diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index b7cb75f..a772310 100644 --- a/.github/workflows/gh-pages.yml +++ b/.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 diff --git a/README.md b/README.md index 79450c0..5f24494 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@

- Kidney-Genetics logo + Kidney-Genetics logo

# Kidney-Genetics - Designing a reproducible and curated database of kidney-related genes diff --git a/edit_docs/.gitignore b/documentation/.gitignore similarity index 76% rename from edit_docs/.gitignore rename to documentation/.gitignore index 9683800..3892ad5 100644 --- a/edit_docs/.gitignore +++ b/documentation/.gitignore @@ -13,4 +13,7 @@ _main.* *.utf8.md !ga.html libs/ -nul \ No newline at end of file +nul + +# the build directory of bookdown +build/ \ No newline at end of file diff --git a/edit_docs/01-analyses-tables.Rmd b/documentation/01-analyses-tables.Rmd similarity index 100% rename from edit_docs/01-analyses-tables.Rmd rename to documentation/01-analyses-tables.Rmd diff --git a/edit_docs/02-analyses-plots.Rmd b/documentation/02-analyses-plots.Rmd similarity index 100% rename from edit_docs/02-analyses-plots.Rmd rename to documentation/02-analyses-plots.Rmd diff --git a/edit_docs/03-high-evidence-curation.Rmd b/documentation/03-high-evidence-curation.Rmd similarity index 100% rename from edit_docs/03-high-evidence-curation.Rmd rename to documentation/03-high-evidence-curation.Rmd diff --git a/edit_docs/04-additional-analyses.Rmd b/documentation/04-additional-analyses.Rmd similarity index 100% rename from edit_docs/04-additional-analyses.Rmd rename to documentation/04-additional-analyses.Rmd diff --git a/edit_docs/05-visualizations.Rmd b/documentation/05-visualizations.Rmd similarity index 100% rename from edit_docs/05-visualizations.Rmd rename to documentation/05-visualizations.Rmd diff --git a/edit_docs/README.md b/documentation/README.md similarity index 72% rename from edit_docs/README.md rename to documentation/README.md index 55b216c..ee0edd9 100644 --- a/edit_docs/README.md +++ b/documentation/README.md @@ -2,7 +2,13 @@ The repository subfolder for the Kidney-Genetics documentation. -To build the documentation execute following commands: +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. +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 \ No newline at end of file +``` \ No newline at end of file diff --git a/edit_docs/_bookdown.yml b/documentation/_bookdown.yml similarity index 97% rename from edit_docs/_bookdown.yml rename to documentation/_bookdown.yml index 8a3d05c..9c94ffe 100644 --- a/edit_docs/_bookdown.yml +++ b/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" \ No newline at end of file diff --git a/edit_docs/_output.yml b/documentation/_output.yml similarity index 100% rename from edit_docs/_output.yml rename to documentation/_output.yml diff --git a/edit_docs/apa.csl b/documentation/apa.csl similarity index 100% rename from edit_docs/apa.csl rename to documentation/apa.csl diff --git a/edit_docs/index.Rmd b/documentation/index.Rmd similarity index 99% rename from edit_docs/index.Rmd rename to documentation/index.Rmd index 621c436..998f312 100644 --- a/edit_docs/index.Rmd +++ b/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"), diff --git a/edit_docs/kidney-genetics.bib b/documentation/kidney-genetics.bib similarity index 100% rename from edit_docs/kidney-genetics.bib rename to documentation/kidney-genetics.bib diff --git a/edit_docs/preamble.tex b/documentation/preamble.tex similarity index 100% rename from edit_docs/preamble.tex rename to documentation/preamble.tex diff --git a/edit_docs/references.Rmd b/documentation/references.Rmd similarity index 100% rename from edit_docs/references.Rmd rename to documentation/references.Rmd diff --git a/edit_docs/static/img/figures/curation_flow_diagram.drawio b/documentation/static/img/figures/curation_flow_diagram.drawio similarity index 100% rename from edit_docs/static/img/figures/curation_flow_diagram.drawio rename to documentation/static/img/figures/curation_flow_diagram.drawio diff --git a/edit_docs/static/img/figures/curation_flow_diagram.png b/documentation/static/img/figures/curation_flow_diagram.png similarity index 100% rename from edit_docs/static/img/figures/curation_flow_diagram.png rename to documentation/static/img/figures/curation_flow_diagram.png diff --git a/edit_docs/static/img/figures/raw/curation_flow_diagram_raw.drawio b/documentation/static/img/figures/raw/curation_flow_diagram_raw.drawio similarity index 100% rename from edit_docs/static/img/figures/raw/curation_flow_diagram_raw.drawio rename to documentation/static/img/figures/raw/curation_flow_diagram_raw.drawio diff --git a/edit_docs/static/img/figures/updated/curation_flow_diagram_current.drawio b/documentation/static/img/figures/updated/curation_flow_diagram_current.drawio similarity index 100% rename from edit_docs/static/img/figures/updated/curation_flow_diagram_current.drawio rename to documentation/static/img/figures/updated/curation_flow_diagram_current.drawio diff --git a/edit_docs/static/img/logo/kidney-genetics_logo.png b/documentation/static/img/logo/kidney-genetics_logo.png similarity index 100% rename from edit_docs/static/img/logo/kidney-genetics_logo.png rename to documentation/static/img/logo/kidney-genetics_logo.png diff --git a/edit_docs/static/img/logo/kidney-genetics_logo.svg b/documentation/static/img/logo/kidney-genetics_logo.svg similarity index 100% rename from edit_docs/static/img/logo/kidney-genetics_logo.svg rename to documentation/static/img/logo/kidney-genetics_logo.svg diff --git a/edit_docs/static/img/visualizations/Kidney-Genetics and Nephro Candidate Score_CADS_20230713.pptx b/documentation/static/img/visualizations/Kidney-Genetics and Nephro Candidate Score_CADS_20230713.pptx old mode 100755 new mode 100644 similarity index 100% rename from edit_docs/static/img/visualizations/Kidney-Genetics and Nephro Candidate Score_CADS_20230713.pptx rename to documentation/static/img/visualizations/Kidney-Genetics and Nephro Candidate Score_CADS_20230713.pptx diff --git a/edit_docs/static/img/visualizations/Kidney-Genetics_AG Halbritter_20230705.pptx b/documentation/static/img/visualizations/Kidney-Genetics_AG Halbritter_20230705.pptx old mode 100755 new mode 100644 similarity index 100% rename from edit_docs/static/img/visualizations/Kidney-Genetics_AG Halbritter_20230705.pptx rename to documentation/static/img/visualizations/Kidney-Genetics_AG Halbritter_20230705.pptx diff --git a/edit_docs/static/img/visualizations/Kidney-Genetics_AG Halbritter_20231205.pptx b/documentation/static/img/visualizations/Kidney-Genetics_AG Halbritter_20231205.pptx old mode 100755 new mode 100644 similarity index 100% rename from edit_docs/static/img/visualizations/Kidney-Genetics_AG Halbritter_20231205.pptx rename to documentation/static/img/visualizations/Kidney-Genetics_AG Halbritter_20231205.pptx diff --git a/edit_docs/static/img/visualizations/Kidney-Genetics_DGfN_20231007.pptx b/documentation/static/img/visualizations/Kidney-Genetics_DGfN_20231007.pptx similarity index 100% rename from edit_docs/static/img/visualizations/Kidney-Genetics_DGfN_20231007.pptx rename to documentation/static/img/visualizations/Kidney-Genetics_DGfN_20231007.pptx diff --git a/edit_docs/static/img/visualizations/Kidney-Genetics_MRC Symposium_20230928.pptx b/documentation/static/img/visualizations/Kidney-Genetics_MRC Symposium_20230928.pptx old mode 100755 new mode 100644 similarity index 100% rename from edit_docs/static/img/visualizations/Kidney-Genetics_MRC Symposium_20230928.pptx rename to documentation/static/img/visualizations/Kidney-Genetics_MRC Symposium_20230928.pptx diff --git a/edit_docs/style.css b/documentation/style.css similarity index 100% rename from edit_docs/style.css rename to documentation/style.css