From 5921237310824903a2ea1b8cfa3eda5ce8868d09 Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Wed, 4 Oct 2023 16:08:51 +0200
Subject: [PATCH] doc: remove un-needed dependencies

---
 DESCRIPTION | 12 +++---------
 Dockerfile  | 10 ----------
 README.md   | 15 +++++++++++++--
 3 files changed, 16 insertions(+), 21 deletions(-)
 delete mode 100644 Dockerfile

diff --git a/DESCRIPTION b/DESCRIPTION
index 1f172c0..ffe8372 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,12 +1,12 @@
 Package: BiocBook
-Title: Write, containerize, publish and versionize Quarto books with Bioconductor
+Title: Write, containerize, publish and version Quarto books with Bioconductor
 Description: 
     A BiocBook can be created by authors (e.g. R developers, but also 
-    scientists, teachers, communicators, …) who wish to 1) write (compile a 
+    scientists, teachers, communicators, ...) who wish to 1) write (compile a 
     body of biological and/or bioinformatics knowledge), 2) containerize
     (provide Docker images to reproduce the examples illustrated in the compendium), 
     3) publish (deploy an online book to disseminate the compendium), and 4) 
-    versionize (automatically generate specific online book versions 
+    version (automatically generate specific online book versions 
     and Docker images for specific Bioconductor releases). 
 Version: 0.99.8
 Date: 2023-08-03
@@ -42,15 +42,9 @@ Imports:
     quarto,
     renv
 Suggests:
-    BiocManager,
-    BiocVersion,
     BiocStyle,
-    rcmdcheck,
-    BiocCheck,
-    sessioninfo,
     knitr,
     testthat (>= 3.0.0),
-    RefManageR,
     rmarkdown
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 9e9a308..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,10 +0,0 @@
-ARG BIOC_VERSION
-FROM bioconductor/bioconductor_docker:${BIOC_VERSION}
-COPY . /opt/pkg
-
-# 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)'
-
-## Build/install using same approach than BBS
-RUN R CMD INSTALL /opt/pkg
-RUN R CMD build --keep-empty-dirs --no-resave-data /opt/pkg
diff --git a/README.md b/README.md
index cddb767..790bc1a 100644
--- a/README.md
+++ b/README.md
@@ -14,11 +14,18 @@ A `BiocBook` can be created by authors (e.g. `R` developers, but also scientists
 1. *Write*: compile a **body of biological and/or bioinformatics knowledge**;
 2. *Containerize*: provide **Docker images** to reproduce the examples illustrated in the compendium;
 3. *Publish*: deploy an **online book** to disseminate the compendium; 
-4. *Versionize*: **automatically** generate specific online book versions and Docker images for specific [Bioconductor releases](https://contributions.bioconductor.org/use-devel.html). 
+4. *Version*: **automatically** generate specific online book versions and Docker images for specific [Bioconductor releases](https://contributions.bioconductor.org/use-devel.html). 
 
 ## Installation
 
-To install the most recent version of `BiocBook`, you can use:
+To install `BiocBook` from Bioconductor, proceed as follows:
+
+```r
+if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
+BiocManager::install("BiocBook")
+```
+
+To install `BiocBook` development version, you can use:
 
 ```r
 install.packages("devtools")
@@ -52,6 +59,10 @@ preview(bb)
 publish(bb)
 ```
 
+Please read `BiocBook` vignette: `vignette("BiocBook")`. 
+
+You can also check out the [`BiocBookDemo` book](https://js2264.github.io/BiocBookDemo/devel/) to know more about `BiocBook`. 
+
 ## Acknowledgments
 
 This works was inspired by and closely follows the strategy used in coordination