diff --git a/CHANGELOG.md b/CHANGELOG.md index 718d8d91..55e9ee63 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,12 @@ * `cellmapper_linear`: Write the unmasked variants as `mask_var: null` rather than `mask_var: None`, which YAML reads as the string `"None"` and which would resolve to `adata.var["None"]` (PR #38). +* `comp_method`: Run `check_config.py` as part of the component tests, so method metadata is validated like control methods and metrics already are (PR #37). + +* `knnr_py`, `knnr_r`, `lm`, `guanlab_dengkw_pm`: Move `documentation_url` and `repository_url` out of `info` and into the top-level `links` (PR #37). + +* `novel`, `simple_mlp`: Add a placeholder Nextflow resource label. Viash renders no process for a `nextflow_script` component, so the label is inert -- it is only there because `check_config` requires one. Can be removed once openproblems-bio/core#41 is released (PR #37). + ## BUG FIXES * Fix the component paths, build paths and `rename_keys` separator in the helper scripts, which prevented `scripts/create_datasets/test_resources.sh` and both `run_test.sh` scripts from running at all (PR #22). diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml index c3c56508..9414b6ea 100644 --- a/src/api/comp_method.yaml +++ b/src/api/comp_method.yaml @@ -24,6 +24,8 @@ arguments: direction: output required: true test_resources: + - type: python_script + path: /common/component_tests/check_config.py - type: python_script path: /common/component_tests/run_and_check_output.py - path: /resources_test/task_predict_modality/openproblems_neurips2021/bmmc_cite/swap diff --git a/src/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/methods/guanlab_dengkw_pm/config.vsh.yaml index e10d658c..925b5591 100644 --- a/src/methods/guanlab_dengkw_pm/config.vsh.yaml +++ b/src/methods/guanlab_dengkw_pm/config.vsh.yaml @@ -11,10 +11,11 @@ description: | singular vectors. references: doi: 10.1101/2022.04.11.487796 +links: + documentation: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw + repository: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw info: preferred_normalization: log_cp10k - documentation_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw - repository_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw competition_submission_id: 170636 arguments: - name: "--distance_method" diff --git a/src/methods/knnr_py/config.vsh.yaml b/src/methods/knnr_py/config.vsh.yaml index ca8df0d8..2c87c75f 100644 --- a/src/methods/knnr_py/config.vsh.yaml +++ b/src/methods/knnr_py/config.vsh.yaml @@ -5,9 +5,10 @@ summary: K-nearest neighbor regression in Python. description: K-nearest neighbor regression in Python. references: doi: 10.2307/1403797 +links: + documentation: https://scikit-learn.org/stable/modules/neighbors.html + repository: https://github.com/scikit-learn/scikit-learn info: - documentation_url: https://scikit-learn.org/stable/modules/neighbors.html - repository_url: https://github.com/scikit-learn/scikit-learn preferred_normalization: log_cp10k arguments: - name: "--distance_method" diff --git a/src/methods/knnr_r/config.vsh.yaml b/src/methods/knnr_r/config.vsh.yaml index 0af5de3d..8a163d93 100644 --- a/src/methods/knnr_r/config.vsh.yaml +++ b/src/methods/knnr_r/config.vsh.yaml @@ -5,9 +5,10 @@ summary: K-nearest neighbor regression in R. description: K-nearest neighbor regression in R. references: doi: 10.2307/1403797 +links: + documentation: https://cran.r-project.org/package=FNN + repository: https://github.com/cran/FNN info: - documentation_url: https://cran.r-project.org/package=FNN - repository_url: https://github.com/cran/FNN preferred_normalization: log_cp10k arguments: - name: "--distance_method" diff --git a/src/methods/lm/config.vsh.yaml b/src/methods/lm/config.vsh.yaml index b41977ba..6f6223b8 100644 --- a/src/methods/lm/config.vsh.yaml +++ b/src/methods/lm/config.vsh.yaml @@ -5,9 +5,10 @@ summary: Linear model regression. description: A linear model regression method. references: doi: 10.2307/2346786 +links: + documentation: https://cran.r-project.org/package=RcppArmadillo + repository: https://github.com/RcppCore/RcppArmadillo info: - repository_url: https://github.com/RcppCore/RcppArmadillo - documentation_url: https://cran.r-project.org/package=RcppArmadillo preferred_normalization: log_cp10k arguments: - name: "--distance_method" diff --git a/src/methods/novel/novel/config.vsh.yaml b/src/methods/novel/novel/config.vsh.yaml index a30a31e4..f372f394 100644 --- a/src/methods/novel/novel/config.vsh.yaml +++ b/src/methods/novel/novel/config.vsh.yaml @@ -20,4 +20,7 @@ dependencies: - name: methods/novel_train - name: methods/novel_predict runners: - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + # inert placeholder -- remove when check_config is updated (openproblems-bio/core#41) + label: [lowtime, lowmem, lowcpu] diff --git a/src/methods/simple_mlp/simple_mlp/config.vsh.yaml b/src/methods/simple_mlp/simple_mlp/config.vsh.yaml index fe5ca358..6b61d154 100644 --- a/src/methods/simple_mlp/simple_mlp/config.vsh.yaml +++ b/src/methods/simple_mlp/simple_mlp/config.vsh.yaml @@ -25,3 +25,6 @@ dependencies: - name: methods/simple_mlp_predict runners: - type: nextflow + directives: + # inert placeholder -- remove when check_config is updated (openproblems-bio/core#41) + label: [lowtime, lowmem, lowcpu]