Cucim

Latest version: v23.10.0

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23.10.00

🐛 Bug Fixes

- Use `conda mambabuild` not `mamba mambabuild` ([607](https://github.com/rapidsai/cucim/pull/607)) [bdice](https://github.com/bdice)

📖 Documentation

- minor updates to release 23.08 changelog ([605](https://github.com/rapidsai/cucim/pull/605)) [grlee77](https://github.com/grlee77)

🛠️ Improvements

- Update image names ([609](https://github.com/rapidsai/cucim/pull/609)) [AyodeAwe](https://github.com/AyodeAwe)
- Use `copy-pr-bot` ([606](https://github.com/rapidsai/cucim/pull/606)) [ajschmidt8](https://github.com/ajschmidt8)

23.08.00

🚨 Breaking Changes

- Sync cuCIM API with scikit-image 0.21 ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)
- The `random_state` argument of medial_axis and unsupervised_wiener is now deprecated and will be removed in the future. The new argument name, `seed`, should be used instead. ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)
- The existing function `cucim.skimage.color.get_xyz_coords` has been renamed `cucim.skimage.color.xyz_tristimulus_values`. The former function name is deprecated and will be removed in the future. ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)

🐛 Bug Fixes

- Remove libwebp-base upper bound. ([599](https://github.com/rapidsai/cucim/pull/599)) [bdice](https://github.com/bdice)
- Fix ignore_run_exports_from. ([596](https://github.com/rapidsai/cucim/pull/596)) [bdice](https://github.com/bdice)
- Add ignore_run_exports for CUDA 11 ([593](https://github.com/rapidsai/cucim/pull/593)) [raydouglass](https://github.com/raydouglass)
- Use linalg & inline `_get_manders_overlap_coeff` ([578](https://github.com/rapidsai/cucim/pull/578)) [jakirkham](https://github.com/jakirkham)
- Fix canny and butterworth (recent CuPy and NumPy compatibility) ([574](https://github.com/rapidsai/cucim/pull/574)) [grlee77](https://github.com/grlee77)
- A bug was fixed in 2D shear calculations for AffineTransform. ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)
- A bug was fixed in the energy calculation of `cucim.skimage.segmentation.chan_vese`. This fix may result in different output from previous versions. ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)

🛠️ Improvements

- The formerly private function `_invariant_denoise` has been renamed `denoise_invariant` and is now part of the public `cucim.skimage.restoration` API ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)
- A new `return_mapping` option was added to `cucim.skimage.segmentation.join_segmentations`. This provides an additional output with a mapping between the labels in the joined segmentation and the original ones. ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)
- Added support for y-axis shear to the 2D AffineTransform. ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)
- Postponed the assessment of GPU memory for testing ([601](https://github.com/rapidsai/cucim/pull/601)) [gigony](https://github.com/gigony)
- Do not use x86_64 GDS binaries for aarch64 ([590](https://github.com/rapidsai/cucim/pull/590)) [gigony](https://github.com/gigony)
- remove checks for versions of scikit-image that are no longer supported ([587](https://github.com/rapidsai/cucim/pull/587)) [grlee77](https://github.com/grlee77)
- Allow scikit-image 0.21.0 ([580](https://github.com/rapidsai/cucim/pull/580)) [jakirkham](https://github.com/jakirkham)
- Drop unneeded selector on `libwebp-base` ([579](https://github.com/rapidsai/cucim/pull/579)) [jakirkham](https://github.com/jakirkham)
- switch from bundled lazy loading code to the public lazy_loader package ([575](https://github.com/rapidsai/cucim/pull/575)) [grlee77](https://github.com/grlee77)
- Sync cuCIM API with scikit-image 0.21 ([573](https://github.com/rapidsai/cucim/pull/573)) [grlee77](https://github.com/grlee77)
- cuCIM: Build CUDA 12 packages ([572](https://github.com/rapidsai/cucim/pull/572)) [jakirkham](https://github.com/jakirkham)
- use rapids-upload-docs script ([570](https://github.com/rapidsai/cucim/pull/570)) [AyodeAwe](https://github.com/AyodeAwe)
- Remove documentation build scripts for Jenkins ([567](https://github.com/rapidsai/cucim/pull/567)) [ajschmidt8](https://github.com/ajschmidt8)

23.06.00

🚨 Breaking Changes

- Support Python 3.9 build/tests ([547](https://github.com/rapidsai/cucim/pull/547)) [shwina](https://github.com/shwina)

🐛 Bug Fixes

- Fix SHA256 check failure in test suite ([564](https://github.com/rapidsai/cucim/pull/564)) [grlee77](https://github.com/grlee77)
- Handle space character in ./run download_testdata ([556](https://github.com/rapidsai/cucim/pull/556)) [gigony](https://github.com/gigony)
- Fix `return_error=&39;always&39;` behavior in phase_cross_correlation ([549](https://github.com/rapidsai/cucim/pull/549)) [grlee77](https://github.com/grlee77)
- Only load versioned `libcufile` ([548](https://github.com/rapidsai/cucim/pull/548)) [jakirkham](https://github.com/jakirkham)
- add a 20 minute timeout for pytest runs on CI ([545](https://github.com/rapidsai/cucim/pull/545)) [grlee77](https://github.com/grlee77)
- protect against possible out of bounds memory access in 2D distance transform ([540](https://github.com/rapidsai/cucim/pull/540)) [grlee77](https://github.com/grlee77)

📖 Documentation

- Fix doc building via `run build_package` ([553](https://github.com/rapidsai/cucim/pull/553)) [grlee77](https://github.com/grlee77)
- update changelog for release 23.04.00 and 23.04.01 ([552](https://github.com/rapidsai/cucim/pull/552)) [grlee77](https://github.com/grlee77)

🛠️ Improvements

- Allow numpy 1.24. ([563](https://github.com/rapidsai/cucim/pull/563)) [bdice](https://github.com/bdice)
- run docs nightly too ([560](https://github.com/rapidsai/cucim/pull/560)) [AyodeAwe](https://github.com/AyodeAwe)
- Update cupy dependency ([558](https://github.com/rapidsai/cucim/pull/558)) [vyasr](https://github.com/vyasr)
- Remove libjpeg dependency ([557](https://github.com/rapidsai/cucim/pull/557)) [gigony](https://github.com/gigony)
- Enable sccache hits from local builds ([551](https://github.com/rapidsai/cucim/pull/551)) [AyodeAwe](https://github.com/AyodeAwe)
- Revert shared workflows branch ([550](https://github.com/rapidsai/cucim/pull/550)) [ajschmidt8](https://github.com/ajschmidt8)
- Support Python 3.9 build/tests ([547](https://github.com/rapidsai/cucim/pull/547)) [shwina](https://github.com/shwina)
- Remove usage of rapids-get-rapids-version-from-git ([546](https://github.com/rapidsai/cucim/pull/546)) [jjacobelli](https://github.com/jjacobelli)
- Use ARC V2 self-hosted runners for GPU jobs ([538](https://github.com/rapidsai/cucim/pull/538)) [jjacobelli](https://github.com/jjacobelli)
- Remove underscore in build string. ([528](https://github.com/rapidsai/cucim/pull/528)) [bdice](https://github.com/bdice)

23.04.01

🛠️ Improvements

- Pin libwebp-base ([541](https://github.com/rapidsai/cucim/pull/541)) [ajschmidt8](https://github.com/ajschmidt8)

23.04.00

🚨 Breaking Changes

- Fix inefficiency in handling clipping of image range in `resize` and other transforms ([516](https://github.com/rapidsai/cucim/pull/516)) [grlee77](https://github.com/grlee77)

🐛 Bug Fixes

- Fix bug in median filter with non-uniform footprint ([521](https://github.com/rapidsai/cucim/pull/521)) [grlee77](https://github.com/grlee77)
- use cp.around instead of cp.round for CuPy 10.x compatiblity ([508](https://github.com/rapidsai/cucim/pull/508)) [grlee77](https://github.com/grlee77)
- Fix error in LZ4-compressed Zarr writing demo ([506](https://github.com/rapidsai/cucim/pull/506)) [grlee77](https://github.com/grlee77)
- Normalize whitespace. ([474](https://github.com/rapidsai/cucim/pull/474)) [bdice](https://github.com/bdice)

🛠️ Improvements

- allow scikit-image 0.20 as well ([536](https://github.com/rapidsai/cucim/pull/536)) [grlee77](https://github.com/grlee77)
- Pass `AWS_SESSION_TOKEN` and `SCCACHE_S3_USE_SSL` vars to conda build ([525](https://github.com/rapidsai/cucim/pull/525)) [ajschmidt8](https://github.com/ajschmidt8)
- Update aarch64 to GCC 11 ([524](https://github.com/rapidsai/cucim/pull/524)) [bdice](https://github.com/bdice)
- Update to GCC 11 ([522](https://github.com/rapidsai/cucim/pull/522)) [bdice](https://github.com/bdice)
- Upgrade dockcross and pybind11 ([519](https://github.com/rapidsai/cucim/pull/519)) [gigony](https://github.com/gigony)
- Binary morphology: omit weights array when possible ([517](https://github.com/rapidsai/cucim/pull/517)) [grlee77](https://github.com/grlee77)
- Fix inefficiency in handling clipping of image range in `resize` and other transforms ([516](https://github.com/rapidsai/cucim/pull/516)) [grlee77](https://github.com/grlee77)
- Fix GHA build workflow ([515](https://github.com/rapidsai/cucim/pull/515)) [AjayThorve](https://github.com/AjayThorve)
- Reduce error handling verbosity in CI tests scripts ([511](https://github.com/rapidsai/cucim/pull/511)) [AjayThorve](https://github.com/AjayThorve)
- Update shared workflow branches ([510](https://github.com/rapidsai/cucim/pull/510)) [ajschmidt8](https://github.com/ajschmidt8)
- Remove gpuCI scripts. ([505](https://github.com/rapidsai/cucim/pull/505)) [bdice](https://github.com/bdice)
- Move date to build string in `conda` recipe ([497](https://github.com/rapidsai/cucim/pull/497)) [ajschmidt8](https://github.com/ajschmidt8)

23.02.00

🚨 Breaking Changes

- Add disambiguation option to phase_cross_correlation (skimage 0.20 feature) ([486](https://github.com/rapidsai/cucim/pull/486)) [grlee77](https://github.com/grlee77)

🐛 Bug Fixes

- apply bug fix to vendored ndimage code ([494](https://github.com/rapidsai/cucim/pull/494)) [grlee77](https://github.com/grlee77)
- Closes 490 -- fixes bug in hue jitter ([491](https://github.com/rapidsai/cucim/pull/491)) [benlansdell](https://github.com/benlansdell)
- Fix random seed used in test_3d_similarity_estimation ([472](https://github.com/rapidsai/cucim/pull/472)) [grlee77](https://github.com/grlee77)

📖 Documentation

- Fix documentation author ([475](https://github.com/rapidsai/cucim/pull/475)) [bdice](https://github.com/bdice)

🚀 New Features

- Add colocalization measures ([488](https://github.com/rapidsai/cucim/pull/488)) [grlee77](https://github.com/grlee77)
- Add disambiguation option to phase_cross_correlation (skimage 0.20 feature) ([486](https://github.com/rapidsai/cucim/pull/486)) [grlee77](https://github.com/grlee77)

🛠️ Improvements

- Update shared workflow branches ([501](https://github.com/rapidsai/cucim/pull/501)) [ajschmidt8](https://github.com/ajschmidt8)
- Update `isort` version to 5.12.0 ([492](https://github.com/rapidsai/cucim/pull/492)) [ajschmidt8](https://github.com/ajschmidt8)
- Improve rank filtering performance by removing use of footprint kernel when possible ([485](https://github.com/rapidsai/cucim/pull/485)) [grlee77](https://github.com/grlee77)
- use vendored version of cupy.pad with added performance optimizations ([482](https://github.com/rapidsai/cucim/pull/482)) [grlee77](https://github.com/grlee77)
- add docs builds to Github Actions ([481](https://github.com/rapidsai/cucim/pull/481)) [AjayThorve](https://github.com/AjayThorve)
- Update `numpy` version specifier ([480](https://github.com/rapidsai/cucim/pull/480)) [ajschmidt8](https://github.com/ajschmidt8)
- Build CUDA `11.8` and Python `3.10` Packages ([476](https://github.com/rapidsai/cucim/pull/476)) [ajschmidt8](https://github.com/ajschmidt8)
- Add GitHub Actions Workflows. ([471](https://github.com/rapidsai/cucim/pull/471)) [bdice](https://github.com/bdice)
- Fix conflicts in "Forward-merge branch-22.12 to branch-23.02" ([468](https://github.com/rapidsai/cucim/pull/468)) [jakirkham](https://github.com/jakirkham)
- Enable copy_prs. ([465](https://github.com/rapidsai/cucim/pull/465)) [bdice](https://github.com/bdice)

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