From e7582aae04ec288fe2260d1174c54f6f5f1560b0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 4 Sep 2024 11:53:30 +0200 Subject: [PATCH] update images (#464) * update images * fix numpy issues * fix scib kbet by pinning scipy to <= 1.13 (see theislab/scib#412) * remove unnecessary workaround * add workaround to other mse component * update viash test to only run on the main branch or in PRs Former-commit-id: 9493835133c6b033f2bf44fb174f2472883667af --- .github/workflows/viash-test.yml | 21 +------------------ CONTRIBUTING.qmd | 2 +- .../check_dataset_schema/config.vsh.yaml | 2 +- src/common/check_yaml_schema/config.vsh.yaml | 2 +- src/common/create_component/script.py | 4 ++-- src/common/create_task_readme/config.vsh.yaml | 2 +- src/common/extract_metadata/config.vsh.yaml | 2 +- src/common/extract_scores/config.vsh.yaml | 2 +- .../check_obsolete_terms/config.vsh.yaml | 2 +- .../generate_qc/config.vsh.yaml | 2 +- .../get_api_info/config.vsh.yaml | 2 +- .../get_dataset_info/config.vsh.yaml | 2 +- .../get_method_info/config.vsh.yaml | 2 +- .../get_metric_info/config.vsh.yaml | 2 +- .../get_results/config.vsh.yaml | 2 +- .../get_task_info/config.vsh.yaml | 2 +- .../yaml_to_json/config.vsh.yaml | 2 +- .../loaders/cellxgene_census/config.vsh.yaml | 2 +- .../config.vsh.yaml | 2 +- .../config.vsh.yaml | 4 ++-- .../config.vsh.yaml | 2 +- .../loaders/openproblems_v1/config.vsh.yaml | 2 +- .../config.vsh.yaml | 2 +- .../normalization/atac_tfidf/config.vsh.yaml | 2 +- .../normalization/l1_sqrt/config.vsh.yaml | 4 ++-- .../normalization/log_cp/config.vsh.yaml | 2 +- .../log_scran_pooling/config.vsh.yaml | 2 +- .../normalization/prot_clr/config.vsh.yaml | 2 +- .../normalization/sqrt_cp/config.vsh.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 2 +- src/datasets/processors/knn/config.vsh.yaml | 2 +- src/datasets/processors/pca/config.vsh.yaml | 2 +- .../processors/subsample/config.vsh.yaml | 2 +- src/datasets/processors/svd/config.vsh.yaml | 2 +- .../check_migration_status/config.vsh.yaml | 2 +- src/migration/list_git_shas/config.vsh.yaml | 2 +- src/migration/update_bibtex/config.vsh.yaml | 2 +- .../batch_embed/config.vsh.yaml | 2 +- .../global_embed/config.vsh.yaml | 2 +- .../global_feature/config.vsh.yaml | 2 +- .../global_graph/config.vsh.yaml | 2 +- .../celltype_embed/config.vsh.yaml | 2 +- .../celltype_jitter_embed/config.vsh.yaml | 2 +- .../batch_embed/config.vsh.yaml | 2 +- .../batch_feature/config.vsh.yaml | 2 +- .../batch_graph/config.vsh.yaml | 2 +- .../celltype_embed/config.vsh.yaml | 2 +- .../celltype_feature/config.vsh.yaml | 2 +- .../celltype_graph/config.vsh.yaml | 2 +- .../global_embed/config.vsh.yaml | 2 +- .../global_feature/config.vsh.yaml | 2 +- .../global_graph/config.vsh.yaml | 2 +- .../methods/bbknn/config.vsh.yaml | 2 +- .../methods/combat/config.vsh.yaml | 2 +- .../methods/fastmnn_embedding/config.vsh.yaml | 2 +- .../methods/fastmnn_feature/config.vsh.yaml | 2 +- .../methods/liger/config.vsh.yaml | 2 +- .../methods/mnn_correct/config.vsh.yaml | 2 +- .../methods/pyliger/config.vsh.yaml | 2 +- .../methods/scalex_embed/config.vsh.yaml | 2 +- .../methods/scalex_feature/config.vsh.yaml | 2 +- .../methods/scanorama_embed/config.vsh.yaml | 2 +- .../methods/scanorama_feature/config.vsh.yaml | 2 +- .../methods/scanvi/config.vsh.yaml | 2 +- .../methods/scvi/config.vsh.yaml | 2 +- .../metrics/asw_batch/config.vsh.yaml | 2 +- .../metrics/asw_label/config.vsh.yaml | 2 +- .../cell_cycle_conservation/config.vsh.yaml | 2 +- .../clustering_overlap/config.vsh.yaml | 2 +- .../graph_connectivity/config.vsh.yaml | 2 +- .../metrics/hvg_overlap/config.vsh.yaml | 2 +- .../isolated_label_asw/config.vsh.yaml | 2 +- .../metrics/isolated_label_f1/config.vsh.yaml | 2 +- .../metrics/kbet/config.vsh.yaml | 3 ++- .../metrics/lisi/config.vsh.yaml | 2 +- .../metrics/pcr/config.vsh.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../embed_to_graph/config.vsh.yaml | 2 +- .../feature_to_embed/config.vsh.yaml | 2 +- .../no_denoising/config.vsh.yaml | 2 +- .../perfect_denoising/config.vsh.yaml | 2 +- .../denoising/methods/alra/config.vsh.yaml | 2 +- .../methods/knn_smoothing/config.vsh.yaml | 2 +- .../denoising/methods/magic/config.vsh.yaml | 2 +- .../denoising/methods/saver/config.vsh.yaml | 2 +- .../denoising/metrics/mse/config.vsh.yaml | 2 +- .../denoising/metrics/poisson/config.vsh.yaml | 2 +- .../denoising/process_dataset/config.vsh.yaml | 2 +- .../random_features/config.vsh.yaml | 2 +- .../spectral_features/config.vsh.yaml | 2 +- .../true_features/config.vsh.yaml | 2 +- .../methods/densmap/config.vsh.yaml | 2 +- .../methods/diffusion_map/config.vsh.yaml | 2 +- .../methods/ivis/config.vsh.yaml | 2 +- .../methods/lmds/config.vsh.yaml | 2 +- .../methods/neuralee/config.vsh.yaml | 2 +- .../methods/pca/config.vsh.yaml | 2 +- .../methods/phate/config.vsh.yaml | 2 +- .../methods/pymde/config.vsh.yaml | 2 +- .../methods/simlr/config.vsh.yaml | 2 +- .../methods/tsne/config.vsh.yaml | 2 +- .../methods/umap/config.vsh.yaml | 2 +- .../clustering_performance/config.vsh.yaml | 2 +- .../metrics/coranking/config.vsh.yaml | 2 +- .../density_preservation/config.vsh.yaml | 2 +- .../distance_correlation/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../majority_vote/config.vsh.yaml | 2 +- .../random_labels/config.vsh.yaml | 2 +- .../true_labels/config.vsh.yaml | 2 +- .../methods/knn/config.vsh.yaml | 2 +- .../logistic_regression/config.vsh.yaml | 2 +- .../methods/mlp/config.vsh.yaml | 2 +- .../methods/naive_bayes/config.vsh.yaml | 2 +- .../methods/scanvi/config.vsh.yaml | 2 +- .../methods/scanvi_scarches/config.vsh.yaml | 2 +- .../seurat_transferdata/config.vsh.yaml | 2 +- .../methods/xgboost/config.vsh.yaml | 2 +- .../metrics/accuracy/config.vsh.yaml | 2 +- .../metrics/f1/config.vsh.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../random_features/config.vsh.yaml | 2 +- .../true_features/config.vsh.yaml | 2 +- .../methods/fastmnn/config.vsh.yaml | 2 +- .../harmonic_alignment/config.vsh.yaml | 2 +- .../methods/procrustes/config.vsh.yaml | 2 +- .../methods/scot/config.vsh.yaml | 2 +- .../metrics/knn_auc/config.vsh.yaml | 2 +- .../metrics/mse/config.vsh.yaml | 4 ++-- .../process_dataset/config.vsh.yaml | 2 +- .../meanpergene/config.vsh.yaml | 2 +- .../random_predict/config.vsh.yaml | 2 +- .../control_methods/solution/config.vsh.yaml | 2 +- .../control_methods/zeros/config.vsh.yaml | 2 +- .../methods/guanlab_dengkw_pm/config.vsh.yaml | 2 +- .../methods/knnr_py/config.vsh.yaml | 2 +- .../methods/knnr_r/config.vsh.yaml | 2 +- .../methods/lm/config.vsh.yaml | 2 +- .../methods/lmds_irlba_rf/config.vsh.yaml | 2 +- .../methods/newwave_knnr/config.vsh.yaml | 2 +- .../methods/novel/predict/config.vsh.yaml | 2 +- .../methods/novel/train/config.vsh.yaml | 2 +- .../methods/random_forest/config.vsh.yaml | 2 +- .../simple_mlp/predict/config.vsh.yaml | 2 +- .../methods/simple_mlp/train/config.vsh.yaml | 2 +- .../metrics/correlation/config.vsh.yaml | 2 +- .../metrics/mse/config.vsh.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../random_proportions/config.vsh.yaml | 2 +- .../true_proportions/config.vsh.yaml | 2 +- .../dataset_simulator/config.vsh.yaml | 2 +- .../methods/cell2location/config.vsh.yaml | 2 +- .../methods/destvi/config.vsh.yaml | 2 +- .../methods/nmfreg/config.vsh.yaml | 2 +- .../methods/nnls/config.vsh.yaml | 2 +- .../methods/rctd/config.vsh.yaml | 2 +- .../methods/seurat/config.vsh.yaml | 2 +- .../methods/stereoscope/config.vsh.yaml | 2 +- .../methods/tangram/config.vsh.yaml | 2 +- .../methods/vanillanmf/config.vsh.yaml | 2 +- .../metrics/r2/config.vsh.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- 163 files changed, 168 insertions(+), 186 deletions(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index e7ebcf4875..b6bab576ed 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -3,34 +3,15 @@ name: viash test on: pull_request: push: - branches: [ '**' ] + branches: [ main ] jobs: - run_ci_check_job: - runs-on: ubuntu-latest - outputs: - run_ci: ${{ steps.github_cli.outputs.check }} - steps: - - name: 'Check if branch has an existing pull request and the trigger was a push' - id: github_cli - run: | - pull_request=$(gh pr list -R ${{ github.repository }} -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url') - # If the branch has a PR and this run was triggered by a push event, do not run - if [[ "$pull_request" != "null" && "$GITHUB_REF_NAME" != "main" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then - echo "check=false" >> $GITHUB_OUTPUT - else - echo "check=true" >> $GITHUB_OUTPUT - fi - env: - GITHUB_TOKEN: ${{ secrets.GTHB_PAT }} # phase 1 list: - needs: run_ci_check_job env: s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest - if: "needs.run_ci_check_job.outputs.run_ci == 'true'" outputs: matrix: ${{ steps.set_matrix.outputs.matrix }} diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 995c02d361..6b6e33ae07 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -185,7 +185,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: [scikit-learn] diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index d25bf5766e..08449c3e7d 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 test_setup: - type: python packages: viashpy diff --git a/src/common/check_yaml_schema/config.vsh.yaml b/src/common/check_yaml_schema/config.vsh.yaml index 40a62fd2c8..b87bec5429 100644 --- a/src/common/check_yaml_schema/config.vsh.yaml +++ b/src/common/check_yaml_schema/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 822d0eac87..8c954a66d4 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -141,11 +141,11 @@ def generate_resources(par, script_path) -> str: def generate_docker_platform(par) -> str: """Set up the docker platform for Python.""" if par["language"] == "python": - image_str = "ghcr.io/openproblems-bio/base_python:1.0.4" + image_str = "openproblems/base_python:1.0.0" setup_type = "python" package_example = "scib==1.1.5" elif par["language"] == "r": - image_str = "ghcr.io/openproblems-bio/base_r:1.0.4" + image_str = "openproblems/base_r:1.0.0" setup_type = "r" package_example = "tidyverse" return strip_margin(f'''\ diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index 6ba0a726c7..d268974ce8 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: dest: openproblems-v2/_viash.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, processx] diff --git a/src/common/extract_metadata/config.vsh.yaml b/src/common/extract_metadata/config.vsh.yaml index 0636812619..76e73cb975 100644 --- a/src/common/extract_metadata/config.vsh.yaml +++ b/src/common/extract_metadata/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 test_setup: - type: python packages: viashpy diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 46fb174924..72270b7a95 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/ontology/check_obsolete_terms/config.vsh.yaml b/src/common/ontology/check_obsolete_terms/config.vsh.yaml index dbb0506098..fc006f6cf9 100644 --- a/src/common/ontology/check_obsolete_terms/config.vsh.yaml +++ b/src/common/ontology/check_obsolete_terms/config.vsh.yaml @@ -70,7 +70,7 @@ functionality: - path: /resources_test/common/cellxgene_census platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r packages: [ dplyr, tidyr, tibble, ontologyIndex, processx ] \ No newline at end of file diff --git a/src/common/process_task_results/generate_qc/config.vsh.yaml b/src/common/process_task_results/generate_qc/config.vsh.yaml index 9b3b07dc01..68a5d19682 100644 --- a/src/common/process_task_results/generate_qc/config.vsh.yaml +++ b/src/common/process_task_results/generate_qc/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_api_info/config.vsh.yaml b/src/common/process_task_results/get_api_info/config.vsh.yaml index 2026c007ab..0e7eb1696e 100644 --- a/src/common/process_task_results/get_api_info/config.vsh.yaml +++ b/src/common/process_task_results/get_api_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_dataset_info/config.vsh.yaml b/src/common/process_task_results/get_dataset_info/config.vsh.yaml index 75f4952738..10247a22ba 100644 --- a/src/common/process_task_results/get_dataset_info/config.vsh.yaml +++ b/src/common/process_task_results/get_dataset_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_method_info/config.vsh.yaml b/src/common/process_task_results/get_method_info/config.vsh.yaml index ee606c852e..053bbac53c 100644 --- a/src/common/process_task_results/get_method_info/config.vsh.yaml +++ b/src/common/process_task_results/get_method_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_metric_info/config.vsh.yaml b/src/common/process_task_results/get_metric_info/config.vsh.yaml index e6555bca36..ee5833b5b9 100644 --- a/src/common/process_task_results/get_metric_info/config.vsh.yaml +++ b/src/common/process_task_results/get_metric_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_results/config.vsh.yaml b/src/common/process_task_results/get_results/config.vsh.yaml index 5e1b716731..cd639fad4d 100644 --- a/src/common/process_task_results/get_results/config.vsh.yaml +++ b/src/common/process_task_results/get_results/config.vsh.yaml @@ -42,7 +42,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ purrr, yaml, rlang, dplyr, tidyr, readr, lubridate, dynutils, processx ] diff --git a/src/common/process_task_results/get_task_info/config.vsh.yaml b/src/common/process_task_results/get_task_info/config.vsh.yaml index b74c67c3e7..2e8fbd2b66 100644 --- a/src/common/process_task_results/get_task_info/config.vsh.yaml +++ b/src/common/process_task_results/get_task_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/yaml_to_json/config.vsh.yaml b/src/common/process_task_results/yaml_to_json/config.vsh.yaml index de54b44cce..7231cdcdbf 100644 --- a/src/common/process_task_results/yaml_to_json/config.vsh.yaml +++ b/src/common/process_task_results/yaml_to_json/config.vsh.yaml @@ -11,6 +11,6 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow - type: native diff --git a/src/datasets/loaders/cellxgene_census/config.vsh.yaml b/src/datasets/loaders/cellxgene_census/config.vsh.yaml index f59547174a..667e1c6a6b 100644 --- a/src/datasets/loaders/cellxgene_census/config.vsh.yaml +++ b/src/datasets/loaders/cellxgene_census/config.vsh.yaml @@ -151,7 +151,7 @@ functionality: path: test.py platforms: - type: docker - #image: ghcr.io/openproblems-bio/base_python:1.0.4 + #image: openproblems/base_python:1.0.0 image: python:3.11 setup: - type: python diff --git a/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml b/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml index 91fad8769f..7ee4166d9d 100644 --- a/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml +++ b/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml @@ -114,7 +114,7 @@ functionality: path: test.py platforms: - type: docker - #image: ghcr.io/openproblems-bio/base_python:1.0.4 + #image: openproblems/base_python:1.0.0 image: python:3.11 setup: - type: python diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml index f8837cba6d..96dad30e76 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml @@ -68,7 +68,7 @@ functionality: # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: - label: [highmem, midcpu , midtime] \ No newline at end of file + label: [highmem, midcpu, midtime] \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml index a6d79c701d..b2141482f1 100644 --- a/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml @@ -74,7 +74,7 @@ functionality: # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ highmem, midcpu, midtime] \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 5a53755b82..a07a60d0ac 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -72,7 +72,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: apt packages: git diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index 0f07dbff62..812e52be62 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -80,7 +80,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: apt packages: git diff --git a/src/datasets/normalization/atac_tfidf/config.vsh.yaml b/src/datasets/normalization/atac_tfidf/config.vsh.yaml index 3240fec43f..5a8f56306a 100644 --- a/src/datasets/normalization/atac_tfidf/config.vsh.yaml +++ b/src/datasets/normalization/atac_tfidf/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index a133bdee48..212eadc968 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -16,12 +16,12 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: - scprep - - numpy + - numpy<2 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml index dd02663380..a040258526 100644 --- a/src/datasets/normalization/log_cp/config.vsh.yaml +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: "Number of counts per cell" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 3431e8174b..4cbf81ff5a 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ Matrix, rlang, scran, BiocParallel ] diff --git a/src/datasets/normalization/prot_clr/config.vsh.yaml b/src/datasets/normalization/prot_clr/config.vsh.yaml index 351cc0569a..8f6bbe269f 100644 --- a/src/datasets/normalization/prot_clr/config.vsh.yaml +++ b/src/datasets/normalization/prot_clr/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml index 7da0165229..4d95636f4c 100644 --- a/src/datasets/normalization/sqrt_cp/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: "Number of counts per cell" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index d2702d90d6..aed18c6d38 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 652676ab90..9908fe9086 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 027faf1e08..7f0213b922 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index bbfacdf832..4e52e93db5 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: - path: /resources_test/common/pancreas platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 test_setup: - type: python packages: diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml index e59865da5e..bbad17f58c 100644 --- a/src/datasets/processors/svd/config.vsh.yaml +++ b/src/datasets/processors/svd/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: [scikit-learn] diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml index a2dea51e00..bd8107381c 100644 --- a/src/migration/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -25,6 +25,6 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow - type: native diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml index 53fc63aabb..c70366612a 100644 --- a/src/migration/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" diff --git a/src/migration/update_bibtex/config.vsh.yaml b/src/migration/update_bibtex/config.vsh.yaml index 0df07b66c2..147e0b6c22 100644 --- a/src/migration/update_bibtex/config.vsh.yaml +++ b/src/migration/update_bibtex/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: git+https://github.com/sciunto-org/python-bibtexparser@main diff --git a/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml index 9e7a05b56f..c2484fbaa2 100644 --- a/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml index 229f5e7352..95212518c5 100644 --- a/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml index d480b4bb3e..b20701c8f1 100644 --- a/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml index afaed6346a..86886ce263 100644 --- a/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml index 4dec4675f4..6c853a7719 100644 --- a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml index 07ec9dfc68..e945e3bc58 100644 --- a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml index 09e1d2d731..d8bcee01d4 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml index c26ac8027e..5f98284bb9 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml index 761cfc6ccd..72a12c5031 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml index aeef32e5e7..b4457498c9 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml index 843b45cd36..7c483739c2 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml index 13fa6213e7..6015185616 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml index 7b8efce8e8..0343c37817 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml index 09551d3078..f49ee146a1 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml index fb0db3f66c..1b92cbc70a 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: - path: ../../utils.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 99f8346ed4..8eff37339f 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 198b20dc3d..f94333627d 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, highmem, lowcpu] diff --git a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml index 11eb009031..cd885da3cd 100644 --- a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: ../fastmnn_feature/script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/r:1.1.0 + image: openproblems/base_r:1.0.0 setup: - type: r bioc: diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml index b3036f278c..e28406eb54 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/r:1.1.0 + image: openproblems/base_r:1.0.0 setup: - type: r bioc: batchelor diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index bc5ec32a64..4c638d467b 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/r:1.1.0 + image: openproblems/base_r:1.0.0 setup: - type: apt packages: cmake diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml index 683bc17af9..1c999fa540 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/r:1.1.0 + image: openproblems/base_r:1.0.0 setup: - type: r bioc: diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index f0489da337..cf16b2e684 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml index e448d11006..3437df19c9 100644 --- a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml index f25023f730..1874bc190e 100644 --- a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index 68161f0ebc..b5dcd8f54a 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index e70e68bb48..3f735ddffd 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index becf9467c2..5615fd72cd 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index 68485a188c..45eb09d5cf 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index c8ac04f374..be6567271c 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -40,7 +40,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 21e40aad42..068381b9e3 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 42fe1c8fa8..3852029a60 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -37,7 +37,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index ee74fb410b..8d92033e40 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -51,7 +51,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml index 77e5191d33..6384feca62 100644 --- a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml @@ -37,7 +37,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml index 803c535420..a8025783d6 100644 --- a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml index d3d62877b5..65e1970c4f 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml @@ -30,7 +30,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml index f36550ca4b..6b8f0703bf 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml @@ -42,7 +42,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml index f2d83d8030..aca556a8fc 100644 --- a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml @@ -42,7 +42,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/r:1.1.0 + image: openproblems/base_r:1.0.0 setup: - type: r github: theislab/kBET @@ -51,6 +51,7 @@ platforms: - scib==1.1.5 - rpy2>=3 - anndata2ri + - scipy<=1.13 - type: nextflow directives: label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml index dc87c769e4..750574f84a 100644 --- a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index 4eb6c0f854..d3391fb528 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -34,7 +34,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index 0dbe5f3bcd..73ea5815c3 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index 0bbaf29256..e841081a91 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index ca576977b6..e08013c63b 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -14,7 +14,7 @@ functionality: path: /src/common/helper_functions/read_anndata_partial.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, midmem, lowcpu] diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index ec3ed2469d..64a35f9986 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index c36581e205..b16862360b 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, midmem, midcpu] diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index 1354b5c00c..374d317fce 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ Matrix, rsvd ] diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index 975d729990..b0c55ae0d8 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 0d2ff14c98..380666a1b5 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -54,7 +54,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python pip: [scprep, magic-impute, scipy, scikit-learn<1.2] diff --git a/src/tasks/denoising/methods/saver/config.vsh.yaml b/src/tasks/denoising/methods/saver/config.vsh.yaml index fcd3e4b88a..3c997fc36f 100644 --- a/src/tasks/denoising/methods/saver/config.vsh.yaml +++ b/src/tasks/denoising/methods/saver/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r github: mohuangx/SAVER diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index 3260c2694a..8330a8de31 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index 5d239b0c92..e523a9306e 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python pip: scprep diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index 6c30e6ab12..c9b5b06c1a 100644 --- a/src/tasks/denoising/process_dataset/config.vsh.yaml +++ b/src/tasks/denoising/process_dataset/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: - path: helper.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index cc5a4be442..6c0d36ad44 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, highmem, highcpu] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml index 8e409f7bbc..b3ae5aa95b 100644 --- a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 43f660d34d..a83d393072 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index 778ee410bb..ff5764a561 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml index e8ad2b1f99..ced082c708 100644 --- a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -22,7 +22,7 @@ functionality: default: 3 platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r bioc: destiny diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index 9f72001546..aa3c5ca0b4 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml index 98a7cd53a4..2b651271a9 100644 --- a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ Matrix, lmds ] diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 130cd7faf2..0d3d0234c4 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -44,7 +44,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index ec86b6725f..11d3841fb6 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scanpy diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index 1c2dd68e2b..ff63659780 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml index 1948fd51ea..2f733bb714 100644 --- a/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: pymde diff --git a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml index 210801ac0e..ba4b7b3b84 100644 --- a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml @@ -45,7 +45,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r packages: [ grDevices ] diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 9dbc917e0f..cedaba0484 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: apt packages: diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index 6b4b222fef..a073e9dbe3 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -39,7 +39,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml index 56757c0a02..67f1078f13 100644 --- a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml @@ -51,7 +51,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: [ scikit-learn, scanpy, leidenalg ] diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index b7a82fe3d7..6787e88f7e 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -157,7 +157,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ coRanking ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index c421f6a479..4b1e9f3a32 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -30,7 +30,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml index 44ff1950e5..b08c93db2c 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 2e66527bd4..5f75fa8e26 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index 292318947d..d6f62e0c7e 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, highmem, highcpu] diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index 641cc89b71..8f0915a1dd 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index 52f4c6a072..728157a644 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scanpy diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index c464a3a9dc..ec536fcc7d 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index a083f1ff20..499fa69e81 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: [scikit-learn, jsonschema] diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index 2497d5c803..88f4c2d5af 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index 944ed6e4f7..9c7e92fc68 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml b/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml index 2a09c7fa5d..90f6e72a52 100644 --- a/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml +++ b/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index b271878a5c..6c36ead072 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 setup: - type: python packages: diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index ddd18f4e91..ccf2f449b4 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 setup: - type: python pypi: scvi-tools>=1.1.0 diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 2bdac1c370..d51b532917 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ Matrix>=1.5.3, Seurat, rlang ] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index d0892b9e8c..516308fbdd 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: xgboost diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index cad211fd77..8fc7021ffa 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index d059a236bb..f5abc0caa6 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index 63724de9cd..aa010876cb 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [highmem, midcpu , midtime] diff --git a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml index efe3dd5e42..8c021c3bdf 100644 --- a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml index 0fefd7f49b..bc897dd821 100644 --- a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml index db343218b7..4e143ec67b 100644 --- a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r bioc: batchelor diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml index 466c26d160..3146db56e0 100644 --- a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python github: diff --git a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml index e0c95afcc2..db7b49383b 100644 --- a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml index 5ea1a45164..e86fe4438a 100644 --- a/src/tasks/match_modalities/methods/scot/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: apt packages: git diff --git a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml index d629f20c38..e7067a20b5 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml index a6fadd43f1..b1dfc15746 100644 --- a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -20,11 +20,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: - - numpy + - numpy<2 - scipy - scprep - type: nextflow diff --git a/src/tasks/match_modalities/process_dataset/config.vsh.yaml b/src/tasks/match_modalities/process_dataset/config.vsh.yaml index 4560b350b3..35dc757809 100644 --- a/src/tasks/match_modalities/process_dataset/config.vsh.yaml +++ b/src/tasks/match_modalities/process_dataset/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [highmem, midcpu , midtime] diff --git a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml index 87696bd678..9521b90508 100644 --- a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml index d36e02d3c0..3324c53a91 100644 --- a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml index 64cf880a97..350b0e79ea 100644 --- a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml index d557556c32..344df9c338 100644 --- a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml index a81ed56cb3..8663123ad9 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml index 4ef88dd62b..543ee71fa1 100644 --- a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [hightime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml index cda809b109..448b3ca0b8 100644 --- a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ lmds, FNN, proxyC] diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml index 98d3268abd..3fdbc0f243 100644 --- a/src/tasks/predict_modality/methods/lm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ lmds, RcppArmadillo, pbapply] diff --git a/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml b/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml index 37906c9c96..ba86f0631e 100644 --- a/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [lmds, ranger, pbapply, irlba] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index 1e01b4fc6a..385f1234bb 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ lmds, FNN, proxy, proxyC ] diff --git a/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml b/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml index 2efc42a59f..72e3292407 100644 --- a/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: - path: ../helper_functions.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 setup: - type: python packages: diff --git a/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml b/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml index a6ae6a4bb8..87ea471301 100644 --- a/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: - path: ../helper_functions.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 setup: - type: python packages: diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml index 110582e07c..a1ee69041d 100644 --- a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ lmds, ranger, pbapply] diff --git a/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml b/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml index e5806b395c..ef972e416f 100644 --- a/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: platforms: - type: docker # image: pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 # run_args: ["--gpus all --ipc=host"] setup: - type: python diff --git a/src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml b/src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml index 9a063324b8..8bcf75b97d 100644 --- a/src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: platforms: - type: docker # image: pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 # run_args: ["--gpus all --ipc=host"] setup: - type: python diff --git a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml index c3837e990a..9d297a147d 100644 --- a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml @@ -56,7 +56,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ proxyC, testthat, dynutils ] diff --git a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml index a80c7a15a6..78fbcc8efc 100644 --- a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index fdf7e3ab39..ec52472896 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 - type: nextflow directives: label: [hightime, highmem, highcpu] diff --git a/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml b/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml index a0ccc70c61..4134e7b7d5 100644 --- a/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: numpy diff --git a/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml b/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml index 7979f59c1e..0c58473acc 100644 --- a/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: native - type: nextflow directives: diff --git a/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml b/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml index a0151c8bc3..5295a9e79d 100644 --- a/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml @@ -191,7 +191,7 @@ functionality: dest: resources_test/common/cxg_mouse_pancreas_atlas platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: [numpy, scanpy] diff --git a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml index 42b99b0d9e..14ca1fb518 100644 --- a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml @@ -71,7 +71,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml index a415bd760c..3a642e0a23 100644 --- a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml index 97320cb550..0d32f2d410 100644 --- a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml index 537c7140cf..100458b95a 100644 --- a/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml index 2d2f82ca47..57ab923a75 100644 --- a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ Matrix, pak ] diff --git a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml index c82a1c9a7b..86c15cff30 100644 --- a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [Matrix, Seurat] diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml index f9a74dd9ff..4c8ca98bb1 100644 --- a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml index e1320e750e..652b276927 100644 --- a/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: tangram-sc diff --git a/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml index 7341cee6f2..7b04a40e93 100644 --- a/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml b/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml index bc5585f2b6..96679c5be4 100644 --- a/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml @@ -22,7 +22,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml b/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml index 292318947d..d6f62e0c7e 100644 --- a/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 - type: nextflow directives: label: [midtime, highmem, highcpu]