From 0f6d7233a9fc4db1c1f6b3251a72c70684f143b7 Mon Sep 17 00:00:00 2001 From: Bernt Popp Date: Wed, 20 Dec 2023 14:42:48 +0100 Subject: [PATCH] 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 | 4 ++-- README.md | 2 +- {edit_docs => documentation}/.gitignore | 5 ++++- .../01-analyses-tables.Rmd | 0 .../02-analyses-plots.Rmd | 0 .../03-high-evidence-curation.Rmd | 0 .../04-additional-analyses.Rmd | 0 .../05-visualizations.Rmd | 0 {edit_docs => documentation}/README.md | 17 +++++++++-------- {edit_docs => documentation}/_bookdown.yml | 2 +- {edit_docs => documentation}/_output.yml | 0 {edit_docs => documentation}/apa.csl | 0 {edit_docs => documentation}/index.Rmd | 2 +- .../kidney-genetics.bib | 0 {edit_docs => documentation}/preamble.tex | 0 {edit_docs => documentation}/references.Rmd | 0 .../img/figures/curation_flow_diagram.drawio | 0 .../img/figures/curation_flow_diagram.png | Bin .../raw/curation_flow_diagram_raw.drawio | 0 .../curation_flow_diagram_current.drawio | 0 .../static/img/logo/kidney-genetics_logo.png | Bin .../static/img/logo/kidney-genetics_logo.svg | 0 ...d Nephro Candidate Score_CADS_20230713.pptx | Bin ...Kidney-Genetics_AG Halbritter_20230705.pptx | Bin ...Kidney-Genetics_AG Halbritter_20231205.pptx | Bin .../Kidney-Genetics_DGfN_20231007.pptx | Bin ...Kidney-Genetics_MRC Symposium_20230928.pptx | Bin {edit_docs => documentation}/style.css | 0 28 files changed, 18 insertions(+), 14 deletions(-) rename {edit_docs => documentation}/.gitignore (76%) rename {edit_docs => documentation}/01-analyses-tables.Rmd (100%) rename {edit_docs => documentation}/02-analyses-plots.Rmd (100%) rename {edit_docs => documentation}/03-high-evidence-curation.Rmd (100%) rename {edit_docs => documentation}/04-additional-analyses.Rmd (100%) rename {edit_docs => documentation}/05-visualizations.Rmd (100%) rename {edit_docs => documentation}/README.md (72%) rename {edit_docs => documentation}/_bookdown.yml (97%) rename {edit_docs => documentation}/_output.yml (100%) rename {edit_docs => documentation}/apa.csl (100%) rename {edit_docs => documentation}/index.Rmd (99%) rename {edit_docs => documentation}/kidney-genetics.bib (100%) rename {edit_docs => documentation}/preamble.tex (100%) rename {edit_docs => documentation}/references.Rmd (100%) rename {edit_docs => documentation}/static/img/figures/curation_flow_diagram.drawio (100%) rename {edit_docs => documentation}/static/img/figures/curation_flow_diagram.png (100%) rename {edit_docs => documentation}/static/img/figures/raw/curation_flow_diagram_raw.drawio (100%) rename {edit_docs => documentation}/static/img/figures/updated/curation_flow_diagram_current.drawio (100%) rename {edit_docs => documentation}/static/img/logo/kidney-genetics_logo.png (100%) rename {edit_docs => documentation}/static/img/logo/kidney-genetics_logo.svg (100%) rename {edit_docs => documentation}/static/img/visualizations/Kidney-Genetics and Nephro Candidate Score_CADS_20230713.pptx (100%) mode change 100755 => 100644 rename {edit_docs => documentation}/static/img/visualizations/Kidney-Genetics_AG Halbritter_20230705.pptx (100%) mode change 100755 => 100644 rename {edit_docs => documentation}/static/img/visualizations/Kidney-Genetics_AG Halbritter_20231205.pptx (100%) mode change 100755 => 100644 rename {edit_docs => documentation}/static/img/visualizations/Kidney-Genetics_DGfN_20231007.pptx (100%) rename {edit_docs => documentation}/static/img/visualizations/Kidney-Genetics_MRC Symposium_20230928.pptx (100%) mode change 100755 => 100644 rename {edit_docs => documentation}/style.css (100%) 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