Series class accepts .slp files
#79
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WalkthroughThe recent updates focus on enhancing compatibility with newer Python versions, refining the handling of series data in the Changes
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Actionable comments posted: 2
Out of diff range and nitpick comments (2)
sleap_roots/series.py (2)
45-45: Ensure the new attributeseries_nameis properly documented.Consider adding a brief description in the class docstring for the
series_nameattribute to explain its purpose and usage.
Line range hint
387-387: Useisinstance()for type checking.- if type(data_folders) != list: + if not isinstance(data_folders, list):Using
isinstance()is more Pythonic and supports subclass checking.
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Files selected for processing (1)
- sleap_roots/series.py (8 hunks)
Additional Context Used
Ruff (2)
sleap_roots/series.py (2)
387-387: Do not compare types, use
isinstance()
405-405: Do not compare types, use
isinstance()
Additional comments not posted (2)
sleap_roots/series.py (2)
56-57: Updated method signature forloadto includeseries_name.The inclusion of
series_nameas an optional parameter enhances flexibility in data handling.
396-412: Functionfind_all_slp_seriescorrectly extracts unique series names from .slp files.This function enhances the software's capability to handle .slp files, aligning with the PR's objectives.
| if series_name is None: | ||
| if h5_path is not None: | ||
| series_name = Path(h5_path).name.split(".")[0] | ||
| else: | ||
| raise ValueError("series_name or h5_path must be provided.") |
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Add error handling for both series_name and h5_path being None.
- raise ValueError("series_name or h5_path must be provided.")
+ raise ValueError("Either 'series_name' or 'h5_path' must be provided.")This change clarifies the error message, making it more informative.
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.
| if series_name is None: | |
| if h5_path is not None: | |
| series_name = Path(h5_path).name.split(".")[0] | |
| else: | |
| raise ValueError("series_name or h5_path must be provided.") | |
| if series_name is None: | |
| if h5_path is not None: | |
| series_name = Path(h5_path).name.split(".")[0] | |
| else: | |
| raise ValueError("Either 'series_name' or 'h5_path' must be provided.") |
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Actionable comments posted: 0
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Files selected for processing (2)
- environment.yml (1 hunks)
- pyproject.toml (1 hunks)
Files skipped from review as they are similar to previous changes (1)
- pyproject.toml
Additional comments not posted (1)
environment.yml (1)
8-8: Update to Python 3.11 noted. Ensure compatibility of all dependencies with this Python version.
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Actionable comments posted: 5
Out of diff range and nitpick comments (10)
sleap_roots/__init__.py (2)
Line range hint
14-14: Consider removing or using thesleap_roots.trait_pipelinesimport as it is currently unused.
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16-20: The specific imports fromsleap_roots.trait_pipelinesare unused. Consider removing them or adding them to__all__if they need to be exposed as public API.tests/test_series.py (1)
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79-79: The functiontest_series_nameis redefined. This could lead to unexpected behavior in testing. Consider renaming one of the functions or combining their logic if applicable.README.md (6)
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24-24: It seems there might be a missing closing bracket]for the markdown link. Please check and correct if necessary.
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141-141: Consider adding a comma after "environment" for better readability: "activate your conda environment, which includes JupyterLab (recommended)".
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157-157: Remove the trailing space at the end of this line to maintain clean and consistent formatting.
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207-207: Remove the trailing space at the end of this line to maintain clean and consistent formatting.
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27-27: Multiple consecutive blank lines found. Consider reducing to a single blank line to maintain clean formatting.
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160-160: Multiple consecutive blank lines found. Consider reducing to a single blank line to maintain clean formatting.sleap_roots/series.py (1)
Line range hint
388-388: Useisinstance()for type checking instead of comparing types directly. This is more Pythonic and supports subclass checking.- if type(data_folders) != list: + if not isinstance(data_folders, list):
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Files selected for processing (5)
- README.md (1 hunks)
- sleap_roots/init.py (1 hunks)
- sleap_roots/series.py (8 hunks)
- tests/test_series.py (4 hunks)
- tests/test_trait_pipelines.py (5 hunks)
Additional Context Used
LanguageTool (2)
README.md (2)
Near line 24: Unpaired symbol: ‘]’ seems to be missing
Context: ...ntation per pipeline is available here: [sleap-roots HackMD](https://hackmd.io/DM...
Near line 141: Possible missing comma found.
Context: ...oks`. To use them, activate your conda environment which includes JupyterLab (recommended)...
Ruff (15)
sleap_roots/__init__.py (9)
14-14:
sleap_roots.trait_pipelinesimported but unused; consider removing, adding to__all__, or using a redundant alias
16-16:
sleap_roots.trait_pipelines.DicotPipelineimported but unused; consider removing, adding to__all__, or using a redundant alias
17-17:
sleap_roots.trait_pipelines.TraitDefimported but unused; consider removing, adding to__all__, or using a redundant alias
18-18:
sleap_roots.trait_pipelines.YoungerMonocotPipelineimported but unused; consider removing, adding to__all__, or using a redundant alias
19-19:
sleap_roots.trait_pipelines.OlderMonocotPipelineimported but unused; consider removing, adding to__all__, or using a redundant alias
20-20:
sleap_roots.trait_pipelines.MultipleDicotPipelineimported but unused; consider removing, adding to__all__, or using a redundant alias
22-22:
sleap_roots.series.Seriesimported but unused; consider removing, adding to__all__, or using a redundant alias
22-22:
sleap_roots.series.find_all_h5_seriesimported but unused; consider removing, adding to__all__, or using a redundant alias
22-22:
sleap_roots.series.find_all_slp_seriesimported but unused; consider removing, adding to__all__, or using a redundant aliassleap_roots/series.py (2)
388-388: Do not compare types, use
isinstance()
406-406: Do not compare types, use
isinstance()tests/test_series.py (3)
2-2:
numpyimported but unused
4-4:
sleap_roots.series.find_all_slp_seriesimported but unused
79-79: Redefinition of unused
test_series_namefrom line 60tests/test_trait_pipelines.py (1)
9-9:
sleap_roots.series.find_all_slp_seriesimported but unused
| @@ -19,7 +19,7 @@ | |||
| OlderMonocotPipeline, | |||
| MultipleDicotPipeline, | |||
| ) | |||
| from sleap_roots.series import Series, find_all_series | |||
| from sleap_roots.series import Series, find_all_h5_series, find_all_slp_series | |||
There was a problem hiding this comment.
The imports from sleap_roots.series are unused in this file. Consider removing them or using them appropriately.
| @@ -1,7 +1,7 @@ | |||
| import sleap_io as sio | |||
| import numpy as np | |||
There was a problem hiding this comment.
The numpy import is unused in this file. Consider removing it unless it's needed for future tests.
| @@ -1,7 +1,7 @@ | |||
| import sleap_io as sio | |||
| import numpy as np | |||
| import pytest | |||
| from sleap_roots.series import Series, find_all_series | |||
| from sleap_roots.series import Series, find_all_h5_series, find_all_slp_series | |||
There was a problem hiding this comment.
The import find_all_slp_series is unused in this file. Consider removing it to clean up the code.
| @@ -6,13 +6,19 @@ | |||
| OlderMonocotPipeline, | |||
| MultipleDicotPipeline, | |||
| ) | |||
| from sleap_roots.series import Series, find_all_series | |||
| from sleap_roots.series import Series, find_all_h5_series, find_all_slp_series | |||
There was a problem hiding this comment.
The import find_all_slp_series is unused in this file. Consider removing it to clean up the code.
| Returns: | ||
| A list of unique series names derived from the filenames. | ||
| """ | ||
| if type(data_folders) != list: |
There was a problem hiding this comment.
Use isinstance() for type checking instead of comparing types directly. This is more Pythonic and supports subclass checking.
- if type(data_folders) != list:
+ if not isinstance(data_folders, list):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.
| if type(data_folders) != list: | |
| if not isinstance(data_folders, list): |
There was a problem hiding this comment.
Actionable comments posted: 0
Review Details
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Review profile: CHILL
Files selected for processing (4)
- notebooks/Series.ipynb (1 hunks)
- sleap_roots/series.py (9 hunks)
- tests/test_series.py (4 hunks)
- tests/test_trait_pipelines.py (5 hunks)
Files not reviewed due to errors (3)
- notebooks/Series.ipynb (no review received)
- tests/test_trait_pipelines.py (no review received)
- sleap_roots/series.py (no review received)
Additional Context Used
Ruff (6)
sleap_roots/series.py (2)
388-388: Do not compare types, use
isinstance()
406-406: Do not compare types, use
isinstance()tests/test_series.py (3)
2-2:
numpyimported but unused
4-4:
sleap_roots.series.find_all_slp_seriesimported but unused
74-74: Redefinition of unused
test_series_namefrom line 60tests/test_trait_pipelines.py (1)
9-9:
sleap_roots.series.find_all_slp_seriesimported but unused
Additional comments not posted (12)
tests/test_series.py (12)
12-12: LGTM! The fixture correctly initializes aSeriesinstance with dummy data.
17-17: LGTM! The fixture correctly creates a dummy video file path.
Line range hint
25-25: LGTM! The fixture correctly creates a dummy labels file path.
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33-33: LGTM! The fixture correctly creates aSeriesinstance using dummy paths.
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41-41: LGTM! The fixture correctly creates a dummy CSV file path.
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49-49: LGTM! The test correctly checks theseries_nameattribute.
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57-57: LGTM! The test correctly checks theget_framemethod.
89-89: LGTM! The test correctly checks theloadmethod with specific parameters.
97-97: LGTM! The test correctly checks thefind_all_h5_seriesfunction with a specific folder.
Line range hint
105-105: LGTM! The test correctly checks theloadmethod with specific parameters for rice data.
Line range hint
113-113: LGTM! The test correctly checks theget_framemethod with specific parameters for rice data.
136-136: LGTM! The test correctly checks thefind_all_h5_seriesfunction with a specific folder for rice data.
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Files selected for processing (1)
- notebooks/Series.ipynb (1 hunks)
Files skipped from review as they are similar to previous changes (1)
- notebooks/Series.ipynb
Seriesclass but necessary for the plotting functionseries_nameis now an attribute that uniquely identifies the sampleseries_namecan be found using theh5_pathor directly inputfind_all_slp_seriesadded to find uniqueseries_namefrom .slp files in a list of data foldersSummary by CodeRabbit
New Features
Seriesclass with a new attribute for series naming and improved parameter handling in the loading method.Series.ipynbfor managing series data using thesleap_rootspackage.Enhancements
Refactor
find_all_h5_seriestofind_all_slp_series.Documentation
Bug Fixes