Add support for Python 3.12, update to umap-learn==0.5.6 (rapidsai#6060)

Contributes to rapidsai/build-planning#40 This PR adds support for Python 3.12. Other changes required for this: * updating `umap-learn`, `0.5.3 -> 0.5.6` (https://github.com/rapidsai/cuml/pull/6060/files#r1745915933) ## Notes for Reviewers This is part of ongoing work to add Python 3.12 support across RAPIDS. It temporarily introduces a build/test matrix including Python 3.12, from rapidsai/shared-workflows#213. A follow-up PR will revert back to pointing at the `branch-24.10` branch of `shared-workflows` once all RAPIDS repos have added Python 3.12 support. ### This will fail until all dependencies have been updates to Python 3.12 CI here is expected to fail until all of this project's upstream dependencies support Python 3.12. This can be merged whenever all CI jobs are passing. Authors: - James Lamb (https://github.com/jameslamb) - Bradley Dice (https://github.com/bdice) Approvers: - Bradley Dice (https://github.com/bdice) URL: rapidsai#6060
trxcllnt · Sep 12, 2024 · 28641bb · 28641bb
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diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -28,7 +28,7 @@ concurrency:
 jobs:
   cpp-build:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@python-3.12
     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-workflows/.github/workflows/custom-job.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@python-3.12
     with:
       arch: "amd64"
       branch: ${{ inputs.branch }}
@@ -51,7 +51,7 @@ jobs:
   python-build:
     needs: [cpp-build]
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@python-3.12
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
@@ -60,15 +60,15 @@ jobs:
   upload-conda:
     needs: [cpp-build, python-build]
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-upload-packages.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-upload-packages.yaml@python-3.12
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
       date: ${{ inputs.date }}
       sha: ${{ inputs.sha }}
   wheel-build-cuml:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@python-3.12
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
@@ -84,7 +84,7 @@ jobs:
   wheel-publish-cuml:
     needs: wheel-build-cuml
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-publish.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-publish.yaml@python-3.12
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -26,18 +26,18 @@ jobs:
       - wheel-tests-cuml
       - devcontainer
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/pr-builder.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/pr-builder.yaml@python-3.12
   checks:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@python-3.12
     with:
       enable_check_generated_files: false
       ignored_pr_jobs: >-
         optional-job-conda-python-tests-cudf-pandas-integration
   clang-tidy:
     needs: checks
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@python-3.12
     with:
       build_type: pull-request
       node_type: "cpu8"
@@ -47,55 +47,55 @@ jobs:
   conda-cpp-build:
     needs: checks
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@python-3.12
     with:
       build_type: pull-request
   conda-cpp-tests:
     needs: conda-cpp-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-tests.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-tests.yaml@python-3.12
     with:
       build_type: pull-request
   conda-cpp-checks:
     needs: conda-cpp-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-post-build-checks.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-post-build-checks.yaml@python-3.12
     with:
       build_type: pull-request
       enable_check_symbols: true
       symbol_exclusions: raft_cutlass
   conda-python-build:
     needs: conda-cpp-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@python-3.12
     with:
       build_type: pull-request
   conda-python-tests-singlegpu:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@python-3.12
     with:
       build_type: pull-request
       script: "ci/test_python_singlegpu.sh"
   optional-job-conda-python-tests-cudf-pandas-integration:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@python-3.12
     with:
       matrix_filter: map(select(.ARCH == "amd64"))
       build_type: pull-request
       script: "ci/test_python_integration.sh"
   conda-python-tests-dask:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@python-3.12
     with:
       build_type: pull-request
       script: "ci/test_python_dask.sh"
   conda-notebook-tests:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@python-3.12
     with:
       build_type: pull-request
       node_type: "gpu-v100-latest-1"
@@ -105,7 +105,7 @@ jobs:
   docs-build:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@python-3.12
     with:
       build_type: pull-request
       node_type: "gpu-v100-latest-1"
@@ -115,7 +115,7 @@ jobs:
   wheel-build-cuml:
     needs: checks
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@python-3.12
     with:
       build_type: pull-request
       script: ci/build_wheel.sh
@@ -125,13 +125,13 @@ jobs:
   wheel-tests-cuml:
     needs: wheel-build-cuml
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@python-3.12
     with:
       build_type: pull-request
       script: ci/test_wheel.sh
   devcontainer:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/build-in-devcontainer.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/build-in-devcontainer.yaml@python-3.12
     with:
       arch: '["amd64"]'
       cuda: '["12.5"]'

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -16,7 +16,7 @@ on:
 jobs:
   conda-cpp-checks:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-post-build-checks.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-post-build-checks.yaml@python-3.12
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}
@@ -26,15 +26,15 @@ jobs:
       symbol_exclusions: raft_cutlass
   conda-cpp-tests:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-tests.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-tests.yaml@python-3.12
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}
       date: ${{ inputs.date }}
       sha: ${{ inputs.sha }}
   conda-python-tests-singlegpu:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@python-3.12
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}
@@ -43,7 +43,7 @@ jobs:
       script: "ci/test_python_singlegpu.sh"
   conda-python-tests-dask:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@python-3.12
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}
@@ -52,7 +52,7 @@ jobs:
       script: "ci/test_python_dask.sh"
   wheel-tests-cuml:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.10
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@python-3.12
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}

diff --git a/BUILD.md b/BUILD.md
@@ -18,7 +18,7 @@ To install cuML from source, ensure the following dependencies are met:
 It is recommended to use conda for environment/package management. If doing so, development environment .yaml files are located in `conda/environments/all_*.yaml`. These files contains most of the dependencies mentioned above (notable exceptions are `gcc` and `zlib`). To create a development environment named `cuml_dev`, you can use the follow commands:
 
 ```bash
-conda create -n cuml_dev python=3.11
+conda create -n cuml_dev python=3.12
 conda env update -n cuml_dev --file=conda/environments/all_cuda-118_arch-x86_64.yaml
 conda activate cuml_dev
 ```

diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml
@@ -58,7 +58,7 @@ dependencies:
 - pytest-cov
 - pytest-xdist
 - pytest==7.*
-- python>=3.10,<3.12
+- python>=3.10,<3.13
 - raft-dask==24.10.*,>=0.0.0a0
 - rapids-build-backend>=0.3.0,<0.4.0.dev0
 - rapids-dask-dependency==24.10.*,>=0.0.0a0
@@ -68,13 +68,14 @@ dependencies:
 - scikit-learn==1.5
 - scipy>=1.8.0
 - seaborn
+- setuptools
 - sphinx-copybutton
 - sphinx-markdown-tables
 - sphinx<6
 - statsmodels
 - sysroot_linux-64==2.17
 - treelite==4.3.0
-- umap-learn==0.5.3
+- umap-learn==0.5.6
 - pip:
   - dask-glm==0.3.0
 name: all_cuda-118_arch-x86_64
diff --git a/conda/environments/all_cuda-125_arch-x86_64.yaml b/conda/environments/all_cuda-125_arch-x86_64.yaml
@@ -54,7 +54,7 @@ dependencies:
 - pytest-cov
 - pytest-xdist
 - pytest==7.*
-- python>=3.10,<3.12
+- python>=3.10,<3.13
 - raft-dask==24.10.*,>=0.0.0a0
 - rapids-build-backend>=0.3.0,<0.4.0.dev0
 - rapids-dask-dependency==24.10.*,>=0.0.0a0
@@ -64,13 +64,14 @@ dependencies:
 - scikit-learn==1.5
 - scipy>=1.8.0
 - seaborn
+- setuptools
 - sphinx-copybutton
 - sphinx-markdown-tables
 - sphinx<6
 - statsmodels
 - sysroot_linux-64==2.17
 - treelite==4.3.0
-- umap-learn==0.5.3
+- umap-learn==0.5.6
 - pip:
   - dask-glm==0.3.0
 name: all_cuda-125_arch-x86_64
diff --git a/conda/recipes/cuml-cpu/meta.yaml b/conda/recipes/cuml-cpu/meta.yaml
@@ -35,7 +35,7 @@ requirements:
     - pandas
     - scikit-learn=1.2
     - hdbscan>=0.8.38,<0.8.39
-    - umap-learn=0.5.3
+    - umap-learn=0.5.6
     - nvtx
 
 tests:                                 # [linux64]

diff --git a/dependencies.yaml b/dependencies.yaml
@@ -472,8 +472,12 @@ dependencies:
             packages:
               - python=3.11
           - matrix:
+              py: "3.12"
             packages:
-              - python>=3.10,<3.12
+              - python=3.12
+          - matrix:
+            packages:
+              - python>=3.10,<3.13
   test_libcuml:
     common:
       - output_types: conda
@@ -509,8 +513,9 @@ dependencies:
           - seaborn
           - *scikit_learn
           - statsmodels
-          - umap-learn==0.5.3
+          - umap-learn==0.5.6
           - pynndescent
+          - setuptools  # Needed on Python 3.12 for dask-glm, which requires pkg_resources but Python 3.12 doesn't have setuptools by default
       - output_types: conda
         packages:
           - pip

diff --git a/python/cuml/pyproject.toml b/python/cuml/pyproject.toml
@@ -105,6 +105,7 @@ classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
 [project.optional-dependencies]
@@ -124,8 +125,9 @@ test = [
     "pytest==7.*",
     "scikit-learn==1.5",
     "seaborn",
+    "setuptools",
     "statsmodels",
-    "umap-learn==0.5.3",
+    "umap-learn==0.5.6",
 ] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 
 [project.urls]