From d19f1b55a369afb932b8fd7be685c9d703db47b2 Mon Sep 17 00:00:00 2001 From: maxime Date: Mon, 17 Nov 2025 16:52:00 +0100 Subject: [PATCH 1/5] updating torch version --- .github/workflows/main.yml | 2 ++ pyproject.toml | 2 +- requirements_cuda.txt | 5 +++++ 3 files changed, 8 insertions(+), 1 deletion(-) create mode 100644 requirements_cuda.txt diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d326d010..a497df09 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -19,6 +19,8 @@ jobs: - name: Install dependencies run: | + pip uninstall mamba-ssm causal-conv1d flash-attn -y + pip install --no-cache-dir -r ./requirements_cuda.txt pip install -r requirements-dev.txt pip install .[mamba-ssm] diff --git a/pyproject.toml b/pyproject.toml index 242e22eb..139576cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ dependencies = [ 'scikit-learn>=1.5.0', 'scipy==1.13.1', 'gitpython==3.1.43', - 'torch==2.6.0', + 'torch==2.7.0', 'accelerate==1.4.0', 'transformers==4.49.0', 'loompy==3.0.7', diff --git a/requirements_cuda.txt b/requirements_cuda.txt new file mode 100644 index 00000000..3ab09792 --- /dev/null +++ b/requirements_cuda.txt @@ -0,0 +1,5 @@ +--extra-index-url https://pypi.nvidia.com +# rapids-singlecell[rapids12] +https://github.com/state-spaces/mamba/releases/download/v2.2.4/mamba_ssm-2.2.4+cu12torch2.6cxx11abiFALSE-cp311-cp311-linux_x86_64.whl +https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.5.0.post8/causal_conv1d-1.5.0.post8+cu12torch2.6cxx11abiFALSE-cp311-cp311-linux_x86_64.whl +https://github.com/Dao-AILab/flash-attention/releases/download/v2.7.4.post1/flash_attn-2.7.4.post1+cu12torch2.6cxx11abiFALSE-cp311-cp311-linux_x86_64.whl \ No newline at end of file From 98ca9fcdaec6bfd02f08a14e31a11a4edc66a607 Mon Sep 17 00:00:00 2001 From: maxime Date: Mon, 17 Nov 2025 16:55:48 +0100 Subject: [PATCH 2/5] updating torch version --- requirements_cuda.txt | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/requirements_cuda.txt b/requirements_cuda.txt index 3ab09792..8fc98260 100644 --- a/requirements_cuda.txt +++ b/requirements_cuda.txt @@ -1,5 +1,6 @@ --extra-index-url https://pypi.nvidia.com # rapids-singlecell[rapids12] -https://github.com/state-spaces/mamba/releases/download/v2.2.4/mamba_ssm-2.2.4+cu12torch2.6cxx11abiFALSE-cp311-cp311-linux_x86_64.whl -https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.5.0.post8/causal_conv1d-1.5.0.post8+cu12torch2.6cxx11abiFALSE-cp311-cp311-linux_x86_64.whl -https://github.com/Dao-AILab/flash-attention/releases/download/v2.7.4.post1/flash_attn-2.7.4.post1+cu12torch2.6cxx11abiFALSE-cp311-cp311-linux_x86_64.whl \ No newline at end of file +https://github.com/state-spaces/mamba/releases/download/v2.2.4/mamba_ssm-2.2.4+cu12torch2.7cxx11abiFALSE-cp311-cp311-linux_x86_64.whl +https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.5.0.post8/causal_conv1d-1.5.0.post8+cu12torch2.7cxx11abiFALSE-cp311-cp311-linux_x86_64.whl +https://github.com/Dao-AILab/flash-attention/releases/download/v2.7.4.post1/flash_attn-2.7.4.post1+cu12torch2.7cxx11abiFALSE-cp311-cp311-linux_x86_64.whl + From 9726b99b0b05c2fefaf95591d95ea47b23320d92 Mon Sep 17 00:00:00 2001 From: maxime Date: Mon, 17 Nov 2025 16:59:27 +0100 Subject: [PATCH 3/5] updating versions mamba causal --- pyproject.toml | 4 ++-- requirements_cuda.txt | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 139576cd..35ae4ff0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,8 +46,8 @@ dependencies = [ [project.optional-dependencies] mamba-ssm = [ - 'mamba-ssm==2.2.4', - 'causal-conv1d==1.5.0.post8', + 'mamba-ssm==2.2.5', + 'causal-conv1d==1.5.1', ] evo-2 = [ diff --git a/requirements_cuda.txt b/requirements_cuda.txt index 8fc98260..20038bf5 100644 --- a/requirements_cuda.txt +++ b/requirements_cuda.txt @@ -1,6 +1,6 @@ --extra-index-url https://pypi.nvidia.com # rapids-singlecell[rapids12] -https://github.com/state-spaces/mamba/releases/download/v2.2.4/mamba_ssm-2.2.4+cu12torch2.7cxx11abiFALSE-cp311-cp311-linux_x86_64.whl -https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.5.0.post8/causal_conv1d-1.5.0.post8+cu12torch2.7cxx11abiFALSE-cp311-cp311-linux_x86_64.whl +https://github.com/state-spaces/mamba/releases/download/v2.2.5/mamba_ssm-2.2.5+cu12torch2.7cxx11abiFALSE-cp311-cp311-linux_x86_64.whl +https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.5.1/causal_conv1d-1.5.1+cu12torch2.7cxx11abiFALSE-cp311-cp311-linux_x86_64.whl https://github.com/Dao-AILab/flash-attention/releases/download/v2.7.4.post1/flash_attn-2.7.4.post1+cu12torch2.7cxx11abiFALSE-cp311-cp311-linux_x86_64.whl From a17ab28b69bcee9110a14096c6a61e2aaace7dc2 Mon Sep 17 00:00:00 2001 From: maxime Date: Mon, 17 Nov 2025 17:06:59 +0100 Subject: [PATCH 4/5] taking out pip installs CI --- .github/workflows/main.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a497df09..d326d010 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -19,8 +19,6 @@ jobs: - name: Install dependencies run: | - pip uninstall mamba-ssm causal-conv1d flash-attn -y - pip install --no-cache-dir -r ./requirements_cuda.txt pip install -r requirements-dev.txt pip install .[mamba-ssm] From 6bcc0f29187bb789e1079faebc407f8f9ece67d6 Mon Sep 17 00:00:00 2001 From: Benoit Putzeys <157973952+bputzeys@users.noreply.github.com> Date: Mon, 17 Nov 2025 17:37:19 +0100 Subject: [PATCH 5/5] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 35ae4ff0..81f6e0ce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] name = "helical" -version = "1.4.12" +version = "1.4.13" authors = [ { name="Helical Team", email="support@helical-ai.com" }, ]