chore(syncweaver): update tracked sources from CCBR/MOSuite@v0.4.0

Author: kelly-sovacool

.syncweaver-lock.json

@@ -5,8 +5,8 @@
   "sources": {
     "code/MOSuite": {
       "repo_url": "https://github.com/CCBR/MOSuite",
-      "ref": "FigOutSync",
-      "git_sha": "f2177f7c4b1efc6960e96361442e7be099c532c9"
+      "ref": "v0.4.0",
+      "git_sha": "ef1bdf806d153515e8ecbb8a8d2bfc518a418e05"
     }
   }
 }

code/MOSuite/.Rbuildignore

@@ -1,38 +1,38 @@
-^renv$
-^renv\.lock$
 ^_pkgdown\.yml$
+^[.]?air[.]toml$
 ^\.github$
 ^\.lintr$
+^\.posit$
 ^\.pre-commit-config\.yaml$
 ^\.prettierignore$
 ^\.prettierrc$
 ^\.Rproj\.user$
+^\.vscode$
 ^CITATION\.cff$
 ^codemeta\.json$
 ^data-raw$
 ^doc$
-^Dockerfile$
 ^docker$
+^Dockerfile$
 ^docs$
 ^figures$
+^inst/quarto/report_files$
 ^LICENSE\.md$
 ^Meta$
+^moo_input\.rds$
 ^MOSuite\.Rproj$
 ^pkgdown$
-^README\.Rmd$
-^README\.html$
-^README_files$
-^Rplots\.pdf$
-^moo_input\.rds$
 ^plot-volc-enh\.json$
-^volc-sum-params\.json$
-^report_files$
-^inst/quarto/report_files$
+^README.*$
+^renv\.lock$
+^renv$
+^report
+^Rplots\.pdf$
+^SECURITY\.md$
 ^tests/figures$
+^vignettes/cli\.Rmd$
 ^vignettes/figures/$
 ^vignettes/memory\.Rmd$
-^vignettes/cli\.Rmd$
+^volc-sum-params\.json$
 VennDiagram.*\.log
-^[.]?air[.]toml$
-^\.vscode$
-^SECURITY\.md$
+^\.posit/assistant$

code/MOSuite/.github/workflows/R-CMD-check.yaml

@@ -6,7 +6,6 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   workflow_dispatch:
 
 concurrency:
@@ -23,8 +22,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'release' }
-          - { os: ubuntu-latest, r: 'oldrel-1' }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel-1" }
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     env:
@@ -51,7 +50,7 @@ jobs:
       - uses: actions/checkout@v6
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: '4.5'
+          r-version: "4.5"
           use-public-rspm: true
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

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

@@ -3,7 +3,6 @@ name: auto-format
 on:
   workflow_dispatch:
   pull_request:
-    branches: [ main, master ]
 
 permissions:
   contents: write
@@ -40,7 +39,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: '4.5'
+          r-version: "4.5"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

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

@@ -16,7 +16,7 @@ on:
       orchestrator-repo:
         description: Optional orchestrator repository override in OWNER/REPO format.
         required: false
-        default: CCBR/syncweaver
+        default: NIDAP-Community/syncweaver-orchestrator
         type: string
 
 permissions:
@@ -28,7 +28,7 @@ jobs:
     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' }}
+      ORCHESTRATOR_REPO: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs['orchestrator-repo'] || vars['orchestrator-repo'] || 'NIDAP-Community/syncweaver-orchestrator' }}
     steps:
       - name: Validate dispatch payload
         shell: bash

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

@@ -20,7 +20,7 @@ repos:
       - id: trailing-whitespace
   # spell check
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.2
+    rev: v2.4.3
     hooks:
       - id: codespell
         args: ["-I=.github/WORDLIST.txt"]
@@ -30,10 +30,9 @@ repos:
     hooks:
       - id: air-format
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9028
+    rev: v0.4.3.9029
     hooks:
       - id: parsable-R
-      - id: readme-rmd-rendered
       - id: use-tidy-description
       - id: lintr
         args: [--warn_only]

code/MOSuite/AGENTS.md

@@ -0,0 +1,58 @@
+# multiOmicsSuite
+
+## Description
+
+multiOmicsSuite (`MOSuite`) is an R package for differential multi-omic analysis.
+It defines an S7 class called `multiOmicDataSet` to store data and analyses from
+multi-omic experiments.
+
+Development of MOSuite follows the R packages 2nd edition (https://r-pkgs.org/),
+with a few minor exceptions noted below.
+Helper functions from `usethis` and `devtools` are used extensively for development tasks.
+
+## Package conventions
+
+- **Internal functions should have roxygen2 documentation** (with `@keywords internal`). Do not strip roxygen docs from internal functions.
+- R code should pass `lintr` and `air format` (run `air format .` from the package root).
+- 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.
+
+## Commit messages
+
+- Commit messages must follow [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/) (as enforced in `CONTRIBUTING.md`).
+- Generate messages from staged changes only (`git diff --staged`); do not include unrelated work.
+- Commits should be atomic: one logical change per commit.
+- If mixed changes are present, split into multiple logical commits; the number of commits does not need to equal the number of files changed.
+- Subject format must be: `<type>(optional-scope): short imperative summary` (<=72 chars), e.g., `fix(profile): update release table parser`.
+- Add a body only when needed to explain **why** and notable impact; never include secrets, tokens, PHI, or large diffs.
+- For AI-assisted commits, add this final italicized footer line in the commit message body: _commit message is ai-generated_
+
+## Pull request (PR) process
+
+- When opening a PR, use the request template (`.github/PULL_REQUEST_TEMPLATE.md`) and fill out all sections of the template in the PR description.
+- Do not allow the developer to proceed with opening a PR if it does not fill out all sections of the template.
+- Before a PR can be moved from draft to "ready for review", all of the relevant checklist items must be checked, and any
+irrelevant checklist items should be crossed out.
+- If code is AI-generated, the PR should be labeled `generated-by-AI`. There should be a brief, concise statement in the PR description of how AI was used in creating the PR (model used, high-level prompt intent, manual review confirmation).
+- When new features, bug fixes, or other behavioral changes are introduced to the code,
+unit tests must be added or updated to cover the new or changed functionality.
+- If there are any API or other user-facing changes, the documentation must be updated both inline via roxygen comments and long-form docs in the `vignettes/` directory as R Markdown files.
+- The `R-CMD-check` github actions workflow must pass before the PR can be approved.
+
+### Changelog
+
+The changelog for the repository is maintained in `NEWS.md`  at the root of the repository.
+Each pull request that introduces user-facing changes must include a concise
+entry with the PR number and author username tagged.
+Developer-only changes (i.e. updates to CI workflows, development notes, etc.)
+should never be included in the changelog.
+
+Example:
+
+```
+## development version
+
+- Fix bug in `detect_absolute_paths()` to ignore comments. (#123, @username)
+```