chore: syncweaver init + add MOSuite v0.3.2

.codeocean/environment.json

@@ -1,7 +1,6 @@
 {
 	"version": 1,
-	"base_image": "codeocean/mosuite-minimal:v0.3.1",
-	"post_install": true,
+	"base_image": "codeocean/mosuite-minimal:v0.3.2",
 	"options": {
 		"registry_host_arg": true,
 		"git_ask_pass": true,

.gitattributes

@@ -1 +1,2 @@
-/code/MOSuite linguist-vendored
+/code/MOSuite linguist-vendored
+code/MOSuite linguist-vendored

.github/workflows/syncweaver-host-contribute-patch.yml

@@ -0,0 +1,191 @@
+name: syncweaver-contribute-patch
+
+on:
+  workflow_dispatch:
+    inputs:
+      source_path:
+        description: Optional tracked source path override; if omitted, source_path is resolved from lockfile.
+        required: false
+        type: string
+      repo_url:
+        description: Optional source repository identifier (URL or OWNER/REPO) used to resolve source_path from lockfile.
+        required: false
+        type: string
+      source_repository:
+        description: Optional source repository in OWNER/REPO format; if omitted, derives from lockfile repo_url.
+        required: false
+        type: string
+      lockfile:
+        description: Path to the syncweaver lockfile.
+        required: false
+        default: .syncweaver-lock.json
+        type: string
+      patch_path:
+        description: Optional patch path override; if omitted, uses source entry patch value from lockfile.
+        required: false
+        type: string
+      source_base_ref:
+        description: Optional source repository base branch for PR; if omitted, uses source entry ref from lockfile.
+        required: false
+        type: string
+      syncweaver-version:
+        description: syncweaver version/ref to install (e.g. version tag, branch name, or commit SHA). Will use docker image if available.
+        required: false
+        type: string
+        default: main
+
+permissions:
+  contents: read
+
+jobs:
+  resolve-patch-metadata:
+    runs-on: ubuntu-latest
+    outputs:
+      source_path: ${{ steps.resolve.outputs.source_path }}
+      repo_url: ${{ steps.resolve.outputs.repo_url }}
+      source_repository: ${{ steps.resolve.outputs.source_repository }}
+      patch_path: ${{ steps.resolve.outputs.patch_path }}
+      source_base_ref: ${{ steps.resolve.outputs.source_base_ref }}
+      lockfile: ${{ env.LOCKFILE }}
+    env:
+      SOURCE_PATH: ${{ github.event.inputs.source_path || '' }}
+      REPO_URL: ${{ github.event.inputs.repo_url || '' }}
+      SOURCE_REPOSITORY: ${{ github.event.inputs.source_repository || '' }}
+      LOCKFILE: ${{ github.event.inputs.lockfile || '.syncweaver-lock.json' }}
+      PATCH_PATH: ${{ github.event.inputs.patch_path || '' }}
+      SOURCE_BASE_REF: ${{ github.event.inputs.source_base_ref || '' }}
+      SYNCWEAVER_VERSION: ${{ github.event.inputs['syncweaver-version'] || github.event.client_payload['syncweaver-version'] || 'main' }}
+    steps:
+      - name: Checkout host repository
+        uses: actions/checkout@v6
+
+      - name: Setup syncweaver
+        uses: CCBR/syncweaver/actions/setup-syncweaver@main
+        with:
+          syncweaver-version: ${{ env.SYNCWEAVER_VERSION }}
+
+      - name: Resolve source and patch metadata
+        id: resolve
+        shell: bash
+        env:
+          SOURCE_PATH_INPUT: ${{ env.SOURCE_PATH }}
+          REPO_URL_INPUT: ${{ env.REPO_URL }}
+          SOURCE_REPOSITORY_INPUT: ${{ env.SOURCE_REPOSITORY }}
+          LOCKFILE_PATH: ${{ env.LOCKFILE }}
+          PATCH_PATH_INPUT: ${{ env.PATCH_PATH }}
+          SOURCE_BASE_REF_INPUT: ${{ env.SOURCE_BASE_REF }}
+          SYNCWEAVER_HOST_CWD: ${{ github.workspace }}
+        run: |
+          set -euo pipefail
+          syncweaver-python -m syncweaver.contribute_patch
+
+      - name: Print resolved metadata
+        shell: bash
+        run: |
+          set -euo pipefail
+          echo "source_path=${{ steps.resolve.outputs.source_path }}"
+          echo "repo_url=${{ steps.resolve.outputs.repo_url }}"
+          echo "source_repository=${{ steps.resolve.outputs.source_repository }}"
+          echo "patch_path=${{ steps.resolve.outputs.patch_path }}"
+          echo "source_base_ref=${{ steps.resolve.outputs.source_base_ref }}"
+
+  contribute-patch:
+    runs-on: ubuntu-latest
+    needs: resolve-patch-metadata
+    permissions:
+      contents: read
+    env:
+      SOURCE_PATH: ${{ needs.resolve-patch-metadata.outputs.source_path }}
+      REPO_URL: ${{ needs.resolve-patch-metadata.outputs.repo_url }}
+      SOURCE_REPOSITORY: ${{ needs.resolve-patch-metadata.outputs.source_repository }}
+      PATCH_PATH: ${{ needs.resolve-patch-metadata.outputs.patch_path }}
+      SOURCE_BASE_REF: ${{ needs.resolve-patch-metadata.outputs.source_base_ref }}
+      LOCKFILE: ${{ needs.resolve-patch-metadata.outputs.lockfile }}
+    steps:
+      - name: Generate CCBR-bot token
+        id: ccbr_bot
+        uses: actions/create-github-app-token@v1
+        with:
+          app-id: ${{ secrets.CCBR_BOT_APP_ID }}
+          private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+
+      - name: Checkout host repository
+        uses: actions/checkout@v6
+        with:
+          path: host
+
+      - name: Checkout source repository
+        uses: actions/checkout@v6
+        with:
+          repository: ${{ env.SOURCE_REPOSITORY }}
+          ref: ${{ env.SOURCE_BASE_REF }}
+          token: ${{ steps.ccbr_bot.outputs.token }}
+          path: source
+
+      - name: Apply patch to source repository
+        id: apply_patch
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          patch_file="$GITHUB_WORKSPACE/host/${PATCH_PATH}"
+          if [[ ! -f "$patch_file" ]]; then
+            echo "Error: patch file not found in host repository: ${PATCH_PATH}" >&2
+            exit 1
+          fi
+
+          branch_stub=$(printf '%s' "$SOURCE_PATH" | tr '/ ' '--' | tr -cd '[:alnum:]._-')
+          if [[ -z "$branch_stub" ]]; then
+            branch_stub="patch"
+          fi
+          branch_name="syncweaver/contribute-patch/${branch_stub}-${GITHUB_RUN_ID}"
+
+          cd "$GITHUB_WORKSPACE/source"
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git switch -c "$branch_name"
+
+          if ! git apply --3way --whitespace=nowarn "$patch_file"; then
+            echo "Error: patch failed to apply cleanly to ${SOURCE_REPOSITORY}@${SOURCE_BASE_REF}" >&2
+            exit 1
+          fi
+
+          if git diff --quiet; then
+            echo "has_changes=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "has_changes=true" >> "$GITHUB_OUTPUT"
+          fi
+          echo "branch_name=$branch_name" >> "$GITHUB_OUTPUT"
+
+      - name: Open pull request in source repository
+        if: steps.apply_patch.outputs.has_changes == 'true'
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.ccbr_bot.outputs.token }}
+          path: source
+          base: ${{ env.SOURCE_BASE_REF }}
+          branch: ${{ steps.apply_patch.outputs.branch_name }}
+          delete-branch: true
+          commit-message: "chore(syncweaver): apply host patch for ${{ env.SOURCE_PATH }}"
+          title: "chore(syncweaver): apply host patch for ${{ env.SOURCE_PATH }}"
+          body: |
+            Automated patch contribution from host repository workflow dispatch.
+
+            Inputs used:
+            - source_path: ${{ env.SOURCE_PATH }}
+            - repo_url: ${{ env.REPO_URL }}
+            - source_repository: ${{ env.SOURCE_REPOSITORY }}
+            - source_base_ref: ${{ env.SOURCE_BASE_REF }}
+            - patch_path: ${{ env.PATCH_PATH }}
+            - lockfile: ${{ env.LOCKFILE }}
+
+            Trigger context:
+            - host_repository: ${{ github.repository }}
+            - workflow_run: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
+      - name: Print no-op summary
+        if: steps.apply_patch.outputs.has_changes == 'false'
+        shell: bash
+        run: |
+          set -euo pipefail
+          echo "Patch applied cleanly but introduced no source changes. No PR created."

.github/workflows/syncweaver-host-update.yml

@@ -0,0 +1,172 @@
+name: syncweaver-host-update
+
+on:
+  repository_dispatch:
+  workflow_dispatch:
+    inputs:
+      source_path:
+        description: Optional tracked source path override for manual runs; if omitted, source_path is resolved from the lockfile.
+        required: false
+        type: string
+      repo_url:
+        description: Optional source repository identifier (URL or OWNER/REPO) used to resolve source_path from lockfile; for repository_dispatch this defaults to client_payload.source_repository.
+        required: false
+        type: string
+      lockfile:
+        description: Path to the syncweaver lockfile.
+        required: false
+        default: .syncweaver-lock.json
+        type: string
+      ref:
+        description: Optional git ref to sync from.
+        required: false
+        type: string
+      remote_subdir:
+        description: Optional remote subdirectory to vendor.
+        required: false
+        type: string
+      syncweaver-version:
+        description: syncweaver version/ref to install (e.g. version tag, branch name, or commit SHA). Will use docker image if available.
+        required: false
+        type: string
+        default: main
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  resolve-source-paths:
+    runs-on: ubuntu-latest
+    outputs:
+      source_paths: ${{ steps.resolve_source_paths.outputs.source_paths }}
+      source_count: ${{ steps.resolve_source_paths.outputs.source_count }}
+      lockfile: ${{ env.LOCKFILE }}
+      ref: ${{ env.REF }}
+      remote_subdir: ${{ env.REMOTE_SUBDIR }}
+      repo_url: ${{ env.REPO_URL }}
+      syncweaver_version: ${{ steps.job_meta.outputs.syncweaver_version }}
+    env:
+      # workflow_dispatch may provide source_path directly; repository_dispatch usually
+      # omits it so the workflow resolves source_path from lockfile + source_repository.
+      SOURCE_PATH: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.source_path || github.event.client_payload.source_path || '' }}
+      # Prefer explicit repo_url, then fall back to source_repository from dispatch payload.
+      REPO_URL: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.repo_url || github.event.client_payload.repo_url || github.event.client_payload.source_repository || '' }}
+      LOCKFILE: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.lockfile || github.event.client_payload.lockfile || '.syncweaver-lock.json' }}
+      REF: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.ref || github.event.client_payload.ref || '' }}
+      REMOTE_SUBDIR: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.remote_subdir || github.event.client_payload.remote_subdir || '' }}
+      SYNCWEAVER_VERSION: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs['syncweaver-version'] || github.event.client_payload['syncweaver-version'] || 'main' }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Setup syncweaver
+        uses: CCBR/syncweaver/actions/setup-syncweaver@main
+        with:
+          syncweaver-version: ${{ env.SYNCWEAVER_VERSION }}
+
+      - name: Capture syncweaver inputs
+        id: job_meta
+        shell: bash
+        run: |
+          set -euo pipefail
+          echo "syncweaver_version=${SYNCWEAVER_VERSION}" >> "$GITHUB_OUTPUT"
+
+      - name: Resolve source paths
+        id: resolve_source_paths
+        shell: bash
+        env:
+          SOURCE_PATH_INPUT: ${{ env.SOURCE_PATH }}
+          REPO_URL_INPUT: ${{ env.REPO_URL }}
+          LOCKFILE_PATH: ${{ env.LOCKFILE }}
+        run: |
+          set -euo pipefail
+          syncweaver-python - <<'PY' >> "$GITHUB_OUTPUT"
+          import json
+          import os
+          import pathlib
+
+          from syncweaver.lockfile import resolve_source_paths_from_lockfile
+
+          source_path_input = os.environ["SOURCE_PATH_INPUT"].strip()
+          repo_url_input = os.environ["REPO_URL_INPUT"].strip()
+          lockfile_path = pathlib.Path(os.environ["LOCKFILE_PATH"])
+
+          try:
+              resolved_source_paths = resolve_source_paths_from_lockfile(
+                  lockfile=lockfile_path,
+                  source_path=source_path_input,
+                  repo_url=repo_url_input,
+              )
+          except ValueError as exc:
+              raise SystemExit(f"Error: {exc}") from exc
+
+          print(f"source_paths={json.dumps(resolved_source_paths)}")
+          print(f"source_count={len(resolved_source_paths)}")
+          PY
+
+      - name: Print resolved source paths
+        shell: bash
+        run: |
+          set -euo pipefail
+          echo "source_count=${{ steps.resolve_source_paths.outputs.source_count }}"
+          echo "source_paths=${{ steps.resolve_source_paths.outputs.source_paths }}"
+
+  update-source:
+    runs-on: ubuntu-latest
+    needs: resolve-source-paths
+    strategy:
+      fail-fast: false
+      matrix:
+        source_path: ${{ fromJson(needs.resolve-source-paths.outputs.source_paths) }}
+    env:
+      LOCKFILE: ${{ needs.resolve-source-paths.outputs.lockfile }}
+      REF: ${{ needs.resolve-source-paths.outputs.ref }}
+      REMOTE_SUBDIR: ${{ needs.resolve-source-paths.outputs.remote_subdir }}
+      REPO_URL: ${{ needs.resolve-source-paths.outputs.repo_url }}
+      SYNCWEAVER_VERSION: ${{ needs.resolve-source-paths.outputs.syncweaver_version }}
+    steps:
+      - name: Generate CCBR-bot token
+        id: ccbr_bot
+        uses: actions/create-github-app-token@v1
+        with:
+          app-id: ${{ vars.CCBR_BOT_APP_ID }}
+          private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          token: ${{ steps.ccbr_bot.outputs.token }}
+
+      - name: Run update-source composite action
+        id: update_source
+        uses: CCBR/syncweaver/actions/update-source@latest
+        with:
+          source_path: ${{ matrix.source_path }}
+          lockfile: ${{ env.LOCKFILE }}
+          ref: ${{ env.REF }}
+          remote_subdir: ${{ env.REMOTE_SUBDIR }}
+          syncweaver-version: ${{ env.SYNCWEAVER_VERSION }}
+
+      - name: Commit changes and open PR
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.ccbr_bot.outputs.token }}
+          branch: syncweaver/update-source/${{ matrix.source_path }}
+          delete-branch: true
+          commit-message: "chore(syncweaver): update ${{ matrix.source_path }} from ${{ steps.update_source.outputs.source_repo }}@${{ steps.update_source.outputs.ref }}"
+          title: "chore(syncweaver): update ${{ matrix.source_path }} from ${{ steps.update_source.outputs.source_repo }}@${{ steps.update_source.outputs.ref }}"
+          body: |
+            Automated source update from the update-source workflow.
+
+            Inputs used:
+            - source_path: ${{ matrix.source_path }}
+            - repo_url: ${{ env.REPO_URL }}
+            - lockfile: ${{ env.LOCKFILE }}
+            - ref: ${{ env.REF }}
+            - remote_subdir: ${{ env.REMOTE_SUBDIR }}
+
+            Resolved from lockfile after update:
+            - source_url: ${{ steps.update_source.outputs.source_url }}
+            - ref: ${{ steps.update_source.outputs.ref }}
+            - remote_subdir: ${{ steps.update_source.outputs.remote_subdir }}

.syncweaver-lock.json

@@ -0,0 +1,12 @@
+{
+  "host": "NIDAP-Community/MOSuite-plot-volcano-summary",
+  "orchestrator": "NIDAP-Community/syncweaver-orchestrator",
+  "syncweaver_version": "0.0.1-dev",
+  "sources": {
+    "code/MOSuite": {
+      "repo_url": "https://github.com/CCBR/MOSuite",
+      "ref": "v0.3.2",
+      "git_sha": "f4465c58a7d04f5feb41d4455a019ca4946a4ca8"
+    }
+  }
+}

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Development version
 
 - Improved the Code Ocean parameter UI for the plot volcano summary capsule (#2, @phoman14).
+- Use MOSuite v0.3.2. (#3, @kelly-sovacool)
 
 ## v4.0