0.12.6
🐛 Bug Fixes
Fix untiling corner-case when no padding in one dimension @rossbar (#673)
What
Closes #665. As noted there, the issue arises from pads of (0, 0) which subsequently lead to 0:0 slices in untiling, giving arrays with shape 0 for that dimension.
AFAICT, the only way to hit this corner case is when one of the dimensions is smaller than model_image_shape, but the other is exactly model_image_shape. If both dimensions are >= model_image_shape, then padding should be False if I'm following the logic correctly.
Why
Bugfix
🧰 Maintenance
Bump version for 0.12.6 release @msschwartz21 (#674)
Update nuclear segmentation and tracking notebooks @msschwartz21 (#671)
This PR updates the three notebooks that are associated with the tracking paper to match our current scripts for training and running the application. I tested each notebook to verify that everything runs.
Update nuclear tracking and segmentation model paths @msschwartz21 (#666)
This PR updates the models used by the NuclearSegmentation and CellTracking applications to the latest versions associated with the upcoming paper.
Cleanup related to transitioning from pylint -> ruff @rossbar (#661)
What
Update codebase to reflect the adoption of ruff instead of pylint.
- Removes pylint configs & pylint ignore flags
- Updates the contributor guide
Why
General cleanup.
Apply pyupgrade to update code style @rossbar (#662)
What
This PR applies pyupgrade (via ruff) to automatically modernize some coding patterns. The way this works: you tell pyupgrade what minimum version of Python you support (3.7 in our case), then it automatically applies linting patterns based on language features in the minimum supported version.
The changes here generally fall in the following categories:
- Stop inheriting from object
- Remove
from __future__imports - Remove super() args in cases of single inheritance
- Automatically convert older-style string formatting to fstrings.
Why
The main improvement is removing cruft related to old Python versions - perhaps the most notable is the removal of the from __future__ imports and related dels in the __init__.py files. The automatic switch to f-strings is also (IMO) a nice improvement.
📚️ Documentation
Update nuclear segmentation and tracking notebooks @msschwartz21 (#671)
This PR updates the three notebooks that are associated with the tracking paper to match our current scripts for training and running the application. I tested each notebook to verify that everything runs.
