From bcaa7a03786c75ecb629c1b9f0d1292c905bcb89 Mon Sep 17 00:00:00 2001 From: divyegala Date: Fri, 24 May 2024 11:35:24 -0700 Subject: [PATCH 1/8] pin hdbscan wheel dependency and switch to using pypi package --- dependencies.yaml | 3 +-- python/pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/dependencies.yaml b/dependencies.yaml index 5d8ac0a94e..055ec4ac1c 100644 --- a/dependencies.yaml +++ b/dependencies.yaml @@ -428,8 +428,7 @@ dependencies: - output_types: pyproject packages: - dask-glm==0.3.0 - # TODO: Can we stop pulling from the master branch now that there was a release in October? - - hdbscan @ git+https://github.com/scikit-learn-contrib/hdbscan.git@master + - hdbscan<=0.8.30 test_notebooks: common: - output_types: [conda, requirements] diff --git a/python/pyproject.toml b/python/pyproject.toml index 9c72a43a9f..dcff8eda2d 100644 --- a/python/pyproject.toml +++ b/python/pyproject.toml @@ -112,7 +112,7 @@ classifiers = [ test = [ "dask-glm==0.3.0", "dask-ml", - "hdbscan @ git+https://github.com/scikit-learn-contrib/hdbscan.git@master", + "hdbscan<=0.8.30", "hypothesis>=6.0,<7", "nltk", "numpydoc", From ddadde7fe5eb0b7a64713341777c4815a0588f19 Mon Sep 17 00:00:00 2001 From: divyegala Date: Fri, 24 May 2024 13:02:13 -0700 Subject: [PATCH 2/8] pin hdbscan to 0.8.36 from pypi --- conda/environments/all_cuda-118_arch-x86_64.yaml | 2 +- conda/environments/all_cuda-122_arch-x86_64.yaml | 2 +- dependencies.yaml | 7 +++---- python/pyproject.toml | 2 +- 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml index cb442367bc..16e79a7fca 100644 --- a/conda/environments/all_cuda-118_arch-x86_64.yaml +++ b/conda/environments/all_cuda-118_arch-x86_64.yaml @@ -22,7 +22,6 @@ dependencies: - doxygen=1.9.1 - gcc_linux-64=11.* - graphviz -- hdbscan<=0.8.30 - hypothesis>=6.0,<7 - ipykernel - ipython @@ -75,4 +74,5 @@ dependencies: - umap-learn==0.5.3 - pip: - dask-glm==0.3.0 + - hdbscan==0.8.36 name: all_cuda-118_arch-x86_64 diff --git a/conda/environments/all_cuda-122_arch-x86_64.yaml b/conda/environments/all_cuda-122_arch-x86_64.yaml index 29492b1f20..ee1c159694 100644 --- a/conda/environments/all_cuda-122_arch-x86_64.yaml +++ b/conda/environments/all_cuda-122_arch-x86_64.yaml @@ -24,7 +24,6 @@ dependencies: - doxygen=1.9.1 - gcc_linux-64=11.* - graphviz -- hdbscan<=0.8.30 - hypothesis>=6.0,<7 - ipykernel - ipython @@ -71,4 +70,5 @@ dependencies: - umap-learn==0.5.3 - pip: - dask-glm==0.3.0 + - hdbscan==0.8.36 name: all_cuda-122_arch-x86_64 diff --git a/dependencies.yaml b/dependencies.yaml index 055ec4ac1c..0f16fc8a38 100644 --- a/dependencies.yaml +++ b/dependencies.yaml @@ -422,13 +422,12 @@ dependencies: - pip - pip: - dask-glm==0.3.0 - # TODO: remove pin once a release that includes fixes for the error - # is released: https://github.com/rapidsai/cuml/issues/5514 - - hdbscan<=0.8.30 + # TODO: Install from conda-forge when available + - hdbscan==0.8.36 - output_types: pyproject packages: - dask-glm==0.3.0 - - hdbscan<=0.8.30 + - hdbscan==0.8.36 test_notebooks: common: - output_types: [conda, requirements] diff --git a/python/pyproject.toml b/python/pyproject.toml index dcff8eda2d..fd880f4596 100644 --- a/python/pyproject.toml +++ b/python/pyproject.toml @@ -112,7 +112,7 @@ classifiers = [ test = [ "dask-glm==0.3.0", "dask-ml", - "hdbscan<=0.8.30", + "hdbscan==0.8.36", "hypothesis>=6.0,<7", "nltk", "numpydoc", From c73fab862d7e827dc99c830352c4336a407648ca Mon Sep 17 00:00:00 2001 From: divyegala Date: Fri, 24 May 2024 17:00:16 -0700 Subject: [PATCH 3/8] hdbscan 0.8.36 conda is released --- conda/environments/all_cuda-118_arch-x86_64.yaml | 2 +- conda/environments/all_cuda-122_arch-x86_64.yaml | 2 +- dependencies.yaml | 4 +--- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml index 16e79a7fca..0e5f7699f1 100644 --- a/conda/environments/all_cuda-118_arch-x86_64.yaml +++ b/conda/environments/all_cuda-118_arch-x86_64.yaml @@ -22,6 +22,7 @@ dependencies: - doxygen=1.9.1 - gcc_linux-64=11.* - graphviz +- hdbscan==0.8.36 - hypothesis>=6.0,<7 - ipykernel - ipython @@ -74,5 +75,4 @@ dependencies: - umap-learn==0.5.3 - pip: - dask-glm==0.3.0 - - hdbscan==0.8.36 name: all_cuda-118_arch-x86_64 diff --git a/conda/environments/all_cuda-122_arch-x86_64.yaml b/conda/environments/all_cuda-122_arch-x86_64.yaml index ee1c159694..d2ffb81316 100644 --- a/conda/environments/all_cuda-122_arch-x86_64.yaml +++ b/conda/environments/all_cuda-122_arch-x86_64.yaml @@ -24,6 +24,7 @@ dependencies: - doxygen=1.9.1 - gcc_linux-64=11.* - graphviz +- hdbscan==0.8.36 - hypothesis>=6.0,<7 - ipykernel - ipython @@ -70,5 +71,4 @@ dependencies: - umap-learn==0.5.3 - pip: - dask-glm==0.3.0 - - hdbscan==0.8.36 name: all_cuda-122_arch-x86_64 diff --git a/dependencies.yaml b/dependencies.yaml index 0f16fc8a38..1df7e95056 100644 --- a/dependencies.yaml +++ b/dependencies.yaml @@ -404,6 +404,7 @@ dependencies: - output_types: [conda, requirements, pyproject] packages: - dask-ml + - hdbscan==0.8.36 - hypothesis>=6.0,<7 - nltk - numpydoc @@ -422,12 +423,9 @@ dependencies: - pip - pip: - dask-glm==0.3.0 - # TODO: Install from conda-forge when available - - hdbscan==0.8.36 - output_types: pyproject packages: - dask-glm==0.3.0 - - hdbscan==0.8.36 test_notebooks: common: - output_types: [conda, requirements] From b2f5b33565135c8412f7ab2301fbc6eb40a09018 Mon Sep 17 00:00:00 2001 From: divyegala Date: Tue, 13 Aug 2024 17:19:33 -0700 Subject: [PATCH 4/8] bring up to date --- conda/environments/all_cuda-118_arch-x86_64.yaml | 2 +- conda/environments/all_cuda-125_arch-x86_64.yaml | 2 +- dependencies.yaml | 2 +- python/cuml/pyproject.toml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml index 1b7562d3e6..91718ce693 100644 --- a/conda/environments/all_cuda-118_arch-x86_64.yaml +++ b/conda/environments/all_cuda-118_arch-x86_64.yaml @@ -22,7 +22,7 @@ dependencies: - doxygen=1.9.1 - gcc_linux-64=11.* - graphviz -- hdbscan==0.8.36 +- hdbscan==0.8.38 - hypothesis>=6.0,<7 - ipykernel - ipython diff --git a/conda/environments/all_cuda-125_arch-x86_64.yaml b/conda/environments/all_cuda-125_arch-x86_64.yaml index d0d8fead3e..248ef7e291 100644 --- a/conda/environments/all_cuda-125_arch-x86_64.yaml +++ b/conda/environments/all_cuda-125_arch-x86_64.yaml @@ -24,7 +24,7 @@ dependencies: - doxygen=1.9.1 - gcc_linux-64=11.* - graphviz -- hdbscan==0.8.36 +- hdbscan==0.8.38 - hypothesis>=6.0,<7 - ipykernel - ipython diff --git a/dependencies.yaml b/dependencies.yaml index a3b947e86d..bdfd57f578 100644 --- a/dependencies.yaml +++ b/dependencies.yaml @@ -466,7 +466,7 @@ dependencies: - output_types: [conda, requirements, pyproject] packages: - dask-ml - - hdbscan==0.8.36 + - hdbscan==0.8.38 - hypothesis>=6.0,<7 - nltk - numpydoc diff --git a/python/cuml/pyproject.toml b/python/cuml/pyproject.toml index c46326edad..6db1fbbcc6 100644 --- a/python/cuml/pyproject.toml +++ b/python/cuml/pyproject.toml @@ -106,7 +106,7 @@ classifiers = [ test = [ "dask-glm==0.3.0", "dask-ml", - "hdbscan==0.8.36", + "hdbscan==0.8.38", "hypothesis>=6.0,<7", "nltk", "numpydoc", From 23877d8f1a8672242b4ef7a8342473aca9c2ee1a Mon Sep 17 00:00:00 2001 From: divyegala Date: Tue, 13 Aug 2024 17:46:22 -0700 Subject: [PATCH 5/8] review suggestions --- conda/recipes/cuml-cpu/meta.yaml | 2 +- dependencies.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conda/recipes/cuml-cpu/meta.yaml b/conda/recipes/cuml-cpu/meta.yaml index e3813db79a..09686ff9dd 100644 --- a/conda/recipes/cuml-cpu/meta.yaml +++ b/conda/recipes/cuml-cpu/meta.yaml @@ -34,7 +34,7 @@ requirements: - numpy>=1.23,<2.0a0 - pandas - scikit-learn=1.2 - - hdbscan<=0.8.30 + - hdbscan>=0.8.38,<0.8.39 - umap-learn=0.5.3 - nvtx diff --git a/dependencies.yaml b/dependencies.yaml index bdfd57f578..87c5b1ac8e 100644 --- a/dependencies.yaml +++ b/dependencies.yaml @@ -466,7 +466,7 @@ dependencies: - output_types: [conda, requirements, pyproject] packages: - dask-ml - - hdbscan==0.8.38 + - hdbscan>=0.8.38,<0.8.39 - hypothesis>=6.0,<7 - nltk - numpydoc From 292355b41e9e690cd9c0ec055f09bb0e4d0d7867 Mon Sep 17 00:00:00 2001 From: divyegala Date: Tue, 13 Aug 2024 17:46:33 -0700 Subject: [PATCH 6/8] review suggestions --- conda/environments/all_cuda-118_arch-x86_64.yaml | 2 +- conda/environments/all_cuda-125_arch-x86_64.yaml | 2 +- python/cuml/pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml index 91718ce693..e8a39e250e 100644 --- a/conda/environments/all_cuda-118_arch-x86_64.yaml +++ b/conda/environments/all_cuda-118_arch-x86_64.yaml @@ -22,7 +22,7 @@ dependencies: - doxygen=1.9.1 - gcc_linux-64=11.* - graphviz -- hdbscan==0.8.38 +- hdbscan>=0.8.38,<0.8.39 - hypothesis>=6.0,<7 - ipykernel - ipython diff --git a/conda/environments/all_cuda-125_arch-x86_64.yaml b/conda/environments/all_cuda-125_arch-x86_64.yaml index 248ef7e291..293028cdb1 100644 --- a/conda/environments/all_cuda-125_arch-x86_64.yaml +++ b/conda/environments/all_cuda-125_arch-x86_64.yaml @@ -24,7 +24,7 @@ dependencies: - doxygen=1.9.1 - gcc_linux-64=11.* - graphviz -- hdbscan==0.8.38 +- hdbscan>=0.8.38,<0.8.39 - hypothesis>=6.0,<7 - ipykernel - ipython diff --git a/python/cuml/pyproject.toml b/python/cuml/pyproject.toml index 6db1fbbcc6..19c7a32160 100644 --- a/python/cuml/pyproject.toml +++ b/python/cuml/pyproject.toml @@ -106,7 +106,7 @@ classifiers = [ test = [ "dask-glm==0.3.0", "dask-ml", - "hdbscan==0.8.38", + "hdbscan>=0.8.38,<0.8.39", "hypothesis>=6.0,<7", "nltk", "numpydoc", From 21769f853c912e72c4ad5fa85a0b688eaf3021e4 Mon Sep 17 00:00:00 2001 From: divyegala Date: Wed, 14 Aug 2024 11:35:47 -0700 Subject: [PATCH 7/8] verbose pytests --- ci/run_cuml_dask_pytests.sh | 2 +- ci/run_cuml_singlegpu_pytests.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/run_cuml_dask_pytests.sh b/ci/run_cuml_dask_pytests.sh index 9a28c6bbcc..7f4d017338 100755 --- a/ci/run_cuml_dask_pytests.sh +++ b/ci/run_cuml_dask_pytests.sh @@ -4,4 +4,4 @@ # Support invoking run_cuml_dask_pytests.sh outside the script directory cd "$(dirname "$(realpath "${BASH_SOURCE[0]}")")"/../python/cuml/cuml/tests/dask -python -m pytest --cache-clear "$@" . +python -m pytest -vvv --cache-clear "$@" . diff --git a/ci/run_cuml_singlegpu_pytests.sh b/ci/run_cuml_singlegpu_pytests.sh index a395baab1b..971cd1c6f3 100755 --- a/ci/run_cuml_singlegpu_pytests.sh +++ b/ci/run_cuml_singlegpu_pytests.sh @@ -4,4 +4,4 @@ # Support invoking run_cuml_singlegpu_pytests.sh outside the script directory cd "$(dirname "$(realpath "${BASH_SOURCE[0]}")")"/../python/cuml/cuml/tests -python -m pytest --cache-clear --ignore=dask -m "not memleak" "$@" . +python -m pytest -vvv --cache-clear --ignore=dask -m "not memleak" "$@" . From c1e4171aea5a0d0b27bfe0e09fd4ef37362379bd Mon Sep 17 00:00:00 2001 From: divyegala Date: Thu, 15 Aug 2024 12:38:52 -0700 Subject: [PATCH 8/8] add cython as run dependency for pytests --- ci/run_cuml_dask_pytests.sh | 2 +- ci/run_cuml_singlegpu_pytests.sh | 2 +- dependencies.yaml | 3 ++- python/cuml/pyproject.toml | 1 + 4 files changed, 5 insertions(+), 3 deletions(-) diff --git a/ci/run_cuml_dask_pytests.sh b/ci/run_cuml_dask_pytests.sh index 7f4d017338..9a28c6bbcc 100755 --- a/ci/run_cuml_dask_pytests.sh +++ b/ci/run_cuml_dask_pytests.sh @@ -4,4 +4,4 @@ # Support invoking run_cuml_dask_pytests.sh outside the script directory cd "$(dirname "$(realpath "${BASH_SOURCE[0]}")")"/../python/cuml/cuml/tests/dask -python -m pytest -vvv --cache-clear "$@" . +python -m pytest --cache-clear "$@" . diff --git a/ci/run_cuml_singlegpu_pytests.sh b/ci/run_cuml_singlegpu_pytests.sh index 971cd1c6f3..a395baab1b 100755 --- a/ci/run_cuml_singlegpu_pytests.sh +++ b/ci/run_cuml_singlegpu_pytests.sh @@ -4,4 +4,4 @@ # Support invoking run_cuml_singlegpu_pytests.sh outside the script directory cd "$(dirname "$(realpath "${BASH_SOURCE[0]}")")"/../python/cuml/cuml/tests -python -m pytest -vvv --cache-clear --ignore=dask -m "not memleak" "$@" . +python -m pytest --cache-clear --ignore=dask -m "not memleak" "$@" . diff --git a/dependencies.yaml b/dependencies.yaml index 87c5b1ac8e..a42da405fb 100644 --- a/dependencies.yaml +++ b/dependencies.yaml @@ -176,7 +176,7 @@ dependencies: common: - output_types: [conda, requirements, pyproject] packages: - - cython>=3.0.0 + - &cython cython>=3.0.0 - &treelite treelite==4.3.0 - output_types: conda packages: @@ -465,6 +465,7 @@ dependencies: common: - output_types: [conda, requirements, pyproject] packages: + - *cython - dask-ml - hdbscan>=0.8.38,<0.8.39 - hypothesis>=6.0,<7 diff --git a/python/cuml/pyproject.toml b/python/cuml/pyproject.toml index 19c7a32160..023639dd2d 100644 --- a/python/cuml/pyproject.toml +++ b/python/cuml/pyproject.toml @@ -104,6 +104,7 @@ classifiers = [ [project.optional-dependencies] test = [ + "cython>=3.0.0", "dask-glm==0.3.0", "dask-ml", "hdbscan>=0.8.38,<0.8.39",