Update references to v2 repo

.github/ISSUE_TEMPLATE/new_task.yml

@@ -4,7 +4,7 @@ labels: [task]
 body:
   - type: markdown
     attributes:
-      value: Thanks for choosing OpenProblems. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/issues?q=label%3Atask+) to see whether a similar task has already been created. If you haven't already, please review the documentation on [how to create a new task](https://openproblems.bio/documentation/create_task/).
+      value: Thanks for choosing OpenProblems. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems/issues?q=label%3Atask+) to see whether a similar task has already been created. If you haven't already, please review the documentation on [how to create a new task](https://openproblems.bio/documentation/create_task/).
   - type: textarea
     attributes:
       label: Task motivation
@@ -16,7 +16,7 @@ body:
   - type: textarea
     attributes:
       label: Proposed ground-truth in datasets
-      description: Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility.
+      description: Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems/src-datasets.html)) which you can peruse through. Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility.
   - type: textarea
     attributes:
       label: Initial set of methods to implement

.github/workflows/release-build.yml

@@ -16,7 +16,6 @@ jobs:
 
     outputs:
       component_matrix: ${{ steps.set_matrix.outputs.components }}
-      workflow_matrix: ${{ steps.set_matrix.outputs.workflows }}
       cache_key: ${{ steps.cache.outputs.cache_key }}
 
     steps:
@@ -56,12 +55,6 @@ jobs:
         src: src
         format: json
 
-    - id: ns_list_workflows
-      uses: viash-io/viash-actions/ns-list@v6
-      with:
-        src: workflows
-        format: json
-
     - id: set_matrix
       run: |
         echo "components=$(jq -c '[ .[] | 
@@ -72,14 +65,6 @@ jobs:
           }
         ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT
 
-        echo "workflows=$(jq -c '[ .[] | 
-          { 
-            "name": (.functionality.namespace + "/" + .functionality.name),
-            "main_script": (.info.config | capture("^(?<dir>.*\/)").dir + "/" + .functionality.test_resources[].path),
-            "entry": .functionality.test_resources[].entrypoint
-          }
-        ]' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT
-
   # phase 2
   build:
     needs: list
@@ -128,56 +113,6 @@ jobs:
 
   ###################################3
   # phase 3
-  integration_test:
-    needs: [ build, list ]
-    if: "${{ needs.list.outputs.workflow_matrix != '[]' }}"
-
-    runs-on: ubuntu-latest
-
-    strategy:
-      fail-fast: false
-      matrix:
-        component: ${{ fromJson(needs.list.outputs.workflow_matrix) }}
-
-    steps:
-    # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.'
-    - uses: data-intuitive/reclaim-the-bytes@v2
-
-    - uses: actions/checkout@v4
-
-    - uses: viash-io/viash-actions/setup@v6
-
-    - uses: nf-core/[email protected]
-
-    # build target dir
-    # use containers from release branch, hopefully these are available
-    - name: Build target dir
-      uses: viash-io/viash-actions/ns-build@v6
-      with:
-        config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'"
-        parallel: true
-
-    # use cache
-    - name: Cache resources data
-      uses: actions/cache@v4
-      timeout-minutes: 5
-      with:
-        path: resources_test
-        key: ${{ needs.list.outputs.cache_key }}
-
-    - name: Run integration test
-      timeout-minutes: 45
-      run: |
-        # todo: replace with viash test command
-        export NXF_VER=22.04.5
-        nextflow run . \
-          -main-script "${{ matrix.component.main_script }}" \
-          -entry ${{ matrix.component.entry }} \
-          -profile docker,mount_temp,no_publish \
-          -c workflows/utils/labels_ci.config
-
-  ###################################3
-  # phase 4
   component_test:
     needs: [ build, list ]
     if: ${{ needs.list.outputs.component_matrix != '[]' && needs.list.outputs.component_matrix != '' }}
@@ -208,4 +143,4 @@ jobs:
           --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \
           "${{ matrix.component.config }}" \
           --cpus 2 \
-          --memory "5gb"
+          --memory "5gb"

.gitignore

@@ -3,9 +3,11 @@ README_files/
 *.DS_Store
 *__pycache__
 *.h5ad
+changelogs
 
 # IDE ignores
 /.idea/
+/.vscode/
 
 # repo specific ignores
 output_bash

.vscode/settings.json

@@ -5,12 +5,6 @@
     "src/common/schemas/task_info.yaml": "src/**/api/task_info.yaml",
     "src/common/schemas/task_method.yaml": "src/tasks/**/methods/**/config.vsh.yaml",
     "src/common/schemas/task_control_method.yaml": "src/tasks/**/control_methods/**/config.vsh.yaml",
-    "src/common/schemas/task_metric.yaml": "src/tasks/**/metrics/**/config.vsh.yaml",
-    "/home/rcannood/.viash/releases/0.8.0/schema.json": [
-      "*.vsh.yaml"
-    ],
-    "/home/rcannood/.viash/releases/0.8.6/schema.json": [
-      "*.vsh.yaml"
-    ]
+    "src/common/schemas/task_metric.yaml": "src/tasks/**/metrics/**/config.vsh.yaml"
   }
 }