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https://github.com/mrustl/mrustl.github.io

My personal website
https://github.com/mrustl/mrustl.github.io

Last synced: 10 days ago
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My personal website

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README 

        
# mrustl.github.io



My personal website is created with [Hugo](https://gohugo.io/) with the fantastic

[Academic](https://sourcethemes.com/academic/) theme. 



The updating/publishing workflow is further enhanced by automatic: 



1. Deployment: with R package [blogdown](https://github.com/rstudio/blogdown) 

with Travis-CI



2. Adding [ORCID](https://orcid.org/) publications to the website by using the R 

package [kwb.orcid](https://github.com/kwb-r/kwb.orcid) and the Python library 

[academic-admin](https://github.com/sourcethemes/academic-admin)



## 1 How to update the website



### Step 1: Create/add new content



Change file(s) in subdirectory ***content***.



In case that blog posts with Rmarkdown are added that require package dependencies:

define these in the **DESCRIPTION** file in the **Imports** and if necessary 

**Remotes** (e.g. if R Package lives on Github like kwb.utils) field.



### Step 2: Check locally



For checking whether the website can be build successfully after adding your 

content do the following



#### Install "blogdown"

```r

if (!require("remotes")) {

  install.packages("remotes", repos = "https://cloud.r-project.org")

}

remotes::install_github("rstudio/blogdown")

```

### Install "hugo" 



with explicitly specifying version number for reproducibility



```r

blogdown::install_hugo(version = "0.52", force = TRUE)

```



### Build/preview site locally



Check whether the website successfully builds locally after the changes



```r

blogdown::serve_site()

```



### Step 2: Commit/push changes to "dev" branch



In case of successfull local build commit and push only the added **content** 

to the **dev** branch. Do not commit the local webiste build stored in the 

**public** folder as well as the output of rendered .Rmd files (as these will 

be automaticall re-build on the Travis-CI)



### Step 3: Automatic build/deployment the website



The deployment is automated with the help of Travis-CI and blogdown very similar to 

the workflow in the [blogdown docu](https://bookdown.org/yihui/blogdown/travis-github.html). 

However instead of specifying all necessary commands only in the `.travis.yml` 

also the files: 



- `_build.sh` and 



- `_deploy.sh` 



are used as both are sucessfully used for automating the update process 

for the [fakin.doc](https://github.com/kwb-r/fakin.doc) website. 



Each push to the repo`s [dev](https://github.com/mrustl/mrustl.github.io/tree/dev) 

branch triggers a Travis [![Travis build](https://travis-ci.org/mrustl/mrustl.github.io.svg?branch=dev)](https://travis-ci.org/mrustl/mrustl.github.io). 



After finalising the Travis [![Travis build](https://travis-ci.org/mrustl/mrustl.github.io.svg?branch=dev)](https://travis-ci.org/mrustl/mrustl.github.io) the website is automatically pushed to the 

repo`s [master](https://github.com/mrustl/mrustl.github.io/tree/master) branch,

which contains all necessary files for serving the website!



### Step 4: Visit the updated website



The content of the updated website is available at [https://mrustl.github.io](https://mrustl.github.io).



## 2 Automatically add ORCID publications to the website



With the following R script it is possible to automatically import all of your 

publications from ORCID:



```r

###############################################################################

### Create .bibtex file with ORCID publications

###############################################################################



# Install dependencies



## Check installed pkgs

installed_pkgs <- rownames(installed.packages())



## Install missing CRAN pkgs

cran_pkgs <- c("remotes", "dplyr", "RefManageR", "reticulate", "data.table")

cran_missing <- !cran_pkgs %in% installed_pkgs



if(any(cran_missing)) {

  install.packages(cran_pkgs[cran_missing] , repos = "https://cloud.r-project.org")

}



## Install latest version of KWB-R GitHub "kwb.orcid" package

remotes::install_github("kwb-r/kwb.orcid")

  

library(magrittr)



secret <- read.csv("secret.csv")

Sys.setenv("ORCID_TOKEN" =  secret$orcid_token)



## Get all of Michael Rustler`s publications from ORCID

orcid <- kwb.orcid::get_kwb_orcids()[4]

publications <- kwb.orcid::create_publications_df_for_orcids(orcids = orcid)



## Put all with DOI in a data.frame 

publications_with_dois <- data.table::rbindlist(publications$`external-ids.external-id`) %>%  

    dplyr::filter(`external-id-type` == "doi")

  



## Create .bibtex from DOIs with RefManageR

## for details see: browseURL("https://github.com/ropensci/RefManageR/")

write_bibtex <- function(dois, file = "publications_orcid.bib", 

                         overwrite = TRUE) {



if(file.exists(file) == FALSE ||  overwrite == TRUE && file.exists(file))  {

  cat(sprintf("Bibtex file '%s'...", file))  

try(RefManageR::GetBibEntryWithDOI(dois,

                               temp.file = file, 

                               delete.file = FALSE))

  cat("Done!")

} else {

   print(sprintf("Bibtex file %s already existing. Specify 'overwrite=TRUE' if 

   you want to overwrite it!", file))

 }

}



## Export all cited publications to  "publications_orcid.bib"

write_bibtex(dois = publications_with_dois$`external-id-value`)



###############################################################################

### Step 2: Import .bibtex file to publications with Python 

###############################################################################



## Download Anaconda with Python 3.7 from website (if not installed)

#browseURL("https://www.anaconda.com/download/")



python_path <- "C:/Users/mrustl.KWB/AppData/Local/Continuum/anaconda3"



Sys.setenv(RETICULATE_PYTHON = python_path)



reticulate::use_python(python_path)



### Define conda environment name with "env"

env <- "academic"



reticulate::conda_create(envname = env)

reticulate::use_condaenv(env)



### Install required Python library "academic" 

### for details see:

# browseURL("https://github.com/sourcethemes/academic-admin")



reticulate::py_install(packages = "academic", 

           envname = env, 

           pip = TRUE, pip_ignore_installed = TRUE) 



## Should existing publications in content/publication folder be overwritten?

overwrite <- TRUE



option_overwrite <- ifelse(overwrite, "--overwrite", "")



### Create and run "import_bibtex.bat" batch file

cmds <- sprintf('call "%s" activate "%s"\ncd "%s"\nacademic import --bibtex "%s"  %s', 

               normalizePath(file.path(python_path, "Scripts/activate.bat")), 

               env,

               normalizePath(getwd()),

               "knitcitations.bib",

               option_overwrite)



writeLines(cmds,con = "import_bibtex.bat")



shell("import_bibtex.bat")



```



Finally check the content of the folder **content/publication**. Your 

ORCID publications should be added there now! 



**Important note:** in case the it was possible to resolve the DOI and create a

valid bibtex entry with the

[knitcitations](https://github.com/cboettig/knitcitations) package these will be

missing in the **content/publication* folder. Check the step where

`knitcitations::citep` is called and watch for errors!



For pushing the changes to your website go through the steps defined in 

[How to update the website](#1-how-to-update-the-website) again!