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

.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": "v0.4.0",
+      "git_sha": "ef1bdf806d153515e8ecbb8a8d2bfc518a418e05"
     }
   }
 }

code/MOSuite/.Rbuildignore

@@ -1,37 +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$
+^\.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

@@ -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: NIDAP-Community/syncweaver-orchestrator
+        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: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs['orchestrator-repo'] || vars['orchestrator-repo'] || 'NIDAP-Community/syncweaver-orchestrator' }}
+    steps:
+      - name: Validate dispatch payload
+        shell: bash
+        run: |
+          set -euo pipefail
+          if [[ -z "${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

@@ -20,20 +20,19 @@ 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"]
   # 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: v0.4.3.9029
     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)
+```