fix: switch to MOSuite FigOutSync

.gitattributes

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

.syncweaver-lock.json

@@ -5,8 +5,8 @@
   "sources": {
     "code/MOSuite": {
       "repo_url": "https://github.com/CCBR/MOSuite",
-      "ref": "v0.3.2",
-      "git_sha": "f4465c58a7d04f5feb41d4455a019ca4946a4ca8"
+      "ref": "FigOutSync",
+      "git_sha": "f2177f7c4b1efc6960e96361442e7be099c532c9"
     }
   }
 }

code/MOSuite/.Rbuildignore

@@ -35,3 +35,4 @@
 VennDiagram.*\.log
 ^[.]?air[.]toml$
 ^\.vscode$
+^SECURITY\.md$

code/MOSuite/.github/workflows/syncweaver-source-dispatch.yml

@@ -0,0 +1,92 @@
+name: syncweaver-source-dispatch
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      source_ref:
+        description: Optional source ref to dispatch (defaults to release tag for release events, or current ref for manual runs).
+        required: false
+        type: string
+      source_repo:
+        description: Optional source repository override in OWNER/REPO format (defaults to current repository).
+        required: false
+        type: string
+      orchestrator-repo:
+        description: Optional orchestrator repository override in OWNER/REPO format.
+        required: false
+        default: CCBR/syncweaver
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  notify-syncweaver:
+    runs-on: ubuntu-latest
+    env:
+      SOURCE_REPOSITORY: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.source_repo || github.repository }}
+      SOURCE_REF: ${{ github.event_name == 'release' && github.event.release.tag_name || github.event.inputs.source_ref || github.ref_name }}
+      ORCHESTRATOR_REPO: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs['orchestrator-repo'] || vars['orchestrator-repo'] || 'CCBR/syncweaver' }}
+    steps:
+      - name: Validate dispatch payload
+        shell: bash
+        run: |
+          set -euo pipefail
+          if [[ -z "${SOURCE_REPOSITORY//[[:space:]]/}" ]]; then
+            echo "Error: source repository cannot be empty." >&2
+            exit 1
+          fi
+          if [[ -z "${SOURCE_REF//[[:space:]]/}" ]]; then
+            echo "Error: source ref cannot be empty." >&2
+            exit 1
+          fi
+          if [[ -z "${ORCHESTRATOR_REPO//[[:space:]]/}" ]]; then
+            echo "Error: orchestrator repository cannot be empty." >&2
+            exit 1
+          fi
+          if [[ "${ORCHESTRATOR_REPO}" != */* ]]; then
+            echo "Error: orchestrator repository must be in OWNER/REPO format." >&2
+            exit 1
+          fi
+          if [[ -z "${{ vars.CCBR_BOT_APP_ID }}" ]]; then
+            echo "Error: vars.CCBR_BOT_APP_ID is required to generate a dispatch token." >&2
+            exit 1
+          fi
+          if [[ -z "${{ secrets.CCBR_BOT_PRIVATE_KEY }}" ]]; then
+            echo "Error: secrets.CCBR_BOT_PRIVATE_KEY is required to generate a dispatch token." >&2
+            exit 1
+          fi
+
+      - name: Resolve orchestrator repository owner and name
+        id: orchestrator_repo
+        shell: bash
+        run: |
+          set -euo pipefail
+          owner="${ORCHESTRATOR_REPO%%/*}"
+          repo="${ORCHESTRATOR_REPO#*/}"
+          if [[ -z "${owner}" || -z "${repo}" ]]; then
+            echo "Error: failed to parse orchestrator repository '${ORCHESTRATOR_REPO}'." >&2
+            exit 1
+          fi
+          echo "owner=${owner}" >> "$GITHUB_OUTPUT"
+          echo "repository=${repo}" >> "$GITHUB_OUTPUT"
+
+      - name: Generate CCBR-bot token
+        id: ccbr_bot
+        uses: actions/create-github-app-token@v3
+        with:
+          client-id: ${{ vars.CCBR_BOT_APP_ID }}
+          private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+          owner: ${{ steps.orchestrator_repo.outputs.owner }}
+          repositories: ${{ steps.orchestrator_repo.outputs.repository }}
+
+      - name: Dispatch syncweaver-update-hosts workflow in orchestrator repo
+        uses: peter-evans/repository-dispatch@v4
+        with:
+          token: ${{ steps.ccbr_bot.outputs.token }}
+          repository: ${{ env.ORCHESTRATOR_REPO }}
+          event-type: syncweaver-update-hosts
+          client-payload: >-
+            {"source_repository": ${{ toJson(env.SOURCE_REPOSITORY) }}, "ref": ${{ toJson(env.SOURCE_REF) }}}

code/MOSuite/.gitignore

@@ -1,21 +1,24 @@
-.Rproj.user
-.Rhistory
-.Rdata
-.httr-oauth
 .DS_Store
-.quarto
-docs
-inst/doc
+*_files/
+**/figures/
+/.github/plans/
+/.httr-oauth
+/.posit/
+/.quarto
+/.Rdata
+/.Rhistory
+/.Rproj.user
+/.vscode/
 /doc/
+/docs
+/inst/doc
 /Meta/
 /README.html
-**/figures/
-VennDiagram.*.log
-*_files/
-tests/testthat/Rplots.pdf
+/tests/testthat/Rplots.pdf
 /tmp
-vignettes/args*.json
-Rplots.pdf
+/vignettes/args*.json
 moo_input.rds
 plot-volc-enh.json
+Rplots.pdf
+VennDiagram.*.log
 volc-sum-params.json

code/MOSuite/.lintr

@@ -3,6 +3,7 @@ linters: linters_with_defaults(
     commented_code_linter = NULL,
     object_name_linter = NULL,
     object_length_linter = object_length_linter(60L),
+    object_usage_linter = NULL,
     return_linter = return_linter(
       return_style = "explicit"
     ),

code/MOSuite/.pre-commit-config.yaml

@@ -26,11 +26,11 @@ repos:
         args: ["-I=.github/WORDLIST.txt"]
   # R formatting
   - repo: https://github.com/posit-dev/air-pre-commit
-    rev: 0.9.0
+    rev: 0.10.0
     hooks:
       - id: air-format
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9025
+    rev: v0.4.3.9028
     hooks:
       - id: parsable-R
       - id: readme-rmd-rendered

code/MOSuite/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MOSuite
 Title: R package for differential multi-omics analysis
-Version: 0.3.2
+Version: 0.3.2.9000
 Authors@R: c(
     person("Kelly", "Sovacool", , "kelly.sovacool@nih.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3283-829X")),

code/MOSuite/NEWS.md

@@ -1,3 +1,10 @@
+## MOSuite development version
+
+- Align plot color defaults with the MOSuite Code Ocean capsule defaults while preserving fallback random colors when a requested palette is too short.
+- Improve top and bottom legend wrapping and automatic legend text sizing for PCA and histogram plots with many or long labels.
+- Align PCA and histogram plotting defaults used by `filter_counts()`, `normalize_counts()`, and `batch_correct_counts()` with the affected Code Ocean capsules: MOSuite-filter-counts, MOSuite-normalize-counts, MOSuite-plot-pca-2D, and MOSuite-plot-pca-3D.
+- Add optional group coloring to `plot_read_depth()` and the `clean_raw_counts()` read-depth output while preserving the single-color default when no group is selected.
+
 ## 0.3.2
 
 - Support ggplot2 v4.0.0 for correlation heatmap plots in `filter_counts()`, `normalize_counts()`, and `batch_correct_counts()`. (#205, @copilot, @kelly-sovacool)