Reach out to `[email protected]`. | ||
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| ## License | ||
| This package is distributed under a BSD 3-Clause License and can be used without | ||
| restrictions. See [`LICENSE`](https://github.com/talmolab/sleap-io/blob/main/LICENSE) for details. |
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Several formatting issues detected: missing blank lines around headings and fenced code blocks, and missing language specification for code blocks.
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+ ```bash
+ ```bash
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