skan - refs/tags/v0.13.0

skan v0.12.3

This minor release updates the minimum numba version to 0.58 to fix a pip resolution error (issue #248, fixed by PR #249, with thanks to new contributor Alister Burt!).

skan v0.12.2

This minor release added an important bug fix from Neil Shephard (#235), preventing a crash when working with float32 images.

skan v0.12.1

This minor release fixed issues with the version switcher in the documentation.

skan v0.12.0

This release adds NumPy 2.0 compatibility (while remaining compatible with 1.x) (#229). It also lays the groundwork for new skeleton editing features with bidirectional Skeleton to NetworkX conversion functions (#224.

We also have a minor deprecation that should improve quality of life in the future: column names in the summary dataframe can now use _ as the separator (instead of -), which allows one to use the pandas attribute access for columns (for example, summary.branch_distance instead of summary['branch-distance']. Use the separator='_' keyword argument to summarize to take advantage of this feature (which will become the default in a future version), or separator='-' to maintain the current behavior even when new versions come out (#215).

The napari plugin now lets you make a Shapes layer fully backed by a Skeleton dataset, including coloring the edges by features in the summary table (#201).

Thanks to Neil Shephard, James Ryan, Jarod Hanko, and Tim Monko for their contributions to this release! 🙏 You can find the full list of changes below:

API changes

• #215: The separators used for column names are configurable, and will transition to _ in the future. This is to make it easier to use the dataframe attribute interface, e.g. summary.branch_distance

New features

• #229: NumPy 2 compatibility
• #224: Create a networkx summary graph from a Skeleton
• #201: Add napari widget to generate shapes layer from a skeletonized label layer

Improvements

• #220: Allow mean pixel value calculation from integer values, not just floats
• #212: Improved error reporting and tests for prune_paths methods

Bug fixes

• #221: Fix documentation builds
• #210: Cache skeletonimage shape for use by the pathlabel_image method

Documentation

• #231: Add 0.12 release notes

Misc

• #232: Use python -m build for wheel and sdist
• #218: Fix pyproject.toml metadata formatting
• #217: Migrate from setup.cfg to pyproject.toml

- Python
Published by github-actions[bot] 8 months ago

skan - refs/tags/v0.12.3

skan v0.12.3

This minor release updates the minimum numba version to 0.58 to fix a pip resolution error (issue #248, fixed by PR #249, with thanks to new contributor Alister Burt!).

skan v0.12.2

This minor release added an important bug fix from Neil Shephard (#235), preventing a crash when working with float32 images.

skan v0.12.1

This minor release fixed issues with the version switcher in the documentation.

skan v0.12.0

This release adds NumPy 2.0 compatibility (while remaining compatible with 1.x) (#229). It also lays the groundwork for new skeleton editing features with bidirectional Skeleton to NetworkX conversion functions (#224.

We also have a minor deprecation that should improve quality of life in the future: column names in the summary dataframe can now use _ as the separator (instead of -), which allows one to use the pandas attribute access for columns (for example, summary.branch_distance instead of summary['branch-distance']. Use the separator='_' keyword argument to summarize to take advantage of this feature (which will become the default in a future version), or separator='-' to maintain the current behavior even when new versions come out (#215).

The napari plugin now lets you make a Shapes layer fully backed by a Skeleton dataset, including coloring the edges by features in the summary table (#201).

Thanks to Neil Shephard, James Ryan, Jarod Hanko, and Tim Monko for their contributions to this release! 🙏 You can find the full list of changes below:

API changes

• #215: The separators used for column names are configurable, and will transition to _ in the future. This is to make it easier to use the dataframe attribute interface, e.g. summary.branch_distance

New features

• #229: NumPy 2 compatibility
• #224: Create a networkx summary graph from a Skeleton
• #201: Add napari widget to generate shapes layer from a skeletonized label layer

Improvements

• #220: Allow mean pixel value calculation from integer values, not just floats
• #212: Improved error reporting and tests for prune_paths methods

Bug fixes

• #221: Fix documentation builds
• #210: Cache skeletonimage shape for use by the pathlabel_image method

Documentation

• #231: Add 0.12 release notes

Misc

• #232: Use python -m build for wheel and sdist
• #218: Fix pyproject.toml metadata formatting
• #217: Migrate from setup.cfg to pyproject.toml

- Python
Published by github-actions[bot] 8 months ago

skan - refs/tags/v0.12.2

skan v0.12.2

This minor release added an important bug fix from Neil Shephard (#235), preventing a crash when working with float32 images.

skan v0.12.1

This minor release fixed issues with the version switcher in the documentation.

skan v0.12.0

This release adds NumPy 2.0 compatibility (while remaining compatible with 1.x) (#229). It also lays the groundwork for new skeleton editing features with bidirectional Skeleton to NetworkX conversion functions (#224.

We also have a minor deprecation that should improve quality of life in the future: column names in the summary dataframe can now use _ as the separator (instead of -), which allows one to use the pandas attribute access for columns (for example, summary.branch_distance instead of summary['branch-distance']. Use the separator='_' keyword argument to summarize to take advantage of this feature (which will become the default in a future version), or separator='-' to maintain the current behavior even when new versions come out (#215).

The napari plugin now lets you make a Shapes layer fully backed by a Skeleton dataset, including coloring the edges by features in the summary table (#201).

Thanks to Neil Shephard, James Ryan, Jarod Hanko, and Tim Monko for their contributions to this release! 🙏 You can find the full list of changes below:

API changes

• #215: The separators used for column names are configurable, and will transition to _ in the future. This is to make it easier to use the dataframe attribute interface, e.g. summary.branch_distance

New features

• #229: NumPy 2 compatibility
• #224: Create a networkx summary graph from a Skeleton
• #201: Add napari widget to generate shapes layer from a skeletonized label layer

Improvements

• #220: Allow mean pixel value calculation from integer values, not just floats
• #212: Improved error reporting and tests for prune_paths methods

Bug fixes

• #221: Fix documentation builds
• #210: Cache skeletonimage shape for use by the pathlabel_image method

Documentation

• #231: Add 0.12 release notes

Misc

• #232: Use python -m build for wheel and sdist
• #218: Fix pyproject.toml metadata formatting
• #217: Migrate from setup.cfg to pyproject.toml

- Python
Published by github-actions[bot] about 1 year ago

skan - refs/tags/v0.12.1

skan v0.12.0

This release adds NumPy 2.0 compatibility (while remaining compatible with 1.x) (#229). It also lays the groundwork for new skeleton editing features with bidirectional Skeleton to NetworkX conversion functions (#224.

We also have a minor deprecation that should improve quality of life in the future: column names in the summary dataframe can now use _ as the separator (instead of -), which allows one to use the pandas attribute access for columns (for example, summary.branch_distance instead of summary['branch-distance']. Use the separator='_' keyword argument to summarize to take advantage of this feature (which will become the default in a future version), or separator='-' to maintain the current behavior even when new versions come out (#215).

The napari plugin now lets you make a Shapes layer fully backed by a Skeleton dataset, including coloring the edges by features in the summary table (#201).

Thanks to Neil Shephard, James Ryan, Jarod Hanko, and Tim Monko for their contributions to this release! 🙏 You can find the full list of changes below:

API changes

• #215: The separators used for column names are configurable, and will transition to _ in the future. This is to make it easier to use the dataframe attribute interface, e.g. summary.branch_distance

New features

• #229: NumPy 2 compatibility
• #224: Create a networkx summary graph from a Skeleton
• #201: Add napari widget to generate shapes layer from a skeletonized label layer

Improvements

• #220: Allow mean pixel value calculation from integer values, not just floats
• #212: Improved error reporting and tests for prune_paths methods

Bug fixes

• #221: Fix documentation builds
• #210: Cache skeletonimage shape for use by the pathlabel_image method

Documentation

• #231: Add 0.12 release notes

Misc

• #232: Use python -m build for wheel and sdist
• #218: Fix pyproject.toml metadata formatting
• #217: Migrate from setup.cfg to pyproject.toml

- Python
Published by github-actions[bot] over 1 year ago

skan - refs/tags/v0.12.0

skan v0.12.0

This release adds NumPy 2.0 compatibility (while remaining compatible with 1.x) (#229). It also lays the groundwork for new skeleton editing features with bidirectional Skeleton to NetworkX conversion functions (#224.

We also have a minor deprecation that should improve quality of life in the future: column names in the summary dataframe can now use _ as the separator (instead of -), which allows one to use the pandas attribute access for columns (for example, summary.branch_distance instead of summary['branch-distance']. Use the separator='_' keyword argument to summarize to take advantage of this feature (which will become the default in a future version), or separator='-' to maintain the current behavior even when new versions come out (#215).

The napari plugin now lets you make a Shapes layer fully backed by a Skeleton dataset, including coloring the edges by features in the summary table (#201).

Thanks to Neil Shephard, James Ryan, Jarod Hanko, and Tim Monko for their contributions to this release! 🙏 You can find the full list of changes below:

API changes

• #215: The separators used for column names are configurable, and will transition to _ in the future. This is to make it easier to use the dataframe attribute interface, e.g. summary.branch_distance

New features

• #229: NumPy 2 compatibility
• #224: Create a networkx summary graph from a Skeleton
• #201: Add napari widget to generate shapes layer from a skeletonized label layer

Improvements

• #220: Allow mean pixel value calculation from integer values, not just floats
• #212: Improved error reporting and tests for prune_paths methods

Bug fixes

• #221: Fix documentation builds
• #210: Cache skeletonimage shape for use by the pathlabel_image method

Documentation

• #231: Add 0.12 release notes

Misc

• #232: Use python -m build for wheel and sdist
• #218: Fix pyproject.toml metadata formatting
• #217: Migrate from setup.cfg to pyproject.toml

- Python
Published by github-actions[bot] over 1 year ago

skan - refs/tags/v0.11.0

skan v0.11.0

This release of skan incorporates several bug fixes, new API features, and documentation improvements. It also finalizes an API change started in 0.10.0: now junction points are always resolved using a minimum spanning tree, and the uniquify_junctions and junction_mode arguments to Skeleton are deprecated (see our FAQ). Finally, this is the first release containing a napari plugin! Currently all it does is skeletonize a Labels layer, but this is just the beginning for GUI-based skeleton analysis.

Thanks to everyone who has helped make this release possible, including Kushaan Gupta, Lucy Liu, Ryan Ly, James Ryan, and Simon Savary! Not to speak of all the contributors who make our upstream libraries possible! 🙏

API changes

• #143: the unique_junctions and junction_mode keyword arguments are removed. Junctions are always resolved by finding the minimum spanning tree of the junction pixels. This PR also speeds up building of the pixel graph.

New features

• #150, #164: add Sholl analysis. (Thanks to Kushaan Gupta for the collaboration that led to this feature!)
• #184: add napari plugin.

Bug fixes

• #152: Some pixel graphs had missing paths in their skeletons because of a mistake in how the graphs were traversed. Thanks Simon Savary for the detailed report that led to the fix! (#147)
• #193, #183: fix the calculation of the buffer size needed for the pixel path graph in the presence of 0-degree nodes (isolated pixels).
• #135: the unique_junctions keyword argument to the Skeleton class is deprecated. Use instead junction_mode. Note however that this option will be removed in 0.11, so you should pin your skan dependency if you need this behavior.
• #139: the skan GUI and corresponding skan.gui module and skan command have all been removed. A new, much more sophisticated napari plugin is in development at https://github.com/kevinyamauchi/napari-skeleton-curator and will be folded into a future version of skan (probably v0.11).

Documentation

• #155, #156, #159: Add documentation on 3D display of skeletons in napari.
• #173, #175, #177: support multiple versions of documentation. (!) (This series of PRs in particular is close to my heart because deprecations and API changes like those listed above are much more painful if the old versions are just erased! Thanks to Lucy Liu for her efforts and expertise here!)
• #194, #195: overhaul of documentation and build infrastructure.

Misc

• #167: drop Python 3.7 support.
• #188, #189, #190: update requirements.

- Python
Published by github-actions[bot] about 3 years ago

skan -

- Python
Published by github-actions[bot] about 3 years ago

skan -

skan v0.10.0rc0

This is a major release of skan that changes, removes, or deprecates much functionality. As skan has grown in popularity, we've been working hard to clean out the warts and kinks in the API, improve compatibility with libraries such as dask, and fix several bugs reported by users. This has brought one major change in how skan computes branch lengths (#135): junctions are now cleaned up by computing their minimum spanning tree rather than by computing their centroid (see the FAQ). This change can be reverted with a keyword argument in this version (junction_mode='centroid'), but will be mandatory in upcoming versions. If you need to preserve the old results, pin skan to <v0.11.

Thanks to Genevieve Buckley, Marianne Corvellec, Zoltan Csati, Marlene da Vitoria Lobo, and Kevin Yamauchi for their contributions!

API changes

• #135: the unique_junctions keyword argument to the Skeleton class is deprecated. Use instead junction_mode. Note however that this option will be removed in 0.11, so you should pin your skan dependency if you need this behavior.
• #139: the skan GUI and corresponding skan.gui module and skan command have all been removed. A new, much more sophisticated napari plugin is in development at https://github.com/kevinyamauchi/napari-skeleton-curator and will be folded into a future version of skan (probably v0.11).

Improvements

• skan tests now pass on GitHub Actions on all platforms (#139).
• skan documentation is now built and deployed on GitHub Actions (#140).
• skan releases are created using GitHub Actions (#141).
• the skan code base is now formatted by yapf (#136).
• skan is now easier to adapt for dask arrays (though there is still much work to be done here) ((#107, #112 and #123).

- Python
Published by github-actions[bot] over 4 years ago

skan -

skan v0.10.0rc0

This is a major release of skan that changes, removes, or deprecates much functionality. As skan has grown in popularity, we've been working hard to clean out the warts and kinks in the API, improve compatibility with libraries such as dask, and fix several bugs reported by users. This has brought one major change in how skan computes branch lengths (#135): junctions are now cleaned up by computing their minimum spanning tree rather than by computing their centroid (see the FAQ). This change can be reverted with a keyword argument in this version (junction_mode='centroid'), but will be mandatory in upcoming versions. If you need to preserve the old results, pin skan to <v0.11.

Thanks to Genevieve Buckley, Marianne Corvellec, Zoltan Csati, Marlene da Vitoria Lobo, and Kevin Yamauchi for their contributions!

API changes

• #135: the unique_junctions keyword argument to the Skeleton class is deprecated. Use instead junction_mode. Note however that this option will be removed in 0.11, so you should pin your skan dependency if you need this behavior.
• #139: the skan GUI and corresponding skan.gui module and skan command have all been removed. A new, much more sophisticated napari plugin is in development at https://github.com/kevinyamauchi/napari-skeleton-curator and will be folded into a future version of skan (probably v0.11).

Improvements

• skan tests now pass on GitHub Actions on all platforms (#139).
• skan documentation is now built and deployed on GitHub Actions (#140).
• skan releases are created using GitHub Actions (#141).
• the skan code base is now formatted by yapf (#136).
• skan is now easier to adapt for dask arrays (though there is still much work to be done here) ((#107, #112 and #123).

- Python
Published by github-actions[bot] over 4 years ago