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Backport #915 to 2.0.x (#918)
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‎CHANGELOG.md‎

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# openpipelines 2.0.0-rc.2
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## BUG FIXES
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* `annotate/popv`: fix popv raising `ValueError` when an accelerator (e.g. GPU) is unavailable (PR #918, backported from PR #915).
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## MINOR CHANGES
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* `dataflow/split_h5mu`: Optimize resource usage of the component (PR #917, backported from PR #913).

‎src/annotate/popv/script.py‎

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save_path_trained_models=temp_dir,
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# hardcoded values
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cl_obo_folder=cl_obo_folder,
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accelerator='cuda' if use_gpu else None
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accelerator='cuda' if use_gpu else 'cpu'
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)
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method_kwargs = {}
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if 'scanorama' in par['methods']:

‎src/annotate/popv/test.py‎

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@@ -43,7 +43,7 @@ def test_popv_with_other_layer(run_component, tmp_path):
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"--input", tmp_path / "input.h5mu",
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"--reference", reference_file,
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"--output", "output.h5mu",
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"--methods", "rf;svm;knn_on_scanorama"
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"--methods", "rf;svm;knn_on_scanorama;knn_on_scvi"
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])
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def test_popv_with_non_overlapping_cells(run_component, tmp_path):

‎target/executable/annotate/celltypist/.config.vsh.yaml‎

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output: "target/executable/annotate/celltypist"
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executable: "target/executable/annotate/celltypist/celltypist"
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viash_version: "0.9.0"
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git_commit: "686217bf7f7dadccb6d8a730b953d8124da01c58"
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git_commit: "110cb5de582bb6fb0f8f8301faf3accca016b93b"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "2.0.0-rc.1-1-g686217bf7f"
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git_tag: "2.0.0-rc.1-2-g110cb5de58"
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package_config:
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name: "openpipeline"
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version: "dev"

‎target/executable/annotate/celltypist/celltypist‎

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LABEL org.opencontainers.image.authors="Jakub Majercik, Weiwei Schultz"
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LABEL org.opencontainers.image.description="Companion container for running component annotate celltypist"
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LABEL org.opencontainers.image.created="2024-11-27T14:19:07Z"
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LABEL org.opencontainers.image.created="2024-11-27T15:31:12Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="686217bf7f7dadccb6d8a730b953d8124da01c58"
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LABEL org.opencontainers.image.revision="110cb5de582bb6fb0f8f8301faf3accca016b93b"
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LABEL org.opencontainers.image.version="2.0.0-rc.2"
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VIASHDOCKER

‎target/executable/annotate/onclass/.config.vsh.yaml‎

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output: "target/executable/annotate/onclass"
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executable: "target/executable/annotate/onclass/onclass"
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viash_version: "0.9.0"
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git_commit: "686217bf7f7dadccb6d8a730b953d8124da01c58"
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git_commit: "110cb5de582bb6fb0f8f8301faf3accca016b93b"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "2.0.0-rc.1-1-g686217bf7f"
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git_tag: "2.0.0-rc.1-2-g110cb5de58"
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package_config:
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name: "openpipeline"
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version: "dev"

‎target/executable/annotate/onclass/onclass‎

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LABEL org.opencontainers.image.authors="Jakub Majercik"
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LABEL org.opencontainers.image.description="Companion container for running component annotate onclass"
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LABEL org.opencontainers.image.created="2024-11-27T14:19:06Z"
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LABEL org.opencontainers.image.created="2024-11-27T15:31:11Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="686217bf7f7dadccb6d8a730b953d8124da01c58"
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LABEL org.opencontainers.image.revision="110cb5de582bb6fb0f8f8301faf3accca016b93b"
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LABEL org.opencontainers.image.version="2.0.0-rc.2"
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VIASHDOCKER

‎target/executable/annotate/popv/.config.vsh.yaml‎

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output: "target/executable/annotate/popv"
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executable: "target/executable/annotate/popv/popv"
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viash_version: "0.9.0"
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git_commit: "686217bf7f7dadccb6d8a730b953d8124da01c58"
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git_commit: "110cb5de582bb6fb0f8f8301faf3accca016b93b"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "2.0.0-rc.1-1-g686217bf7f"
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git_tag: "2.0.0-rc.1-2-g110cb5de58"
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package_config:
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name: "openpipeline"
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version: "dev"

‎target/executable/annotate/popv/popv‎

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@@ -561,9 +561,9 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git
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LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt"
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LABEL org.opencontainers.image.description="Companion container for running component annotate popv"
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LABEL org.opencontainers.image.created="2024-11-27T14:19:06Z"
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LABEL org.opencontainers.image.created="2024-11-27T15:31:11Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="686217bf7f7dadccb6d8a730b953d8124da01c58"
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LABEL org.opencontainers.image.revision="110cb5de582bb6fb0f8f8301faf3accca016b93b"
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LABEL org.opencontainers.image.version="2.0.0-rc.2"
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VIASHDOCKER
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save_path_trained_models=temp_dir,
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# hardcoded values
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cl_obo_folder=cl_obo_folder,
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accelerator='cuda' if use_gpu else None
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accelerator='cuda' if use_gpu else 'cpu'
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)
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method_kwargs = {}
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if 'scanorama' in par['methods']:

‎target/executable/annotate/random_forest_annotation/.config.vsh.yaml‎

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output: "target/executable/annotate/random_forest_annotation"
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executable: "target/executable/annotate/random_forest_annotation/random_forest_annotation"
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viash_version: "0.9.0"
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git_commit: "686217bf7f7dadccb6d8a730b953d8124da01c58"
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git_commit: "110cb5de582bb6fb0f8f8301faf3accca016b93b"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "2.0.0-rc.1-1-g686217bf7f"
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git_tag: "2.0.0-rc.1-2-g110cb5de58"
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package_config:
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name: "openpipeline"
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version: "dev"

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