chore(syncweaver): update tracked sources from CCBR/MOSuite@v0.4.1 (#18)

Co-authored-by: ccbr-bot[bot] <258092125+ccbr-bot[bot]@users.noreply.github.com>

Author: ccbr-bot[bot]

.syncweaver-lock.json

@@ -5,8 +5,8 @@
   "sources": {
     "code/MOSuite": {
       "repo_url": "https://github.com/CCBR/MOSuite",
-      "ref": "v0.4.0",
-      "git_sha": "ef1bdf806d153515e8ecbb8a8d2bfc518a418e05"
+      "ref": "v0.4.1",
+      "git_sha": "4e85d49ab155618d9f6beafd327b6fb87dfa8609"
     }
   }
 }

code/MOSuite/.Rbuildignore

@@ -36,3 +36,4 @@
 ^volc-sum-params\.json$
 VennDiagram.*\.log
 ^\.posit/assistant$
+^AGENTS\.md$

code/MOSuite/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @kelly-sovacool

code/MOSuite/.github/workflows/auto-format.yml

@@ -25,7 +25,7 @@ jobs:
           private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
           owner: ${{ github.repository_owner }}
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           token: ${{ steps.generate-token.outputs.token }}
           fetch-depth: 0
@@ -47,12 +47,6 @@ jobs:
           extra-packages: local::.
           needs: dev
 
-      - name: update Galaxy blueprints
-        shell: Rscript {0}
-        run: |
-          source('inst/extdata/galaxy/galaxy.R')
-          write_package_json_blueprints()
-
       - name: render README.Rmd & docs
         shell: Rscript {0}
         run: |

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

@@ -26,7 +26,7 @@ repos:
         args: ["-I=.github/WORDLIST.txt"]
   # R formatting
   - repo: https://github.com/posit-dev/air-pre-commit
-    rev: 0.10.0
+    rev: 0.11.0
     hooks:
       - id: air-format
   - repo: https://github.com/lorenzwalthert/precommit

code/MOSuite/AGENTS.md

@@ -17,7 +17,7 @@ Helper functions from `usethis` and `devtools` are used extensively for developm
 - Tests should be written with `testthat`.
 - The package must pass `devtools::check()`.
 - R code should adhere to the tidyverse style guide. https://style.tidyverse.org/
-- Only include one return statement at the end of a function, if a return statement is used at all. Explicit returns are preferred but not required for R functions.
+- Only include one return statement at the end of a function. Explicit returns are preferred but not required for R functions.
 
 ## Commit messages
 

code/MOSuite/CITATION.cff

@@ -1,6 +1,6 @@
 Package: MOSuite
 Title: R package for differential multi-omics analysis
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: c(
     person("Kelly", "Sovacool", , "kelly.sovacool@nih.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3283-829X")),
@@ -25,6 +25,7 @@ Depends:
     R (>= 4.1.0)
 Imports:
     assertthat,
+    cli,
     dendextend,
     DESeq2,
     dplyr,
@@ -39,7 +40,6 @@ Imports:
     methods,
     options,
     plotly,
-    png,
     purrr,
     reshape2,
     rlang,

code/MOSuite/DESCRIPTION

@@ -1,6 +1,9 @@
+## MOSuite 0.4.1
+
+- Fix how `plot_volcano_summary()` & `plot_volcano_enhanced` handle detecting column names for features, significance, and fold-change. `plot_volcano_summary()` plot now uses `plot_volcano_enhanced()` for rendering. (#239, @phoman14)
+
 ## MOSuite 0.4.0
 
-- Fix expression heatmap clustering to correctly use the selected gene and sample distance metrics and clustering methods. (#231, @phoman14)
 - Update PCA label, point-size, and histogram behavior. (#230, @phoman14)
 - Add optional count log-transform controls for PCA plots.  (#234, @phoman14)
 - Add a post-clean CPM histogram output in `clean_raw_counts()`. (#234, @phoman14)