Merge branch 'marmunfold' of https://github.com/khanlab/hippunfold in…

…to marmunfold

.github/workflows/bump_version.yml

@@ -1,20 +1,26 @@
+---
 name: Bump version
 on:
   push:
     branches:
       - master
+
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - name: Checkout main branch
+        uses: actions/checkout@v4
 
       - name: Update changelog
         uses: release-drafter/release-drafter@v5
         id: release-drafter
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      # Can replace the below with (until pipeline description) with
+      # khanlab/actions/.github/workflows/workflow-version_task-semverGithub.yml
+      # after adding PAT token
       - name: Get previous release version
         run: |
           echo "PREV_VER=$(cat pyproject.toml | grep -o -E '(version\s=\s)([[:punct:]])([0-9]+\.[0-9]+\.[0-9]+.+)([[:punct:]])' | cut -d ' ' -f 3 | tr -d '"')" >> $GITHUB_ENV
@@ -35,28 +41,27 @@ jobs:
         run: |
           echo "NEW_BUMP=$(($BUMP_VER + 1))" >> $GITHUB_ENV
 
-      - name: Update version in pyproject
-        uses: jacobtomlinson/gha-find-replace@master
+      - name: Update version in pyproject.toml
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'pyproject.toml'
+          include: "pyproject.toml"
           find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version = "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
 
       - name: Update version in pipeline_description (not actually used)
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'hippunfold/pipeline_description.json'
+          include: "hippunfold/pipeline_description.json"
           find: '"Version": "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: '"Version": "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
 
       - name: Update version in config/snakebids.yml
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'hippunfold/config/snakebids.yml'
+          include: "hippunfold/config/snakebids.yml"
           find: 'version: "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version: "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
 
-
       - name: Commit updates
         env:
           SNAKEBIDS_VERSION: ${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}
@@ -66,10 +71,7 @@ jobs:
           git diff-index --quiet HEAD || git commit -m "Bump version to $SNAKEBIDS_VERSION" -a
 
       - name: Push changes
-        uses: ad-m/github-push-action@master
+        uses: ad-m/github-push-action@v0.8.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           tags: false
-
-
-

.github/workflows/dags.yml

@@ -1,66 +1,59 @@
+---
 name: Generate DAG visualizations
-
 on:
   workflow_dispatch:
     inputs:
-      author:
-        description: "Author"
-        required: true
-        default: "github-actions[bot] (user publishing release)"
-      date:
-        description: "Date"
-        required: true
-        default: "YYYY-MM-DD"
       comments:
         description: "Comments"
 
 jobs:
   generate_dag:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
 
     steps:
       - name: Print author
         run: |
-          echo "Author: ${{ github.event.inputs.author }}"
-          echo "Date: ${{ github.event.inputs.date }}"
+          echo "Author: ${{ github.triggering_actor }}"
           echo "Comments: ${{ github.event.inputs.comments }}"
 
-      - uses: actions/checkout@master
+      - name: Checkout main branch
+        uses: actions/checkout@v3
         with:
           ref: refs/heads/master
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Install non-python dependencies
         run: |
           sudo apt-get install -y graphviz-dev graphviz
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install snakebids
 
-      - name: Set-up env for hippunfold 
+      - name: Set-up env for hippunfold
         run: |
           echo "HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models" >> $GITHUB_ENV
           echo "HIPPUNFOLD=./hippunfold/run.py" >> $GITHUB_ENV
+
       - name: Generate rulegraph single T2w bids
         run: |
           $HIPPUNFOLD test_data/bids_singleT2w test_out participant -np --modality T2w --rulegraph | dot -Tsvg > docs/images/rulegraph_T2w.svg
 
       - name: Commit updates
-        env:
-          LATEST_VERSION: ${{ steps.release-drafter.outputs.name }}
         run: |
           git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --local user.name "github-actions[bot]"
-          git diff-index --quiet HEAD || git add docs/images || commit -m "Add updated dags [skip ci]" 
+          git diff-index --quiet HEAD || git add docs/images || commit -m "Add updated dags [skip ci]"
 
       - name: Push changes
-        uses: ad-m/github-push-action@master
+        uses: ad-m/github-push-action@v0.8.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-
-
-

.github/workflows/deploy.yml

@@ -1,16 +1,8 @@
+---
 name: Deploy workflow
-
 on:
   workflow_dispatch:
     inputs:
-      author:
-        description: "Author"
-        required: true
-        default: "github-actions[bot] (user publishing release)"
-      date:
-        description: "Date"
-        required: true
-        default: "YYYY-MM-DD"
       comments:
         description: "Comments"
       branch:
@@ -25,22 +17,24 @@ jobs:
     steps:
       - name: Print author
         run: |
-          echo "Author: ${{ github.event.inputs.author }}"
-          echo "Date: ${{ github.event.inputs.date }}"
+          echo "Author: ${{ github.triggering_actor }}"
           echo "Comments: ${{ github.event.inputs.comments }}"
 
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.inputs.branch }}
 
       - name: Draft change log
         uses: release-drafter/release-drafter@v5
         id: release-drafter
         with:
-          commitish: ${{ github.event.inputs.branch }}        
+          commitish: ${{ github.event.inputs.branch }}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      # Can replace the below with (until pipeline description) with
+      # khanlab/actions/.github/workflows/workflow-version_task-publishGithub.yml
+      # after adding PAT token
       - name: Set new release version
         env:
           RD_RELEASE: ${{ steps.release-drafter.outputs.name }}
@@ -52,27 +46,26 @@ jobs:
           fi
 
       - name: Update version in pyproject.toml
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'pyproject.toml'
+          include: "pyproject.toml"
           find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version = "${{ env.NEW_RELEASE }}"'
 
       - name: Update version in pipeline_description (not actually used)
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'hippunfold/pipeline_description.json'
+          include: "hippunfold/pipeline_description.json"
           find: '"Version": "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: '"Version": "${{ env.NEW_RELEASE }}"'
 
       - name: Update version in config/snakebids.yml
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'hippunfold/config/snakebids.yml'
+          include: "hippunfold/config/snakebids.yml"
           find: 'version: "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version: "${{ env.NEW_RELEASE }}"'
 
-
       - name: Commit updates
         env:
           LATEST_VERSION: ${{ env.NEW_RELEASE }}
@@ -82,7 +75,7 @@ jobs:
           git diff-index --quiet HEAD || git commit -m "Bump version to $LATEST_VERSION" -a
 
       - name: Push changes
-        uses: ad-m/github-push-action@master
+        uses: ad-m/github-push-action@v0.8.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
 
@@ -92,5 +85,3 @@ jobs:
           publish: true
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-

.github/workflows/manual_release_drafter.yml

@@ -1,12 +1,8 @@
+---
 name: Manual release-drafter update
-
 on:
   workflow_dispatch:
     inputs:
-      author:
-        description: "Author"
-        required: true
-        default: "github-actions[bot] (user publishing release)"
       comments:
         description: "Update release drafter notes"
 
@@ -16,11 +12,11 @@ jobs:
     steps:
       - name: Print workflow information
         run: |
-          echo "Author: ${{ github.event.inputs.author }}"
-          echo "Date: ${{ github.event.inputs.date }}"
+          echo "Author: ${{ github.triggering_actor }}"
           echo "Comments: ${{ github.event.inputs.comments }}"
 
-      - uses: actions/checkout@master
+      - name: Checkout main branch
+        uses: actions/checkout@v4
 
       - name: Update changelog
         uses: release-drafter/release-drafter@v5

.github/workflows/push_container.yml

@@ -1,53 +1,18 @@
+---
 # This workflow uses actions that are not certified by GitHub.
 # They are provided by a third-party and are governed by
 # separate terms of service, privacy policy, and support
 # documentation.
 
 name: Publish Docker image
-
-on: 
+on:
   workflow_dispatch:
   release:
     types: [published]
 
 jobs:
   push_to_registries:
-    name: Push Docker image to multiple registries
-    runs-on: ubuntu-latest
-    permissions:
-      packages: write
-      contents: read
-    steps:
-      - name: Check out the repo
-        uses: actions/checkout@master
-
-      - name: Log in to Docker Hub
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-
-      - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@v4
-        with:
-          images: |
-            ${{ github.repository }}
-            ghcr.io/${{ github.repository }}
-          flavor: |
-            latest=auto
-      
-      - name: Build and push Docker images
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
-        with:
-          context: .
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+    uses: khanlab/actions/.github/workflows/[email protected]
+    secrets:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+      DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}