Minor refactoring (#68)

* rename folder

* fix descriptions

* fix gh action

* update readme

.github/workflows/build.yml

@@ -5,8 +5,11 @@ on:
     branches: [ 'main' ]
   workflow_dispatch:
     inputs:
+      target_branch:
+        description: 'Branch to deploy to. If not specified, `build/${BRANCH_NAME}` will be used.'
+        required: false
       version:
-        description: 'Version name to use for the build. If not specified, `${BRANCH_NAME}_build` will be used.'
+        description: 'Version name to use for the build. If not specified, `build/${BRANCH_NAME}` will be used.'
         required: false
 
 jobs:
@@ -15,7 +18,8 @@ jobs:
     runs-on: ubuntu-latest
 
     outputs:
-      version: ${{ steps.version.outputs.version }}
+      target_branch: ${{ steps.defaults.outputs.target_branch }}
+      version: ${{ steps.defaults.outputs.version }}
       component_matrix: ${{ steps.set_matrix.outputs.matrix }}
 
     steps:
@@ -24,13 +28,21 @@ jobs:
     - uses: viash-io/viash-actions/setup@v5
 
     - name: Determine version tag from branch name
-      id: version
+      id: defaults
       run: |
-        if [ -z "$INPUT_VERSION" ]; then
-          echo "version=$(echo $GITHUB_REF | sed 's/refs\/heads\/\(.*\)/\1_build/')" >> $GITHUB_OUTPUT
-        else
-          echo "version=$INPUT_VERSION" >> $GITHUB_OUTPUT
+        BRANCH_NAME=$(echo $GITHUB_REF | sed 's/refs\/heads\///')
+
+        VERSION=${{ github.event.inputs.version }}
+        if [ -z "$VERSION" ]; then
+          VERSION="build/$BRANCH_NAME"
+        fi
+        echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+        TARGET_BRANCH=${{ github.event.inputs.target_branch }}
+        if [ -z "$TARGET_BRANCH" ]; then
+          TARGET_BRANCH="build/$BRANCH_NAME"
         fi
+        echo "target_branch=$TARGET_BRANCH" >> $GITHUB_OUTPUT
 
     - name: Remove target folder from .gitignore
       run: |
@@ -39,15 +51,15 @@ jobs:
 
     - uses: viash-io/viash-actions/ns-build@v5
       with:
-        config_mod: .functionality.version := '${{ steps.version.outputs.version }}'
+        config_mod: .functionality.version := '${{ steps.defaults.outputs.version }}'
         parallel: true
 
     - name: Deploy to target branch
       uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: .
-        publish_branch: ${{ steps.version.outputs.version }}
+        publish_branch: ${{ steps.defaults.outputs.target_branch }}
 
     - id: ns_list
       uses: viash-io/viash-actions/ns-list@v5

README.md

@@ -379,13 +379,12 @@ Arguments:
 
 </div>
 
-
 ## Component type: Method
 
 Path:
 [`src/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/methods)
 
-A regression method.
+A perturbation prediction method
 
 Arguments:
 
@@ -406,7 +405,7 @@ Arguments:
 Path:
 [`src/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/metrics)
 
-A metric to compare two predictions.
+A perturbation prediction metric
 
 Arguments:
 

src/api/comp_control_method.yaml

@@ -6,7 +6,7 @@ functionality:
       label: Control Method
       summary: A control method.
       description: |
-        A control method to predict perturbation effects.
+        A control method to serve as a quality control for the perturbation prediction benchmark.
   arguments:
     - name: --de_train_h5ad
       __merge__: file_de_train_h5ad.yaml

src/api/comp_method.yaml

@@ -1,4 +1,4 @@
-__merge__: comp_method_notest.yaml
+__merge__: wf_method.yaml
 functionality:
   test_resources:
     - type: python_script

src/api/comp_metric.yaml

@@ -4,9 +4,9 @@ functionality:
     type: metric
     type_info:
       label: Metric
-      summary: A metric to compare two predictions.
+      summary: A perturbation prediction metric
       description: |
-        A metric to compare two predictions.
+        A metric to compare a perturbation prediction to the ground truth.
   arguments:
     - name: --de_test_h5ad
       __merge__: file_de_test_h5ad.yaml

src/api/comp_method_notest.yaml → src/api/wf_method.yaml

@@ -4,9 +4,9 @@ functionality:
     type: method
     type_info:
       label: Method
-      summary: A regression method.
+      summary: A perturbation prediction method
       description: |
-        A regression method to predict the expression of one modality from another.
+        A method for predicting the perturbation response of small molecules on certain cell types.
   arguments:
     - name: --de_train_h5ad
       __merge__: file_de_train_h5ad.yaml

src/methods/lgc_ensemble/config.vsh.yaml

@@ -1,4 +1,4 @@
-__merge__: ../../api/comp_method_notest.yaml
+__merge__: ../../api/wf_method.yaml
 
 functionality:
   name: lgc_ensemble

src/process_dataset/bootstrap/config.vsh.yaml

@@ -5,9 +5,9 @@ functionality:
     type: process_dataset
     type_info:
       label: Bootstrap
-      summary: A component to generate bootstraps of a dataset.
+      summary: Bootstrap a dataset
       description: |
-        This component generates bootstraps of a dataset. It takes as input a parquet file and an h5ad file and generates bootstraps of the dataset. The bootstraps are saved as parquet and h5ad files.
+        This component bootstraps a dataset.
   argument_groups:
     - name: Inputs
       arguments:

src/process_dataset/run_limma/config.vsh.yaml

@@ -7,7 +7,7 @@ functionality:
       label: Limma
       summary: Run limma
       description: |
-        Run limma for the parturbation regression task.
+        Run limma for the perturbation regression task.
   arguments:
     - name: --input
       type: file