fix: rename documentation folder, closes #27, closes #5

the previous edit_docs folder is now documentation. The README in the folder is changed to describe the automatic build. Commands need to only be run when in local development. The documentation is automatically build with GitHub actions and deployed to the gh-pages branch.

.github/workflows/gh-pages.yml

@@ -23,7 +23,7 @@ jobs:
         runs-on: ubuntu-20.04
         defaults:
             run:
-              working-directory: ./edit_docs
+              working-directory: ./documentation
         steps:
             - uses: actions/checkout@v4
             - uses: r-lib/actions/setup-r@v2
@@ -54,7 +54,7 @@ jobs:
             - uses: actions/upload-artifact@v4
               with:
                 name: build
-                path: ./edit_docs/build
+                path: ./documentation/build
                 if-no-files-found: error
     checkout-and-deploy:
         runs-on: ubuntu-20.04

README.md

@@ -1,5 +1,5 @@
 <p align="center">
-    <img src="edit_docs/static/img/logo/kidney-genetics_logo.png" alt="Kidney-Genetics logo" width="192" height="192">
+    <img src="documentation/static/img/logo/kidney-genetics_logo.png" alt="Kidney-Genetics logo" width="192" height="192">
 </p>
 
 # Kidney-Genetics - Designing a reproducible and curated database of kidney-related genes

edit_docs/.gitignore → documentation/.gitignore

@@ -13,4 +13,7 @@ _main.*
 *.utf8.md
 !ga.html
 libs/
-nul
+nul
+
+# the build directory of bookdown
+build/

edit_docs/README.md → documentation/README.md

@@ -2,7 +2,13 @@
 
 The repository subfolder for the Kidney-Genetics documentation.
 
-To build the documentation execute following commands:
+<mark style="background-color: red">The documentation is automatically built and deployed to [https://halbritter-lab.github.io/kidney-genetics/](https://halbritter-lab.github.io/kidney-genetics/) using GitHub Actions into the branch hg-pages.</mark>
+The configuration for the GitHub Pages build is in the `.github/workflows` folder.
+
+For local development only, the documentation can be built using the following commands:
+
+```
+To build the documentation locally execute following commands:
 
 ```
 ## load libraries
@@ -11,7 +17,7 @@ library(config)
 
 project_topic <- "nephrology"
 project_name <- "kidney-genetics"
-script_path <- "/edit_docs/"
+script_path <- "/documentation/"
 
 ## read configs
 config_vars_proj <- config::get(file = Sys.getenv("CONFIG_FILE"),
@@ -44,9 +50,4 @@ Rendering HTML widgets for PDF requires webshot and phantomjs [FROM:](https://bo
 ```
 install.packages("webshot")
 webshot::install_phantomjs()
-```
-
-## TODO
-- automatic loading and filtering of current result tables in all Rmd files
-- change scripts to load the gzipped files
-- make a script that runs the above commands to re-generate the pages website
+```

edit_docs/_bookdown.yml → documentation/_bookdown.yml

@@ -19,5 +19,5 @@ download:
   - ["KidneyGenetics_documentation.epub", "EPUB"]
   - ["KidneyGenetics_documentation.docx", "DOCX"]
 view: https://github.com/halbritter-lab/kidney-genetics/tree/master/docs/%s
-edit: https://github.com/halbritter-lab/kidney-genetics/tree/master/edit_docs/%s
+edit: https://github.com/halbritter-lab/kidney-genetics/tree/master/documentation/%s
 output_dir: "build"

edit_docs/index.Rmd → documentation/index.Rmd

@@ -36,7 +36,7 @@ library(shinyLP)      # needed to plot presentations
 ```{r, echo=FALSE, message=FALSE, warning=FALSE}
 project_topic <- "nephrology"
 project_name <- "kidney-genetics"
-script_path <- "/edit_docs/"
+script_path <- "/documentation/"
 
 ## read configs
 config_vars_proj <- config::get(file = Sys.getenv("CONFIG_FILE"),