Release 0.3.0 (#2021)

* updating CHANGELOG.md for release 0.3.0

* scikit-image version issue: replacing selem with footprint

* adding symbolic link to data folder for osm pipeline example

* skipping starmap pipeline example due to high memory requirements (>32Gb)

* correcting Operating System classifier in setup.cfg

CHANGELOG.md

@@ -1,3 +1,43 @@
+## [0.3.0] - 2024-10-05
+- Dropping support for Python 3.8 and setting Python 3.9 as minimum (#2018)
+- Update readthedocs.yml (#2014)
+- Scripts and dependencies updates for Python 3.8 - 3.10 (#2009)
+- Add min_distance parameter to peak_local_max call (#2008)
+- Various Small Fixes/Improvements (#1985)
+- Updated seqFISH Decoding Method: CheckAll Decoder (#1978)
+- Bump dask from 2021.9.0 to 2021.10.0 in /requirements (#1968)
+- Revert "Revert "Fix coords assignment in CombineAdjustFeatures.run (#1965)" (#1966)" (#1967)
+- Revert "Fix coords assignment in CombineAdjustFeatures.run (#1965)" (#1966)
+- Fix coords assignment in CombineAdjustFeatures.run (#1965)
+- Add to_dict and from_dict methods to TransformsList class (#1956)
+- fix notebook tests
+- Fix check-notebooks makefile command; Add python 3.9 to slow-tests
+- Fix Sphinx docs
+- Register pytest markers
+- Remove is_volume param from testing TrackpyLocalMaxPeakFinder invocation
+- Address skimage deprecation of skimage.morphology.watershed
+- Address Xarray pending deprecation for GroupBy.apply
+- Remove usage of deprecated numpy builtin types like np.bool/np.int
+- Add n_processes parameter to FindSpotsAlgorithm.run() abstract method
+- Remove deprecated `indices` param for skimage.feature.peak_local_max
+- Resolve failure when `peak_local_max()` finds no spots
+- Fix failing nearest neighbor trace builder tests
+- Fix composite codebook decoder tests
+- Change default value of BlobDetector exclude_border parameter to False
+- Fix incorrect type annotation and improper `.data()` method call
+- Fix failing morphology utility functions
+- Fix failing LearnTransform Translation class
+- Fix failing Codebook and IntensityTable shape validator
+- Fix failing Codebook.decode_per_round_max() test
+- Update .gitignore file
+- Defer when docker-smoketest github actiosn job is run
+- Bump requirements to clear github actions cache
+- Fix broken github actions Lint job; Fix broken caching
+- Address Mypy type annotation errors
+- Update github actions to use caching; Disable Napari tests for now
+- Use `python -m pip install ...` to perform pip upgrade
+- Replace Travis CI with Github Actions
+
 ## [0.2.2] - 2021-04-29
 - Updates requirements
 - Updates to documentation
@@ -233,6 +273,7 @@
 ## [0.0.33] - 2019.02.14
 - Last release without a changelog!
 
+[0.3.0]: https://github.com/spacetx/starfish/releases/tag/0.3.0
 [0.2.2]: https://github.com/spacetx/starfish/releases/tag/0.2.2
 [0.2.1]: https://github.com/spacetx/starfish/releases/tag/0.2.1
 [0.2.0]: https://github.com/spacetx/starfish/releases/tag/0.2.0

examples/pipelines/baristaseq_pipeline.py

@@ -185,7 +185,7 @@
 from functools import partial
 
 # calculate the background
-opening = partial(opening, selem=disk(5))
+opening = partial(opening, footprint=disk(5))
 
 background = bleed_corrected.apply(
     opening,
@@ -289,4 +289,4 @@ def plot_scaling_result(
     *np.unique(pixel_decoded['target'], return_counts=True)[::-1]
 )
 
-print(pixel_decoded_gene_counts.sort_values(ascending=False)[:20])
+print(pixel_decoded_gene_counts.sort_values(ascending=False)[:20])

examples/pipelines/data

@@ -0,0 +1 @@
+../../notebooks/data

setup.cfg

@@ -25,7 +25,7 @@ classifier =
     Operating System :: POSIX
     Operating System :: Unix
     Operating System :: MacOS :: MacOS X
-    Operating System :: Windows
+    Operating System :: Microsoft :: Windows
     License :: OSI Approved :: MIT License
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3.9