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https://github.com/mrustl/amatzi.github.io
Create website for the great Aendue...
https://github.com/mrustl/amatzi.github.io
Last synced: 10 days ago
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Create website for the great Aendue...
- Host: GitHub
- URL: https://github.com/mrustl/amatzi.github.io
- Owner: mrustl
- License: mit
- Created: 2018-12-13T20:35:54.000Z (about 6 years ago)
- Default Branch: dev
- Last Pushed: 2018-12-15T00:42:05.000Z (about 6 years ago)
- Last Synced: 2024-11-07T01:41:59.502Z (about 2 months ago)
- Language: HTML
- Homepage: https://mrustl.github.io/amatzi.github.io
- Size: 3.09 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# amatzi.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/amatzi.github.io/tree/dev)
branch triggers a Travis [](https://travis-ci.org/mrustl/amatzi.github.io).
After finalising the Travis [](https://travis-ci.org/mrustl/amatzi.github.io) the website is automatically pushed to the
repo`s [master](https://github.com/mrustl/amatzi.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://amatzi.github.io](https://amatzi.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/amatzi.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
[RefManageR](https://github.com/ropensci/RefManageR) package these will be
missing in the **content/publication* folder. Check the step where
`RefManageR::GetBibEntryWithDOI` 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!
## 3 Getting portrait picture
Automatically do this with the magick R package:
### Download, crop and save Andues portrait with magick!
```r
library(magick)
library(magrittr)
url <- file.path("https://www.kompetenz-wasser.de/wp-content/uploads/2017/07",
"andreas_matzinger_kuras-600x400.jpg"")
magick::image_read(url) %>%
magick::image_crop(geometry = magick::geometry_area(250,300, 175, 0)) %>%
magick::image_write("static/img/author.jpg")
```