Enhancements and refactoring: Ruff checks resolved

MilagrosMarin commented 3 weeks ago

This PR closes #441 and #417 by removing the exclusion of ruff checks for dj_pipeline from pyproject.toml.

[x] UPDATE: I’ve added comments in this PR to highlight code changes and make the review process easier for reviewers.
[x] UPDATE2: the following changes have been reverted:
- [x] Revert black formatting ( revert max line length to 88 instead of 105)
- [x] Revert changes in streams.py
- [x] Revert changes about Assertion replacement in tests

This is a summary of the relevant changes that have been implemented, with all checks passing:

Resolved issues for `aeon/dj_pipeline`:

[x] B006: Fixed mutable default argument in plotting.py.
[x] B021: Removed dynamic references and made the docstring static in DeviceDataStream.key_source, ensuring it remains informative.
[x] D101, D102, D103, D105, D106: Added new docstrings.
[x] E501: Corrected most lines that were too long, adding exceptions in a few cases to preserve the intended meaning.
[x] D202, D205: Improved docstring formatting.
[x] F401, F403: Removed unused imported dependencies.
[x] I001: Sorted dependencies.
[x] B905: Added strict=False to the zip function to prevent the function from raising a ValueError if the iterables passed to it do not have the same length.
[x] Security: Replaced hashlib.md5 with hashlib.sha256 due to known vulnerabilities in the MD5 hashing algorithm -> Reverted: Change was reverted, and an ignore rule was added due to potential breakage introduced by the update.
[x] B904: Enhanced exception handling by using as err and raising exceptions with raise ... from err to differentiate errors.
[x] UP038: Used the new X | Y syntax for isinstance calls, as introduced in Python 3.10.
[x] PLR2004: Replaced magic values with constant variables.
[x] SIM108: Refactored visit_analysis to use the ternary operator.
[x] Removed checks from pyproject.toml list: No issues found for B006, B021, S110, UP038, E999, E722, F821, S324, S605, S607, E999, PLR2004.
[x] README.md: Added some text.
[x] Refactor: Updated the read method in the JsonList class within aeon/io/reader.py.
[x] E741: Renamed the variables in gen_hex_grad in aeon/analysis/block_plotting.py.
[x] Refactor: Made improvements to dictionary handling in aeon/analysis/block_plotting.py.
[x] # noqa Exceptions: Added # noqa comments for specific cases, e.g., in reader for F821 and # noqa PLW0127 for visit_analysis.py.

Additional fixes to the rest of the reporitory:

In addition to the above changes, I have also resolved most of the ruff lint issues from the ignored list in pyproject.toml, ensuring all checks passed:

[x] D100, D104, D105, D107: Added missing docstrings.
[x] E201, E202, E203, E231, E702: Corrected whitespace and formatting.
[x] S101: Replaced assertions with exceptions to ensure expected behavior in all scenarios; also added logger=dj.logger where appropriate. -> Reverted assertions replacement in tests and added rule in pyproject since it is acceptable to use for small, simple tests.
[x] PT013: Fixed the import of pytest in tests.
[x] pyproject.toml updated accordingly
[x] All checks passed after the latest changes in this PR.

Deprecation Fix:

Updated all instances of datetime.utcnow() to datetime.now(timezone.utc) to address deprecation issues.

MilagrosMarin commented 3 weeks ago

@ttngu207 I’ve incorporated all the changes we discussed during the PR review.

jkbhagatio commented 2 weeks ago

Can we re- remove ignoring ruff d104 and d100 errors in the pyproject.toml in this PR as well?

lochhh commented 2 weeks ago

Can we re- remove ignoring ruff d104 and d100 errors in the pyproject.toml in this PR as well?

wdym? I thought this was already the case? These are all that's left 🎉 https://github.com/SainsburyWellcomeCentre/aeon_mecha/blob/48493cbc0de8b6e2a5e20bcebc0f30f3f7e6719b/pyproject.toml#L99-L106

MilagrosMarin commented 1 week ago

@lochhh and @ttngu207 , thank you both so much for your reviews! I’ve completed the third round of review for this PR. Since there were many new suggestions in different forms, could you please @lochhh give it a final review? Thank you!

ttngu207 commented 3 days ago

Thanks @MilagrosMarin for addressing all comments. I made another PR here with some final suggestions. And just one last comment about noqa B023 here:

https://github.com/SainsburyWellcomeCentre/aeon_mecha/blob/6279bda3faa16916a2a84226e9ee82e669a88367/aeon/io/reader.py#L164

If it's too much trouble to test this we can also keep the current change.

I have tested this, good to go here

ttngu207 commented 3 days ago

All comments/suggestions have been addressed/resolved PR merged

SainsburyWellcomeCentre / aeon_mecha