Master (#381)

* Add section on network learning (#303)

* Add section on network learning

* Update section on network learning

* Update network learning chapter

Make requested changes
Remove sections on network comparison

* Add network comparison chapter

* Update book.bib

* Update chapters on network learning and comparison

* Update network chapter and contributors (#377)

- Reorder network learning chapter to be less nested
- Move network plots to analysis section
- Add contributors

* #355: Add new data resource (#370)

* #355: Add new data resource

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

* Up

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

* Up

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

* Fix conflicts in book.bib

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

---------

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

* Conversion to BiocBook (#379)

* biocbook: add GHA workflows

* biocbook: move data to extdata

* biocbook: move general/figures to inst/pages/images

* biocbook: add vignettes

* biocbook: add book assets

* biocbook: update package files

* biocbook: purge un-necessary files

* biocbook: migrate Rmd to qmd and fix xrefs

* biocbook: fix aesthetics

* biocbook: add callout acknowledging miaverse in walcome page

* biocbook: improve README to include dev/author instructions

* biocbook: replace `js2264` by `microbiome`

* biocbook: add `BiocBook` to `Suggests` for developers

* biocbook: transfer chaps 60/61 to inst/pages/

* biocbook: include changes from #370 and #377

---------

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Stefanie Peschel <stefpeschel@gmail.com>
Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com>
Co-authored-by: Jacques Serizay <jacquesserizay@gmail.com>

.Rbuildignore

@@ -1,2 +1,10 @@
+^inst/\.quarto$
+^\.png$
+^\.quarto$
+^\.github$
+^LICENSE\.md$
+^NOTES\.md$
+^README\.Rmd$
+^Dockerfile$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.github/.gitignore

@@ -1 +1 @@
-*.html
+*.html

.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/github-pages-deploy-action@v4.4.3
+        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