From e1d8dead6636ebb411e2fe50a2f1b05f40790636 Mon Sep 17 00:00:00 2001 From: Ray Douglass Date: Mon, 24 Jul 2023 16:41:59 -0400 Subject: [PATCH 1/6] v23.10 Updates [skip ci] --- .github/workflows/build.yaml | 8 ++++---- .github/workflows/pr.yaml | 12 ++++++------ .github/workflows/test.yaml | 2 +- README.md | 2 +- VERSION | 2 +- ci/build_docs.sh | 2 +- cpp/plugins/cucim.kit.cumed/VERSION | 2 +- cpp/plugins/cucim.kit.cuslide/VERSION | 2 +- cucim.code-workspace | 8 ++++---- docs/source/conf.py | 4 ++-- python/cucim/README.md | 2 +- python/cucim/VERSION | 2 +- python/cucim/docs/getting_started/index.md | 10 +++++----- python/cucim/docs/index.md | 2 +- 14 files changed, 30 insertions(+), 30 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index f4349bb89..7a8be411e 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -28,7 +28,7 @@ concurrency: jobs: cpp-build: secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.10 with: build_type: ${{ inputs.build_type || 'branch' }} branch: ${{ inputs.branch }} @@ -38,7 +38,7 @@ jobs: if: github.ref_type == 'branch' needs: [python-build] secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.10 with: arch: "amd64" branch: ${{ inputs.branch }} @@ -51,7 +51,7 @@ jobs: python-build: needs: [cpp-build] secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.10 with: build_type: ${{ inputs.build_type || 'branch' }} branch: ${{ inputs.branch }} @@ -60,7 +60,7 @@ jobs: upload-conda: needs: [cpp-build, python-build] secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/conda-upload-packages.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/conda-upload-packages.yaml@branch-23.10 with: build_type: ${{ inputs.build_type || 'branch' }} branch: ${{ inputs.branch }} diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 150debb86..8792ad9ca 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -18,32 +18,32 @@ jobs: - conda-python-tests - docs-build secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/pr-builder.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/pr-builder.yaml@branch-23.10 checks: secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/checks.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/checks.yaml@branch-23.10 conda-cpp-build: needs: checks secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.10 with: build_type: pull-request conda-python-build: needs: conda-cpp-build secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.10 with: build_type: pull-request conda-python-tests: needs: conda-python-build secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.10 with: build_type: pull-request docs-build: needs: conda-python-build secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.10 with: build_type: pull-request node_type: "gpu-v100-latest-1" diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 39b8ac83b..188ceefde 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -16,7 +16,7 @@ on: jobs: conda-python-tests: secrets: inherit - uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.08 + uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.10 with: build_type: nightly branch: ${{ inputs.branch }} diff --git a/README.md b/README.md index 1249e06dd..02a0aa66c 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ pip install scipy scikit-image cupy-cuda110 ### Notebooks -Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.08/notebooks/Welcome.ipynb)) +Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.10/notebooks/Welcome.ipynb)) #### Downloading sample images diff --git a/VERSION b/VERSION index e7ab23867..965a4ca5c 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -23.08.00 +23.10.00 diff --git a/ci/build_docs.sh b/ci/build_docs.sh index 9b228b4eb..349b8a722 100755 --- a/ci/build_docs.sh +++ b/ci/build_docs.sh @@ -24,7 +24,7 @@ rapids-mamba-retry install \ --channel "${PYTHON_CHANNEL}" \ cucim libcucim -export RAPIDS_VERSION_NUMBER="23.08" +export RAPIDS_VERSION_NUMBER="23.10" export RAPIDS_DOCS_DIR="$(mktemp -d)" rapids-logger "Build Python docs" diff --git a/cpp/plugins/cucim.kit.cumed/VERSION b/cpp/plugins/cucim.kit.cumed/VERSION index e7ab23867..965a4ca5c 100644 --- a/cpp/plugins/cucim.kit.cumed/VERSION +++ b/cpp/plugins/cucim.kit.cumed/VERSION @@ -1 +1 @@ -23.08.00 +23.10.00 diff --git a/cpp/plugins/cucim.kit.cuslide/VERSION b/cpp/plugins/cucim.kit.cuslide/VERSION index e7ab23867..965a4ca5c 100644 --- a/cpp/plugins/cucim.kit.cuslide/VERSION +++ b/cpp/plugins/cucim.kit.cuslide/VERSION @@ -1 +1 @@ -23.08.00 +23.10.00 diff --git a/cucim.code-workspace b/cucim.code-workspace index ed540b80b..db4ff8bbd 100644 --- a/cucim.code-workspace +++ b/cucim.code-workspace @@ -33,7 +33,7 @@ "CUCIM_TESTDATA_FOLDER": "${workspaceDirectory}/test_data", // Add cuslide plugin's library path to LD_LIBRARY_PATH "LD_LIBRARY_PATH": "${workspaceDirectory}/build-debug/lib:${workspaceDirectory}/cpp/plugins/cucim.kit.cuslide/build-debug/lib:${workspaceDirectory}/temp/cuda/lib64:${os_env:LD_LIBRARY_PATH}", - "CUCIM_TEST_PLUGIN_PATH": "cucim.kit.cuslide@23.08.00.so" + "CUCIM_TEST_PLUGIN_PATH": "cucim.kit.cuslide@23.10.00.so" }, "cwd": "${workspaceDirectory}", "catch2": { @@ -226,7 +226,7 @@ }, { "name": "CUCIM_TEST_PLUGIN_PATH", - "value": "cucim.kit.cuslide@23.08.00.so" + "value": "cucim.kit.cuslide@23.10.00.so" } ], "console": "externalTerminal", @@ -254,7 +254,7 @@ }, { "name": "CUCIM_TEST_PLUGIN_PATH", - "value": "cucim.kit.cuslide@23.08.00.so" + "value": "cucim.kit.cuslide@23.10.00.so" } ], "console": "externalTerminal", @@ -286,7 +286,7 @@ }, { "name": "CUCIM_TEST_PLUGIN_PATH", - "value": "cucim.kit.cuslide@23.08.00.so" + "value": "cucim.kit.cuslide@23.10.00.so" } ], "console": "externalTerminal", diff --git a/docs/source/conf.py b/docs/source/conf.py index 3fea3380b..5055f6d98 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -72,9 +72,9 @@ # built documents. # # The short X.Y version. -version = '23.08' +version = '23.10' # The full version, including alpha/beta/rc tags. -release = '23.08.00' +release = '23.10.00' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/python/cucim/README.md b/python/cucim/README.md index 1249e06dd..02a0aa66c 100755 --- a/python/cucim/README.md +++ b/python/cucim/README.md @@ -70,7 +70,7 @@ pip install scipy scikit-image cupy-cuda110 ### Notebooks -Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.08/notebooks/Welcome.ipynb)) +Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.10/notebooks/Welcome.ipynb)) #### Downloading sample images diff --git a/python/cucim/VERSION b/python/cucim/VERSION index e7ab23867..965a4ca5c 100644 --- a/python/cucim/VERSION +++ b/python/cucim/VERSION @@ -1 +1 @@ -23.08.00 +23.10.00 diff --git a/python/cucim/docs/getting_started/index.md b/python/cucim/docs/getting_started/index.md index a0228a17e..d17f00ad4 100644 --- a/python/cucim/docs/getting_started/index.md +++ b/python/cucim/docs/getting_started/index.md @@ -14,15 +14,15 @@ ## Installation -Please download the latest SDK package (`cuCIM-v23.08.00-linux.tar.gz`). +Please download the latest SDK package (`cuCIM-v23.10.00-linux.tar.gz`). Untar the downloaded file. ```bash -mkdir -p cuCIM-v23.08.00 -tar -xzvf cuCIM-v23.08.00-linux.tar.gz -C cuCIM-v23.08.00 +mkdir -p cuCIM-v23.10.00 +tar -xzvf cuCIM-v23.10.00-linux.tar.gz -C cuCIM-v23.10.00 -cd cuCIM-v23.08.00 +cd cuCIM-v23.10.00 ``` ## Run command @@ -147,7 +147,7 @@ Its execution would show some metadata information and create two files -- `outp ``` $ ./bin/tiff_image notebooks/input/image.tif . [Plugin: cucim.kit.cuslide] Loading... -[Plugin: cucim.kit.cuslide] Loading the dynamic library from: cucim.kit.cuslide@23.08.00.so +[Plugin: cucim.kit.cuslide] Loading the dynamic library from: cucim.kit.cuslide@23.10.00.so [Plugin: cucim.kit.cuslide] loaded successfully. Version: 0 Initializing plugin: cucim.kit.cuslide (interfaces: [cucim::io::IImageFormat v0.1]) (impl: cucim.kit.cuslide) is_loaded: true diff --git a/python/cucim/docs/index.md b/python/cucim/docs/index.md index e5000f865..6315af2ef 100644 --- a/python/cucim/docs/index.md +++ b/python/cucim/docs/index.md @@ -18,7 +18,7 @@ development/index --> # cuCIM Documentation -Current latest version is [Version 23.08.00](release_notes/v23.08.00.md). +Current latest version is [Version 23.10.00](release_notes/v23.10.00.md). **cuCIM** a toolkit to provide GPU accelerated I/O, image processing & computer vision primitives for N-Dimensional images with a focus on biomedical imaging. From d8960d8dd2a1a0ba98200ebc88806feee006c5e7 Mon Sep 17 00:00:00 2001 From: Gregory Lee Date: Tue, 22 Aug 2023 17:04:13 -0400 Subject: [PATCH 2/6] minor updates to release 23.08 changelog (#605) added description of additional sub-components of the scikit-image 0.21 API sync that was incorporated in release 23.08 Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - Gigon Bae (https://github.com/gigony) - https://github.com/jakirkham URL: https://github.com/rapidsai/cucim/pull/605 --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b29bc2e00..84e66a66e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,8 @@ ## 🚨 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 @@ -11,9 +13,14 @@ - 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) From 774fe39dd1e13989a3dd9030a4d42ecf3e39ebae Mon Sep 17 00:00:00 2001 From: AJ Schmidt Date: Mon, 28 Aug 2023 09:47:01 -0400 Subject: [PATCH 3/6] Use `copy-pr-bot` (#606) [skip ci] --- .github/copy-pr-bot.yaml | 4 ++++ .github/ops-bot.yaml | 1 - 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 .github/copy-pr-bot.yaml diff --git a/.github/copy-pr-bot.yaml b/.github/copy-pr-bot.yaml new file mode 100644 index 000000000..895ba83ee --- /dev/null +++ b/.github/copy-pr-bot.yaml @@ -0,0 +1,4 @@ +# Configuration file for `copy-pr-bot` GitHub App +# https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/ + +enabled: true diff --git a/.github/ops-bot.yaml b/.github/ops-bot.yaml index 4d53902ba..fc90c22b9 100644 --- a/.github/ops-bot.yaml +++ b/.github/ops-bot.yaml @@ -6,5 +6,4 @@ branch_checker: true label_checker: true release_drafter: true external_contributors: false -copy_prs: true recently_updated: true From 97e5cc09b1ec9b941dc05f96ec3906690ffb938a Mon Sep 17 00:00:00 2001 From: Bradley Dice Date: Fri, 8 Sep 2023 12:27:15 -0500 Subject: [PATCH 4/6] Use `conda mambabuild` not `mamba mambabuild` (#607) With the release of conda 23.7.3, `mamba mambabuild` stopped working. With boa installed, `conda mambabuild` uses the mamba solver, so just use that instead. See also https://github.com/rapidsai/cudf/issues/14068. Authors: - Bradley Dice (https://github.com/bdice) Approvers: - Ray Douglass (https://github.com/raydouglass) URL: https://github.com/rapidsai/cucim/pull/607 --- ci/build_cpp.sh | 2 +- ci/build_python.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/build_cpp.sh b/ci/build_cpp.sh index 269a0be40..1cc80d198 100755 --- a/ci/build_cpp.sh +++ b/ci/build_cpp.sh @@ -11,6 +11,6 @@ rapids-print-env rapids-logger "Begin cpp build" -rapids-mamba-retry mambabuild conda/recipes/libcucim +rapids-conda-retry mambabuild conda/recipes/libcucim rapids-upload-conda-to-s3 cpp diff --git a/ci/build_python.sh b/ci/build_python.sh index d12cd4208..ae607aeeb 100755 --- a/ci/build_python.sh +++ b/ci/build_python.sh @@ -15,7 +15,7 @@ CPP_CHANNEL=$(rapids-download-conda-from-s3 cpp) # TODO: Remove `--no-test` flag once importing on a CPU # node works correctly -rapids-mamba-retry mambabuild \ +rapids-conda-retry mambabuild \ --no-test \ --channel "${CPP_CHANNEL}" \ conda/recipes/cucim From 84a79b52f5f5a62ce4bf4a644cb0a867c4c3b596 Mon Sep 17 00:00:00 2001 From: Jake Awe <50372925+AyodeAwe@users.noreply.github.com> Date: Thu, 21 Sep 2023 14:03:00 -0500 Subject: [PATCH 5/6] Update image names (#609) PR updates `rapidsai/ci` references to `rapidsai/ci-conda` Authors: - Jake Awe (https://github.com/AyodeAwe) Approvers: - AJ Schmidt (https://github.com/ajschmidt8) URL: https://github.com/rapidsai/cucim/pull/609 --- .github/workflows/build.yaml | 2 +- .github/workflows/pr.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 7a8be411e..182ae1282 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -43,7 +43,7 @@ jobs: arch: "amd64" branch: ${{ inputs.branch }} build_type: ${{ inputs.build_type || 'branch' }} - container_image: "rapidsai/ci:latest" + container_image: "rapidsai/ci-conda:latest" date: ${{ inputs.date }} node_type: "gpu-v100-latest-1" run_script: "ci/build_docs.sh" diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 8792ad9ca..433a7e33e 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -48,5 +48,5 @@ jobs: build_type: pull-request node_type: "gpu-v100-latest-1" arch: "amd64" - container_image: "rapidsai/ci:latest" + container_image: "rapidsai/ci-conda:latest" run_script: "ci/build_docs.sh" From f3ed5334605d366e15d8559f12943dd72732a201 Mon Sep 17 00:00:00 2001 From: Ray Douglass Date: Wed, 11 Oct 2023 10:29:23 -0400 Subject: [PATCH 6/6] Update Changelog [skip ci] --- CHANGELOG.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84e66a66e..c0c6faf84 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,18 @@ +# cuCIM 23.10.00 (11 Oct 2023) + +## 🐛 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) + # cuCIM 23.08.00 (9 Aug 2023) ## 🚨 Breaking Changes