diff --git a/CHANGELOG.md b/CHANGELOG.md index ece229b1d35..d9b97527d14 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,8 @@ * Fix running `neigbors_leiden_umap` workflow with `-stub` enabled (PR #1026). +* Add missing CUDA enabled `jaxlib` to components that use `scvi-tools` (`scanvi`, `scarches`, `scvi` and `totalvi`) (PR #1028) + # openpipelines 2.1.0 ## BREAKING CHANGES diff --git a/src/annotate/scanvi/config.vsh.yaml b/src/annotate/scanvi/config.vsh.yaml index 27bc8107464..96b22e15779 100644 --- a/src/annotate/scanvi/config.vsh.yaml +++ b/src/annotate/scanvi/config.vsh.yaml @@ -146,6 +146,7 @@ engines: __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .] - type: python packages: + - jax[cuda] - scvi-tools~=1.1.5 test_setup: - type: python diff --git a/src/integrate/scarches/config.vsh.yaml b/src/integrate/scarches/config.vsh.yaml index 1460ef2847b..d5c6d2953d1 100644 --- a/src/integrate/scarches/config.vsh.yaml +++ b/src/integrate/scarches/config.vsh.yaml @@ -147,6 +147,7 @@ engines: - type: python __merge__: [/src/base/requirements/anndata_mudata.yaml, .] packages: + - jax[cuda] - scvi-tools~=1.1.5 test_setup: - type: python diff --git a/src/integrate/scvi/config.vsh.yaml b/src/integrate/scvi/config.vsh.yaml index 7bd5ffa0ec5..f3cef372030 100644 --- a/src/integrate/scvi/config.vsh.yaml +++ b/src/integrate/scvi/config.vsh.yaml @@ -233,6 +233,7 @@ engines: __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .] - type: python packages: + - jax[cuda] - scvi-tools~=1.1.5 test_setup: - type: python diff --git a/src/integrate/totalvi/config.vsh.yaml b/src/integrate/totalvi/config.vsh.yaml index c733ab682ba..9a150326ef0 100644 --- a/src/integrate/totalvi/config.vsh.yaml +++ b/src/integrate/totalvi/config.vsh.yaml @@ -120,6 +120,7 @@ engines: - type: python __merge__: [/src/base/requirements/anndata_mudata.yaml, .] packages: + - jax[cuda] - scvi-tools~=1.1.5 test_setup: - type: python