Deepcell-toolbox

Latest version: v0.12.1

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0.12.0

🧰 Maintenance

<details>
<summary>MAINT: update deprecated code from dependencies and remove warnings filters rossbar (131)</summary>

The current pytest configuration is [suppressing all deprecation warnings](https://github.com/vanvalenlab/deepcell-toolbox/blob/fd398ebf1b21e313870aed745413503dacfb29f2/pytest.ini#L6-L9), which includes warnings from dependency libraries. This makes it much more likely for code to fall out-of-date, as can be seen in [the recent failing CI jobs](https://github.com/vanvalenlab/deepcell-toolbox/actions/runs/3734920418/jobs/6337547681) due to changes in the lastest version of numpy which was just releases (1.24).

This PR addresses the issue in two ways:
1. Updates code to take into account changes in the underlying libraries, and
2. Removes the global warnings filter in favor of fine-grained warnings filtering.

The second bullet involves adding explicit checks for warnings raised by `deepcell-toolbox` itself, to ensure that warnings are being raised correctly in the expected cases.
</details>

<details>
<summary>Add Python3.10 support rossbar (128)</summary>

Adds support for Python 3.10. No changes to the underlying library but some dependency updates were required, the main ones being:
- removing the upper-bound on `pytest`, and
- Dropping the `pytest-pep8` extension, which [hasn't been actively maintained in over 8 years](https://pypi.org/project/pytest-pep8/#history)

We can of course re-add code linting using different tooling - I'm happy to do so but would prefer to leave it for a follow-up PR.
</details>

0.11.2

🧰 Maintenance

<details>
<summary>Release numpy upper bound msschwartz21 (125)</summary>

This PR supports https://github.com/vanvalenlab/deepcell-tf/pull/595 which upgrades tensorflow to 2.8 and allows new versions of numpy.
</details>

0.11.1

🐛 Bug Fixes

<details>
<summary>Correct dice property to return dice statistic msschwartz21 (122)</summary>

Addresses the bug identified in 121.
</details>


🧰 Maintenance

<details>
<summary>Update copyright to 2022 msschwartz21 (123)</summary>

Also bump up version for the next release
</details>

0.11.0

🚀 Features

<details>
<summary>Remove `correct_drift` to support the new `skimage` release 0.19.0. willgraf (119)</summary>

- Use `segmentation.watershed` instead of `morphology.watershed`.
- Remove `correct_drift` (Fixes 6) and `register_translation` is removed in 0.19.x.
- Set array slices with tuples to prevent warnings.
- Update `skimage` version requirements to avoid bug in `peak_local_max` in 0.16.x and 0.17.x.
</details>


🐛 Bug Fixes

<details>
<summary>Pin python-version to 3.8 for PyPI deployment. willgraf (120)</summary>

numpy restriction for the toolbox requires Python < 3.10
</details>

<details>
<summary>Remove `correct_drift` to support the new `skimage` release 0.19.0. willgraf (119)</summary>

- Use `segmentation.watershed` instead of `morphology.watershed`.
- Remove `correct_drift` (Fixes 6) and `register_translation` is removed in 0.19.x.
- Set array slices with tuples to prevent warnings.
- Update `skimage` version requirements to avoid bug in `peak_local_max` in 0.16.x and 0.17.x.
</details>

<details>
<summary>Set Recall, Precision, and SEG to all have same scale. willgraf (118)</summary>

Precision and SEG were being multiplied by 100 while Recall was not. This removes the 100x casting to make all metrics be in the same range [0, 1].

Additionally, fixes the `norecursedirs` value in `pytest.ini` to be space-delimited instead of comma-delimited.

Finally, pins `coveralls<3.3.0` to prevent a breaking change in the latest release.

Fixes 117
</details>


🧰 Maintenance

<details>
<summary>Move `compute_overlap_3D` into `compute_overlap.pyx` willgraf (116)</summary>

No need to have each function in their own files.
</details>

0.10.3

🐛 Bug Fixes

<details>
<summary>Pin `scikit-image` to < 0.19.0. willgraf (119)</summary>

Resolves a breaking change in the new release causing import issues.
</details>

0.10.2

🐛 Bug Fixes

<details>
<summary>Optimize hole filling algorithm ngreenwald (114)</summary>

This PR closes 113. It replaces the previous hole-filling algorithm with an optimized, regionprops-based version. The remaining bottleneck in the post-processing is now peak finding, so the warning message for large images is now raised when `h_maxima` is selected for large images instead of `peak_local_max`
</details>


🧰 Maintenance

<details>
<summary>Bump version to `0.10.2`. willgraf (115)</summary>


</details>

<details>
<summary>Update name from Deepcell to DeepCell to match other projects. willgraf (112)</summary>


</details>

<details>
<summary>Cache the entire Python environment to speed up build times. willgraf (111)</summary>

What
* Cache the entire Python environment in the testing GitHub Action workflow.

Why
* [Drastically speed up build times](https://medium.com/ai2-blog/python-caching-in-github-actions-e9452698e98d).

</details>

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