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Oufattole / meds-torch

MIT License
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Add load_subject_dynamic_data to PyTorch Dataset class #53

Closed payalchandak closed 1 month ago

payalchandak commented 1 month ago

Summary by CodeRabbit

coderabbitai[bot] commented 1 month ago

Walkthrough

The changes introduce a new method load_subject_dynamic_data in the PytorchDataset class, which loads dynamic data slices based on a subject index. This method retrieves the subject ID and time range from the dataset's index and accesses corresponding data from a nested ragged tensor file. Additionally, the existing _seeded_getitem method is modified to call this new method, enhancing the modularity and readability of the code while maintaining the overall structure of the class. The .pre-commit-config.yaml file is also updated to refine pre-commit hooks and their configurations.

Changes

File Path Change Summary
src/meds_torch/data/components/pytorch_dataset.py Added method load_subject_dynamic_data(self, idx: int); modified _seeded_getitem to use the new method and updated assertion message.
.pre-commit-config.yaml Updated pre-commit hooks: changed Python version to 3.12, modified docformatter, set black line length to 110, added autoflake, and adjusted flake8 configurations.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant PytorchDataset
    participant DataLoader

    User->>PytorchDataset: Call _seeded_getitem()
    PytorchDataset->>DataLoader: Load subject dynamic data
    DataLoader-->>PytorchDataset: Return dynamic data
    PytorchDataset-->>User: Return data

🐰 In the meadow where data flows,
A new method blooms and grows.
With each slice, the rabbits cheer,
For loading fast, it brings us near.
So hop along, let’s celebrate,
Dynamic data, oh, how great! 🌼

📜 Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
📥 Commits Files that changed from the base of the PR and between c1ac0d7fa8c1ccec6e3ba4359582d700020148a7 and 0a30d466d0dd4ceb563d715ec847d368776f0f6e.
📒 Files selected for processing (1) * .pre-commit-config.yaml (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1) * .pre-commit-config.yaml
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payalchandak commented 1 month ago

Code quality checks pass locally for me, not sure what's going on with the automated testing 

(eq) payal@narsil:.../meds-torch$ git status
On branch payal/load_subject_dynamic_data
Your branch is up to date with 'origin/payal/load_subject_dynamic_data'.

nothing to commit, working tree clean
(eq) payal@narsil:.../meds-torch$ pre-commit run --all-files
trim trailing whitespace.................................................Passed
fix end of files.........................................................Passed
check docstring is first.................................................Passed
check yaml...............................................................Passed
debug statements (python)................................................Passed
detect private key.......................................................Passed
check that executables have shebangs.................(no files to check)Skipped
check toml...............................................................Passed
check for case conflicts.................................................Passed
check for added large files..............................................Passed
docformatter.............................................................Passed
black....................................................................Passed
isort....................................................................Passed
autoflake................................................................Passed
pyupgrade................................................................Passed
docformatter.............................................................Passed
flake8...................................................................Passed
mdformat.................................................................Passed
codespell................................................................Passed
nbstripout...........................................(no files to check)Skipped
nbqa-black...............................................................Passed
nbqa-isort...............................................................Passed
nbqa-flake8..............................................................Passed
codecov-commenter commented 1 month ago

:warning: Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

Attention: Patch coverage is 90.90909% with 1 line in your changes missing coverage. Please review.

Project coverage is 70.76%. Comparing base (b021a49) to head (8955821). Report is 2 commits behind head on dev.

Files with missing lines Patch % Lines
src/meds_torch/data/components/pytorch_dataset.py 90.90% 1 Missing :warning:

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #53 +/- ## ========================================== + Coverage 70.74% 70.76% +0.01% ========================================== Files 46 46 Lines 2868 2873 +5 ========================================== + Hits 2029 2033 +4 - Misses 839 840 +1 ```

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