Prepare BREAD 0.99.0 for Bioconductor submission

.Rbuildignore

@@ -7,3 +7,8 @@
 ^_pkgdown\.yml$
 ^pkgdown$
 ^tools$
+^data-raw$
+^build_preview$
+^CLAUDE\.md$
+^README\.Rmd$
+^\.git$

.github/CODE_OF_CONDUCT.md

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+# Code of Conduct
+
+BREAD is a Bioconductor package and adopts the
+**[Bioconductor Code of Conduct](https://bioconductor.org/about/code-of-conduct/)**
+in full.
+
+In short: the Bioconductor community is dedicated to providing a welcoming,
+harassment-free experience for everyone, regardless of gender identity and
+expression, sexual orientation, disability, physical appearance, body size,
+race, age, religion, or level of experience. We do not tolerate harassment of
+community members in any form.
+
+Please read the full text, including the list of expected and unacceptable
+behaviours, at <https://bioconductor.org/about/code-of-conduct/>.
+
+## Reporting
+
+Report violations to the package maintainer (see `DESCRIPTION`), or — if the
+report concerns the maintainer, or you would prefer to go outside the project —
+to the Bioconductor Code of Conduct committee using the contact details and
+reporting process described at
+<https://bioconductor.org/about/code-of-conduct/>.
+
+All reports are handled confidentially.

.github/CONTRIBUTING.md

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+# Contributing to BREAD
+
+Thanks for your interest in BREAD. This document covers how to report a
+problem and how to work on the package.
+
+## Reporting bugs and asking questions
+
+- **Bugs and feature requests** → open a [GitHub issue](https://github.com/BacZemin/BREAD/issues).
+  Please include a [reprex](https://reprex.tidyverse.org/) and the output of
+  `sessionInfo()`.
+- **Usage questions** → the
+  [Bioconductor support site](https://support.bioconductor.org) with the
+  `BREAD` tag reaches a wider audience than the issue tracker.
+
+A good bug report for BREAD usually needs three things: the structure of your
+`SummarizedExperiment` (`assayNames()`, `dim()`, `colData()`), the `features`
+`GRanges` you passed, and the exact `fit_bread()` call.
+
+## Development setup
+
+```r
+# clone, then from the package root:
+install.packages(c("devtools", "roxygen2", "testthat"))
+BiocManager::install(c("SummarizedExperiment", "GenomicRanges", "S4Vectors"))
+
+devtools::load_all()
+devtools::test()
+```
+
+Optional backends and vignette dependencies (`brms`, `knowYourCG`,
+`sesameData`) live in `Suggests`; tests that need them skip cleanly when they
+are absent.
+
+## Conventions
+
+- **Documentation is roxygen2.** Never edit `NAMESPACE` or anything in `man/`
+  by hand — run `devtools::document()` and commit the regenerated files.
+- **Every exported object needs a runnable `@examples` block.** Bioconductor
+  requires this. The packaged example data
+  (`system.file("extdata", "vitc_ag06561.rds", package = "BREAD")`) is small
+  and fast enough that examples can fit a real model rather than fake one.
+- **Tests are testthat 3rd edition.** Shared fixtures live in
+  `tests/testthat/helper-toy.R`.
+- **No `library()` calls inside `R/`** — use `@importFrom`.
+- **Style**: tidyverse style guide. Keep lines under 80 characters and
+  functions under 50 lines where practical; BiocCheck flags both.
+- Prefer `vapply()` over `sapply()`, `seq_len()`/`seq_along()` over `1:n`, and
+  `TRUE`/`FALSE` over `T`/`F`.
+
+## Before opening a pull request
+
+```r
+devtools::document()
+devtools::test()
+```
+
+and a full check plus BiocCheck:
+
+```sh
+Rscript tools/run_check.R
+Rscript tools/run_bioccheck.R
+```
+
+Both CI workflows (`R-CMD-check` and `bioc-check`) must be green. The
+`bioc-check` workflow runs on the Bioconductor devel container and is the
+authoritative gate.
+
+Branch from `main` and use a descriptive branch name. Please do not bump the
+version in a PR — that is handled at release time.
+
+## Code of Conduct
+
+This project follows the
+[Bioconductor Code of Conduct](https://bioconductor.org/about/code-of-conduct/).
+By participating you agree to abide by its terms.

.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Something in BREAD behaves incorrectly or errors unexpectedly
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting. For **usage questions** ("how do I ...?"), please
+        use the [Bioconductor support site](https://support.bioconductor.org)
+        with the `BREAD` tag instead.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: What happened?
+      description: What did you expect, and what happened instead?
+    validations:
+      required: true
+
+  - type: textarea
+    id: reprex
+    attributes:
+      label: Reproducible example
+      description: >
+        A self-contained [reprex](https://reprex.tidyverse.org/). The packaged
+        example data is a good basis if your own data cannot be shared.
+      value: |
+        ```r
+        library(BREAD)
+        se  <- readRDS(system.file("extdata", "vitc_ag06561.rds", package = "BREAD"))
+        reg <- readRDS(system.file("extdata", "vitc_regions.rds", package = "BREAD"))
+
+        # your code here
+        ```
+      render: r
+    validations:
+      required: true
+
+  - type: textarea
+    id: data-shape
+    attributes:
+      label: Input structure
+      description: >
+        Output of `assayNames(se)`, `dim(se)`, `colData(se)`, and
+        `length(features)` / `names(mcols(features))`. Most BREAD issues are
+        input-shape issues, so this is usually the fastest route to a fix.
+      render: text
+
+  - type: textarea
+    id: sessioninfo
+    attributes:
+      label: sessionInfo()
+      render: text
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Usage question
+    url: https://support.bioconductor.org
+    about: >
+      For "how do I ...?" questions, please post on the Bioconductor support
+      site and tag it BREAD. Questions there reach more people and stay
+      searchable.
+  - name: Package documentation
+    url: https://baczemin.github.io/BREAD/
+    about: Reference index, vignettes, and the getting-started guide.

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Suggest a capability or improvement for BREAD
+labels: ["enhancement"]
+body:
+  - type: textarea
+    id: problem
+    attributes:
+      label: What problem would this solve?
+      description: >
+        Describe the analysis you are trying to do and where BREAD currently
+        gets in the way. Concrete blocked workflows are more useful than
+        abstract feature names.
+    validations:
+      required: true
+
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed solution
+      description: What would the API look like? A sketched call is ideal.
+      render: r
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+      description: Other packages or workarounds you have tried.
+
+  - type: checkboxes
+    id: roadmap
+    attributes:
+      label: Roadmap
+      options:
+        - label: >
+            I have checked NEWS.md and the open issues to see whether this is
+            already planned.

.github/SUPPORT.md

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+# Getting help with BREAD
+
+## Usage questions
+
+Ask on the **[Bioconductor support site](https://support.bioconductor.org)**
+and tag your post `BREAD`. Questions there are seen by the wider Bioconductor
+community and stay searchable for the next person with the same question.
+
+Good things to include:
+
+- what you are trying to test (the contrast, the regions)
+- `assayNames(se)`, `dim(se)`, and `colData(se)`
+- the `features` object (`length()`, `mcols()` column names)
+- your exact `fit_bread()` call
+- `sessionInfo()`
+
+## Bugs and feature requests
+
+Open an issue at <https://github.com/BacZemin/BREAD/issues> with a
+[reprex](https://reprex.tidyverse.org/). The packaged example data is a good
+basis for a self-contained reproduction:
+
+```r
+se  <- readRDS(system.file("extdata", "vitc_ag06561.rds", package = "BREAD"))
+reg <- readRDS(system.file("extdata", "vitc_regions.rds", package = "BREAD"))
+```
+
+## Documentation
+
+- Package website: <https://baczemin.github.io/BREAD/>
+- `vignette("bread-intro", package = "BREAD")` — getting started
+- `vignette("bread-vitc", package = "BREAD")` — real-data walkthrough

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

@@ -0,0 +1,57 @@
+# R CMD check on a clean runner.
+# Adapted from https://github.com/r-lib/actions/tree/v2/examples
+#
+# Deliberately ubuntu-only to start. macOS and Windows are added to the
+# matrix only once ubuntu is reliably green -- a three-platform matrix that
+# goes red on day one is noise, not signal.
+on:
+  push:
+    branches: [main, polish-for-release]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+name: R-CMD-check
+
+permissions:
+  contents: read
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      # brms/rstan are Suggests and are slow+flaky to build on runners; the
+      # tests that need them already skip_if_not_installed().
+      _R_CHECK_FORCE_SUGGESTS_: false
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          args: 'c("--no-manual", "--as-cran")'