Merge remote-tracking branch 'v2/main'

Former-commit-id: 704afe2

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: [bug]
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: [enhancement]
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/new_task.yml

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+name: New task
+description: Start creating a new benchmarking task in OpenProblems
+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/).
+  - type: textarea
+    attributes:
+      label: Task motivation
+      description: Explain the motivation behind your proposed task. Describe the biological or computational problem you aim to address and why it’s important. Discuss the current state of research in this area and any gaps or challenges that your task could help address. This section should convince readers of the significance and relevance of your task.
+  - type: textarea
+    attributes:
+      label: Task description
+      description: Provide a clear and concise description of your task, detailing the specific problem it aims to solve. Outline the input data types, the expected output, and any assumptions or constraints. Be sure to explain any terminology or concepts that are essential for understanding the task.
+  - 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.
+  - type: textarea
+    attributes:
+      label: Initial set of methods to implement
+      description: List the initial set of methods you plan to implement for your task. Briefly describe each method’s core ideas and algorithms, and explain why you think they are suitable for your task. Consider including both established and cutting-edge methods to provide a comprehensive benchmarking of the state-of-the-art.
+  - type: textarea
+    attributes:
+      label: Proposed control methods
+      description: Outline the control methods you propose for your task. These methods serve as a starting point to test the relative accuracy of new methods in the task and as quality control for the defined metrics. Include both positive controls, which are methods with known outcomes resulting in the best possible metric values, and negative controls, which are simple, naive, or random methods that do not rely on sophisticated techniques or domain knowledge. Explain the rationale for your chosen controls.
+  - type: textarea
+    attributes:
+      label: Proposed Metrics
+      description: Describe the metrics you propose for evaluating the performance of methods in your task. Explain the rationale for selecting these metrics and how they will accurately assess the methods’ success in addressing the task’s challenges. Consider including multiple metrics to capture different aspects of method performance.

.github/PULL_REQUEST_TEMPLATE.md

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+## Describe your changes
+
+## Issue ticket number and link
+Closes #xxxx (Replace xxxx with the GitHub issue number)
+
+## Checklist before requesting a review
+- [ ] I have performed a self-review of my code
+
+- Check the correct box. Does this PR contain:
+  - [ ] Breaking changes
+  - [ ] New functionality
+  - [ ] Major changes
+  - [ ] Minor changes
+  - [ ] Bug fixes
+
+- [ ] Proposed changes are described in the CHANGELOG.md
+
+- [ ] CI Tests succeed and look good!
+
+## Requirements after merging
+
+- [ ] Need to regenerate `common/` resources
+
+- [ ] Need to regenerate task-specific resources. Specify: <all or ...>

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/integration-test.yml

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+name: integration test
+
+on: workflow_dispatch
+
+jobs:
+  # phase 1
+  list:
+    env:
+      s3_bucket: s3://openproblems-data/resources_test/
+    runs-on: ubuntu-latest
+
+    outputs:
+      component_matrix: ${{ steps.set_matrix.outputs.components }}
+      workflow_matrix: ${{ steps.set_matrix.outputs.workflows }}
+      cache_key: ${{ steps.cache.outputs.cache_key }}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: viash-io/viash-actions/setup@v5
+
+    - uses: viash-io/viash-actions/project/sync-and-cache-s3@v5
+      id: cache
+      with:
+        s3_bucket: $s3_bucket
+        dest_path: resources_test
+        cache_key_prefix: resources_test__
+
+    - name: Remove target folder from .gitignore
+      run: |
+        # allow publishing the target folder
+        sed -i 's#^/target/$##g' .gitignore
+
+    - uses: viash-io/viash-actions/ns-build@v5
+      with:
+        config_mod: .functionality.version := 'integration_build'
+        parallel: true
+
+    - name: Deploy to target branch
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: .
+        publish_branch: integration_build
+        exclude_assets: ''
+
+    - id: ns_list
+      uses: viash-io/viash-actions/ns-list@v5
+      with:
+        platform: docker
+        src: src
+        format: json
+
+    - id: set_matrix
+      run: |
+        echo "components=$(jq -c '[ .[] | 
+          { 
+            "name": (.functionality.namespace + (.platforms | map(select(.type == "docker"))[0].namespace_separator) + .functionality.name),
+            "config": .info.config,
+            "dir": .info.config | capture("^(?<dir>.*\/)").dir
+          }
+        ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT
+
+        echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) |
+          { 
+            "name": ($config.functionality.namespace + "/" + $config.functionality.name),
+            "main_script": (($config.info.config | capture("^(?<dir>.*\/)").dir) + "/" + .path),
+            "entry": .entrypoint,
+            "config": $config.info.config
+          }
+        ] | unique' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT
+
+  # phase 2
+  build:
+    needs: list
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        component: ${{ fromJson(needs.list.outputs.component_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@v5
+
+    - name: Build container
+      uses: viash-io/viash-actions/ns-build@v5
+      with:
+        config_mod: .functionality.version := 'integration_build'
+        setup: build
+        src: ${{ matrix.component.dir }}
+
+    - name: Login to container registry
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ secrets.GTHB_USER }}
+        password: ${{ secrets.GTHB_PAT }}
+
+    - name: Push container
+      uses: viash-io/viash-actions/ns-build@v5
+      with:
+        config_mod: .functionality.version := 'integration_build'
+        platform: docker
+        src: ${{ matrix.component.dir }}
+        setup: push
+
+  ###################################
+  # phase 3
+  integration_test:
+    needs: [ build, list ]
+    if: "${{ 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@v5
+
+    - uses: nf-core/[email protected]
+
+    # build target dir
+    # use containers from integration_build branch, hopefully these are available
+    - name: Build target dir
+      uses: viash-io/viash-actions/ns-build@v5
+      with:
+        config_mod: ".functionality.version := 'integration_build'"
+        parallel: true
+
+    # use cache
+    - name: Cache resources data
+      uses: actions/cache@v4
+      timeout-minutes: 5
+      with:
+        path: resources_test
+        key: ${{ needs.list.outputs.cache_key }}
+        fail-on-cache-miss: true
+
+    - name: Run integration test
+      timeout-minutes: 45
+      run: |
+        # todo: replace with viash test command
+        export NXF_VER=22.04.5
+        nextflow run . \
+          -main-script "${{ matrix.component.main_script }}" \
+          -entry "${{ matrix.component.entry }}" \
+          -profile docker,mount_temp,no_publish \
+          -c workflows/utils/labels_ci.config

.github/workflows/main-build.yml

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+name: main build
+
+on:
+  push:
+    branches: [ 'main' ]
+
+jobs:
+  # phase 1
+  list:
+    runs-on: ubuntu-latest
+
+    outputs:
+      component_matrix: ${{ steps.set_matrix.outputs.matrix }}
+      cache_key: ${{ steps.cache.outputs.cache_key }}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: viash-io/viash-actions/setup@v5
+
+    - name: Remove target folder from .gitignore
+      run: |
+        # allow publishing the target folder
+        sed -i 's#^/target/$##g' .gitignore
+
+    - uses: viash-io/viash-actions/ns-build@v5
+      with:
+        config_mod: .functionality.version := 'main_build'
+        parallel: true
+
+    # - name: Build nextflow schemas
+    #   uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4
+    #   with:
+    #     workflows: src
+    #     components: src
+    #     viash_pro_token: ${{ secrets.GTHB_PAT }}
+    #     tools_version: 'main_build'
+
+    # - name: Build parameter files
+    #   uses: viash-io/viash-actions/pro/build-nextflow-params@v4
+    #   with:
+    #     workflows: src
+    #     components: src
+    #     viash_pro_token: ${{ secrets.GTHB_PAT }}
+    #     tools_version: 'main_build'
+
+    - name: Deploy to target branch
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: .
+        publish_branch: main_build
+
+    - id: ns_list
+      uses: viash-io/viash-actions/ns-list@v5
+      with:
+        platform: docker
+        src: src
+        format: json
+
+    - id: set_matrix
+      run: |
+        echo "matrix=$(jq -c '[ .[] | 
+          { 
+            "name": (.functionality.namespace + "/" + .functionality.name),
+            "dir": .info.config | capture("^(?<dir>.*\/)").dir
+          }
+        ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT
+
+  # phase 2
+  build:
+    needs: list
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        component: ${{ fromJson(needs.list.outputs.component_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@v5
+
+    - name: Build container
+      uses: viash-io/viash-actions/ns-build@v5
+      with:
+        config_mod: .functionality.version := 'main_build'
+        platform: docker
+        src: ${{ matrix.component.dir }}
+        setup: build
+
+    - name: Login to container registry
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ secrets.GTHB_USER }}
+        password: ${{ secrets.GTHB_PAT }}
+
+    - name: Push container
+      uses: viash-io/viash-actions/ns-build@v5
+      with:
+        config_mod: .functionality.version := 'main_build'
+        platform: docker
+        src: ${{ matrix.component.dir }}
+        setup: push