Update files based on task_denoising test

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,24 @@
+---
+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

@@ -0,0 +1 @@
+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+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/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,17 @@
+## Describe your changes
+
+<!-- Describe your changes  -->
+
+## 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!

.github/workflows/build.yaml

@@ -1,122 +1,21 @@
-name: build
+name: Build
 
 on:
   push:
     branches: [ 'main' ]
   workflow_dispatch:
     inputs:
-      target_branch:
-        description: 'Branch to deploy to. If not specified, `build-${BRANCH_NAME}` will be used.'
-        required: false
       version:
-        description: 'Version name to use for the build. If not specified, `build-${BRANCH_NAME}` will be used.'
+        description: |
+          The version of the project to build. Example: `1.0.3`.
+
+          If not provided, a development build with a version name
+          based on the branch name will be built. Otherwise, a release
+          build with the provided version will be built.
         required: false
 
 jobs:
-  # phase 1
-  list:
-    runs-on: ubuntu-latest
-
-    outputs:
-      target_branch: ${{ steps.defaults.outputs.target_branch }}
-      version: ${{ steps.defaults.outputs.version }}
-      component_matrix: ${{ steps.set_matrix.outputs.matrix }}
-
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: 'recursive'
-
-    - uses: viash-io/viash-actions/setup@v5
-
-    - name: Determine version tag from branch name
-      id: defaults
-      run: |
-        BRANCH_NAME=$(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" >> $GITHUB_OUTPUT
-
-    - name: Remove target folder from .gitignore
-      run: |
-        # allow publishing the target folder
-        sed -i '/^\/target.*/d' .gitignore
-
-    - uses: viash-io/viash-actions/ns-build@v5
-      with:
-        config_mod: .version := '${{ 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: ${{ steps.defaults.outputs.target_branch }}
-
-    - id: ns_list
-      uses: viash-io/viash-actions/ns-list@v5
-      with:
-        platform: docker
-        src: src
-        format: json
-
-    - id: set_matrix
-      run: |
-        echo "matrix=$(jq -c '[ .[] | 
-          { 
-            "name": (.namespace + "/" + .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: ${{ fromJson(needs.list.outputs.component_matrix) }}
-
-    steps:
-    # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.'
-    - uses: data-intuitive/reclaim-the-bytes@v2
-
-    - uses: actions/checkout@v4
-
-    - uses: viash-io/viash-actions/setup@v5
-
-    - name: Build container
-      uses: viash-io/viash-actions/ns-build@v5
-      with:
-        config_mod: .version := '${{ needs.list.outputs.version }}'
-        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: ${{ secrets.GTHB_PAT }}
-
-    - name: Push container
-      uses: viash-io/viash-actions/ns-build@v5
-      with:
-        config_mod: .version := '${{ needs.list.outputs.version }}'
-        platform: docker
-        src: ${{ matrix.component.dir }}
-        setup: push
+    uses: openproblems-bio/actions/.github/workflows/build.yml@main
+    with:
+      version: ${{ github.event.inputs.version }}

.github/workflows/test.yaml

@@ -1,113 +1,9 @@
-name: test
+name: Test
 
 on:
-  pull_request:
   push:
-    branches: [ '**' ]
+  pull_request:
 
 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 }}
-      cache_key: ${{ steps.cache.outputs.cache_key }}
-
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-        submodules: 'recursive'
-
-    - uses: christian-ci/action-yaml-github-output@v2
-      with:
-        file_path: _viash.yaml
-
-    - uses: viash-io/viash-actions/setup@v5
-
-    - uses: viash-io/viash-actions/project/sync-and-cache-s3@v5
-      id: cache
-      with:
-        s3_bucket: $s3_bucket/$NAME
-        dest_path: resources
-        cache_key_prefix: resources__
-
-    - id: ns_list
-      uses: viash-io/viash-actions/ns-list@v5
-      with:
-        engine: docker
-        format: json
-
-    - id: ns_list_filtered
-      uses: viash-io/viash-actions/project/detect-changed-components@v5
-      with:
-        input_file: "${{ steps.ns_list.outputs.output_file }}"
-
-    - id: set_matrix
-      run: |
-        echo "matrix=$(jq -c '[ .[] | 
-          { 
-            "name": (.namespace + "/" + .name),
-            "config": .info.config
-          }
-        ]' ${{ steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT
-
-  # phase 2
-  viash_test:
-    needs: list
-    if: ${{ needs.list.outputs.matrix != '[]' && needs.list.outputs.matrix != '' }}
-    runs-on: ubuntu-latest
-
-    strategy:
-      fail-fast: false
-      matrix:
-        component: ${{ fromJson(needs.list.outputs.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
-      with:
-        submodules: 'recursive'
-
-    - uses: viash-io/viash-actions/setup@v5
-
-    # use cache
-    - name: Cache resources data
-      uses: actions/cache@v4
-      timeout-minutes: 10
-      with:
-        path: resources
-        key: ${{ needs.list.outputs.cache_key }}
-
-    - name: Run test
-      timeout-minutes: 30
-      run: |
-        VIASH_TEMP=$RUNNER_TEMP/viash viash test \
-          "${{ matrix.component.config }}" \
-          --cpus 2 \
-          --memory "16gb"
+  build:
+    uses: openproblems-bio/actions/.github/workflows/test.yml@main

.gitignore

@@ -1,4 +1,5 @@
 resources
+resources_test
 work
 .nextflow*
 target

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "common"]
 	path = common
-	url = git@github.com:openproblems-bio/common-resources.git
+	url = https://github.com/openproblems-bio/common_resources.git

CHANGELOG.md

@@ -0,0 +1,24 @@
+# task_template x.y.z
+
+## BREAKING CHANGES
+
+<!-- * Restructured `src` directory (PR #3). -->
+
+## NEW FUNCTIONALITY
+
+* Added `control_methods/true_labels` component (PR #5).
+
+* Added `methods/logistic_regression` component (PR #5).
+
+* Added `metrics/accuracy` component (PR #5).
+
+## MAJOR CHANGES
+
+* Updated `api` files (PR #5).
+
+## MINOR CHANGES
+
+* Updated `README.md` (PR #5).
+
+## BUGFIXES
+