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[RELEASE] cucim v21.10 #121

Merged
merged 17 commits into from
Oct 7, 2021
Merged

[RELEASE] cucim v21.10 #121

merged 17 commits into from
Oct 7, 2021

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❄️ Code freeze for branch-21.10 and v21.10 release

What does this mean?

Only critical/hotfix level issues should be merged into branch-21.10 until release (merging of this PR).

What is the purpose of this PR?

  • Update documentation
  • Allow testing for the new release
  • Enable a means to merge branch-21.10 into main for the release

raydouglass and others added 17 commits July 15, 2021 17:03
@raydouglass
DOC v21.10 Updates
d161fce
@GPUtester
Merge pull request #70 from rapidsai/branch-21.08
9f6962e 
[gpuCI] Forward-merge branch-21.08 to branch-21.10 [skip ci]
@GPUtester
Merge pull request #74 from rapidsai/branch-21.08
65f3e42 
[gpuCI] Forward-merge branch-21.08 to branch-21.10 [skip ci]
@GPUtester
Merge pull request #76 from rapidsai/branch-21.08
95b0813 
[gpuCI] Forward-merge branch-21.08 to branch-21.10 [skip ci]
@GPUtester
Merge pull request #77 from rapidsai/branch-21.08
4242848 
[gpuCI] Forward-merge branch-21.08 to branch-21.10 [skip ci]
@GPUtester
Merge pull request #78 from rapidsai/branch-21.08
4696041 
[gpuCI] Forward-merge branch-21.08 to branch-21.10 [skip ci]
@GPUtester
Merge pull request #80 from rapidsai/branch-21.08
21007fd 
[gpuCI] Forward-merge branch-21.08 to branch-21.10 [skip ci]
@GPUtester
Merge pull request #81 from rapidsai/branch-21.08
6cd95fc 
[gpuCI] Forward-merge branch-21.08 to branch-21.10 [skip gpuci]
@dillon-cullinan
ENH Replace gpuci_conda_retry with gpuci_mamba_retry (#69)
e30d2ce 
`mamba` was recently added to gpuCI build environment, testing usage and solvability with this PR which should speed up build times.

Authors:
  - Dillon Cullinan (https://github.com/dillon-cullinan)

Approvers:
  - https://github.com/jakirkham
  - AJ Schmidt (https://github.com/ajschmidt8)

URL: #69
@gigony
Update PyPI cuCIM v21.08.01 README.md and CHANGELOG.md (#87)
f918b22 
Update documents that are related to v21.08.01 for PyPI package release.

Authors:
  - Gigon Bae (https://github.com/gigony)

Approvers:
  - Mark Sadang (https://github.com/msadang)
  - https://github.com/jakirkham

URL: #87
@jakirkham
Merge branch-21.08 into branch-21.10
37f5e40
@raydouglass
Merge pull request #88 from jakirkham/branch-21.10-merge-21.08
27da55a 
Forward-merge branch-21.08 to branch-21.10 [skip gpuci]
@grlee77
fix failing regionprops test cases (#110)
d54c737 
This PR should fix the regionprops test failures [seen recently on CI](https://gpuci.gpuopenanalytics.com/job/rapidsai/job/gpuci/job/cucim/job/prb/job/cucim-gpu-test/CUDA=11.0,GPU_LABEL=gpu-a100,LINUX_VER=centos7,PYTHON=3.7/51/console). Seems related to #4354, but not sure why the prior fix no longer works.

The image is always boolean, so a cast to uint8 should be a safe.

cc @gigony

Authors:
  - Gregory R. Lee (https://github.com/grlee77)
  - Gigon Bae (https://github.com/gigony)

Approvers:
  - Gigon Bae (https://github.com/gigony)
  - Benjamin Zaitlen (https://github.com/quasiben)

URL: #110
@shekhardw
Add transforms for Digital Pathology (#100)
629f207 
Implement transforms for color jitter, image scale intensity, image flip and rotate included for batched RGB images.

This will be used exclusively for digital pathology training pipelines.


closes #105

Authors:
  - https://github.com/shekhardw
  - Gigon Bae (https://github.com/gigony)

Approvers:
  - Gigon Bae (https://github.com/gigony)
  - Gregory R. Lee (https://github.com/grlee77)
  - https://github.com/jakirkham

URL: #100
@gigony
Enable GDS and Support Runtime Context (__enter__, __exit__) for CuFi…
68f6042 
…leDriver and CuImage (#106)

- Enable GDS with GDS v1.0.0
  - Re-enable GDS with public package
  - Found an issue with a GDS static library and working on WSL
    1. Segmentation fault error is happening if we link GDS static library because GDS static library file (libcufile.a) available does not support non-CXX11 ABI (`-D_GLIBCXX_USE_CXX11_ABI=0`).  Python wheel with manylinux2014 needs to be compiled with non-CXX ABI
        - Workaround the static library issue by using a shared library (if exists on the system) instead.
    2. Loading/using GDS shared library(libcufile.so) causes `Assertion failure, file index :cufio-udev  line :143` error on WSL
        - Workaround the WSL issue by not loading GDS shared library (calling `cuFileDriverOpen()`) if the platform is WSL.
- Do not use GDS if in WSL
- Add `__enter__` and `__exit__` for CuFileDriver
- Add `__enter__` and `__exit__` for CuImage


Resolves #3

Authors:
  - Gigon Bae (https://github.com/gigony)

Approvers:
  - https://github.com/jakirkham

URL: #106
@gigony
Add a mechanism for user to know the availability of cucim.CuImage (#107
21d08ee 
)

- Add `cucim.is_available()` method

Users can query if a specific module is available or not.

For example, if cucim.clara module which requires C shared library is not available:
```
>>> import cucim
>>> cucim.is_available()
False
>>> cucim.is_available("skimage")
True
>>> cucim.is_available("core")
True
>>> cucim.is_available("clara")
False
```

Resolves #104
Supports Project-MONAI/MONAI#2987

Authors:
  - Gigon Bae (https://github.com/gigony)

Approvers:
  - Gregory R. Lee (https://github.com/grlee77)
  - https://github.com/jakirkham

URL: #107
@gigony
Support raw RGB tiled TIFF (#108)
4d861fe 
Due to #17 ([BUG] Compression scheme 33003 tile decoding is not implemented), #19 (Check compression method used in the image) was merged so cuCIM has been handling only particular formats (only jpeg/deflate-compressed image).

If the input TIFF image has no-compressed RAW tile image, cuCIM showed the following error message:

> RuntimeError: This format (compression: 1, sample_per_pixel: 1, planar_config: 1, photometric: 1) is not supported yet!. https://github.com/Project-MONAI/MONAI/pull/2987/checks?check_run_id=3667530814#step:7:15641

This patch is to support raw RGB tiled TIFF with fast-path, re-allowing non-compressed image with slow-path (in case the input is not tiled RGB image).

This supports Project-MONAI/MONAI#2987.

Authors:
  - Gigon Bae (https://github.com/gigony)

Approvers:
  - Gregory R. Lee (https://github.com/grlee77)
  - https://github.com/jakirkham

URL: #108
@GPUtester GPUtester requested review from a team as code owners October 5, 2021 18:41
@raydouglass raydouglass merged commit 572520c into main Oct 7, 2021
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7 participants
@GPUtester @raydouglass @dillon-cullinan @gigony @jakirkham @grlee77 @shekhardw