book: switch to BiocBook format

.Rbuildignore

@@ -0,0 +1,8 @@
+^inst/\.quarto$
+^\.png$
+^\.quarto$
+^\.github$
+^LICENSE\.md$
+^NOTES\.md$
+^README\.Rmd$
+^Dockerfile$

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,17 @@
+The Bioconductor community values
+
+* an open approach to science that promotes the sharing of ideas, code, and expertise
+* collaboration
+* diversity and inclusivity
+* a kind and welcoming environment
+* community contributions
+
+In line with these values, Bioconductor is dedicated to providing a welcoming, supportive, collegial, experience free of harassment, intimidation, and bullying regardless of:
+
+* identity: gender, gender identity and expression, sexual orientation, disability, physical appearance, ethnicity, body size, race, age, religion, etc.
+* intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.
+* stage of career
+
+In order to uphold these values, members of the Bioconductor community are required to follow the Code of Conduct.The latest version of Bioconductor project Code of Conduct is available at http://bioconductor.org/about/code-of-conduct/. Please read the Code of Conduct before contributing to this project.
+
+Thank you!

.github/workflows/biocbook.yml

@@ -0,0 +1,111 @@
+name: biocbook
+
+on:
+  push:
+    branches:
+      - devel
+      - RELEASE_**
+
+jobs:
+  build-push:
+    runs-on: ubuntu-latest
+    name: build-book (${{ github.ref_name }})
+    permissions:
+      contents: write
+      packages: write
+
+    steps:
+
+      - name: 🧾 Checkout repository
+        uses: actions/checkout@v3
+
+      - name: ⏳ Collect Workflow Telemetry
+        uses: runforesight/workflow-telemetry-action@v1
+
+      - name: 🐳 Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      - name: 🐳 Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: 📝 Get book info
+        id: info
+        env:
+          OWNER: ${{ github.repository_owner }}
+        run: |
+          Pkgname=$(grep -m1 -E '^Package: +' DESCRIPTION | sed -E 's/.*: +//')
+          echo Pkgname=${Pkgname} >> "${GITHUB_ENV}"
+          pkgname=${Pkgname,,}
+          echo pkgname=${pkgname} >> "${GITHUB_ENV}"
+          owner=${OWNER,,}
+          echo owner=${owner} >> "${GITHUB_ENV}"
+          echo pkgversion=$(grep -m1 -E '^Version: +' DESCRIPTION | sed -E 's/.*: +//') >> "${GITHUB_ENV}"
+
+      - name: 🔐 Log in to the Github Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ env.owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: 🏷 Get metadata for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/${{ env.owner }}/${{ env.pkgname }}
+          tags: |
+            ${{ github.ref_name }}
+            ${{ env.pkgversion }}
+            type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'devel') }}
+
+      - name: 📦 Install, build and check package in local Docker image
+        id: docker
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          load: true
+          tags: ${{ steps.meta.outputs.tags }}
+          build-args: |
+            BIOC_VERSION=${{ github.ref_name }}
+
+      - name: 🚀 Push local Docker image to ghcr.io
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          build-args: |
+            BIOC_VERSION=${{ github.ref_name }}
+
+      - name: 📚 Recover pkg artifacts generated during build in local Docker container (pkg bundle and book) 
+        env:
+          IMG: ${{ steps.docker.outputs.ImageID }}
+        run: |
+          SHA=$(docker container create ${{ env.IMG }})
+          docker container cp ${SHA}:/${{ env.Pkgname }}_${{ env.pkgversion }}.tar.gz .
+          tar --extract --gzip --file ${{ env.Pkgname }}_${{ env.pkgversion }}.tar.gz
+          echo bundle_path=${{ env.Pkgname }}_${{ env.pkgversion }}.tar.gz >> "${GITHUB_ENV}"
+          echo book_path=${{ env.Pkgname }}/inst/doc/book/ >> "${GITHUB_ENV}"
+
+      - name: 🏷 Get gh-branch directory to deploy to
+        run: |
+          echo target_folder=$(echo ${{ github.ref_name }} | sed 's,RELEASE_,,' | tr '_' '.') >> "${GITHUB_ENV}"
+
+      - name: 🚀 Deploy book to Github Pages on versioned branch
+        uses: JamesIves/[email protected]
+        with:
+          folder: ${{ env.book_path }}/ 
+          target-folder: docs/${{ env.target_folder }}/ 
+          branch: gh-pages
+          clean: false 
+
+      - name: 💾 Upload package bundle artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: bundle
+          path: ${{ env.bundle_path }}
+
+      - name: 💾 Upload book artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: book
+          path: ${{ env.book_path }}

.github/workflows/rworkflows.yml

@@ -0,0 +1,53 @@
+## Adapted from neurogenomics/rworkflows: rworkflows::use_workflow()
+
+name: rworkflows
+'on':
+  push:
+    branches:
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - devel
+    - RELEASE_**
+
+jobs:
+  rworkflows:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+        # - os: macOS-latest
+        #   bioc: release
+        #   r: auto
+        #   cont: ~
+        #   rspm: ~
+        # - os: windows-latest
+        #   bioc: release
+        #   r: auto
+        #   cont: ~
+        #   rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ false }}
+        run_vignettes: ${{ false }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ false }}
+        run_pkgdown: ${{ false }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1

DESCRIPTION

@@ -22,6 +22,9 @@ Depends:
     fourDNData
 Imports:
     plyinteractions, 
+    terra, 
+    Rfast, 
+    WGCNA, 
     diffHic, 
     strawr, 
     hicrep,
@@ -37,9 +40,9 @@ Imports:
     rebook,
     quarto,
     sessioninfo 
+Suggests:
 Remotes:
-    github::TaoYang-dev/hicrep,
-    github::tidyomics/plyinteractions
+    github::TaoYang-dev/hicrep
 biocViews:
     HiC,
     DNA3DStructure

Dockerfile

@@ -1,21 +1,10 @@
 ARG BIOC_VERSION
-ARG VERSION
-
-# Pull the base image from bioconductor/bioconductor_docker
 FROM bioconductor/bioconductor_docker:${BIOC_VERSION}
+COPY . /opt/pkg
 
-LABEL org.opencontainers.image.source=https://github.com/js2264/OHCA
-LABEL org.opencontainers.image.documentation=https://js2264.github.io/OHCA
-LABEL org.opencontainers.image.authors="OHCA authors"
-LABEL org.opencontainers.image.description="Orchestrating Hi-C analysis with Bioconductor"
-LABEL org.opencontainers.image.licenses=MIT
-LABEL org.opencontainers.image.version ${VERSION}
+# Install book package 
+RUN Rscript -e 'repos <- BiocManager::repositories() ; remotes::install_local(path = "/opt/pkg/", repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE) ; sessioninfo::session_info(installed.packages()[,"Package"], include_base = TRUE)'
 
-# Install quarto
-# Install OHCA package suite
-# Install OHCA package itself
-# Print info 
-# Cleanup files
-WORKDIR /opt/OHCA
-COPY . /opt/OHCA
-RUN make 
+## Build/install using same approach than BBS
+RUN R CMD INSTALL /opt/pkg
+RUN quarto install tinytex && R CMD build --keep-empty-dirs --no-resave-data /opt/pkg

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2023
+COPYRIGHT HOLDER: Jacques Serizay

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2023 Jacques Serizay
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.