Merge pull request #20 from lnnrtwttkhn/osip

Merge update for OSIP talk
lnnrtwttkhn · Jan 20, 2023 · 019605e · 019605e
2 parents e0ed9a1 + ea869bf
commit 019605e
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diff --git a/.Rprofile b/.Rprofile
@@ -1 +1,8 @@
-source("renv/activate.R")
+# if the current directory is called "/home" and the parent directory contains
+# a file called ".dockerenv", we know we are in a docker container
+# in this case DO NOT activate renv
+if ( here::here() == "/home" && file.exists(here::here("../.dockerenv")) == TRUE )  {
+} else {
+  # source("renv/activate.R")
+}
+
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -4,7 +4,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     container:
-      image: lennartwittkuhn/talk-rdm
+      image: lennartwittkuhn/talk-rdm:amd64
     steps:
       - name: Checkout
         uses: actions/checkout@v2

diff --git a/.gitignore b/.gitignore
@@ -3,4 +3,5 @@ libs
 *.html
 input
 public
-*.pdf
+*.pdf
+.Rhistory
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM r-base:4.0.3
+FROM r-base:4.2.2
 
 RUN apt-get update
 
@@ -7,7 +7,7 @@ RUN echo 'options(Ncpus=4, repos=structure(c(CRAN="https://cloud.r-project.org")
 RUN echo 'installOrQuit <- function(p) {tryCatch(install.packages(p), warning=function(e){q(status=1)})}' >> ~/.Rprofile
 
 # external dependencies
-RUN apt-get install -y pandoc pandoc-citeproc && apt-get clean
+RUN apt-get install -y pandoc && apt-get clean
 
 # prefer binary R packages, if they are available
 RUN apt-get update && apt-get install -y \

diff --git a/Makefile b/Makefile
@@ -5,6 +5,19 @@ talk-rdm.html: talk-rdm.Rmd
 
 public/index.html: index.Rmd talk-rdm.Rmd archive
 	Rscript -e "rmarkdown::render('index.Rmd', output_dir = 'public', output_file = 'index.html')"
-
+
+.PHONY: local
 local: talk-rdm.Rmd
 	Rscript -e "xaringan::inf_mr('talk-rdm.Rmd')"
+
+.PHONY: docker-build 
+docker-build:
+	docker build --platform linux/amd64 -t lennartwittkuhn/talk-rdm:amd64 .
+
+.PHONY: docker-push
+docker-push:
+	docker push lennartwittkuhn/talk-rdm:amd64
+
+.PHONY: docker-pull
+docker-pull:
+	docker image pull lennartwittkuhn/talk-rdm:amd64
diff --git a/README.md b/README.md
@@ -12,6 +12,7 @@ Slides are available at: https://lennartwittkuhn.com/talk-rdm/
 
 | When | What | Host |
 |---|---|---|
+| 18<sup>th</sup> of January 2023 | [Open Science Initiative at the Department of Psychology (OSIP)](https://tu-dresden.de/mn/psychologie/die-fakultaet/open-science#) at [TU Dresden](https://tu-dresden.de/) |
 | 13<sup>th</sup> of September 2022 | [5<sup>th</sup> RDM-Workshop 2022 on Research Data Management in the Max Planck Society](https://rdm.mpdl.mpg.de/mpdl-services/workshops/5-fdm-workshop-2022/) | [Max Planck Digital Library (MPDL)](https://www.mpdl.mpg.de/en/) |
 | 20<sup>th</sup> of October 2021 | LNDG Lab meeting | [Lifespan Neural Dynamics Group (LNDG)](https://www.mpib-berlin.mpg.de/research/research-centers/lip/projects/lndg) at the [Max Planck Institute for Human Development](https://www.mpib-berlin.mpg.de/en) |
 | 18<sup>th</sup> of October 2021 | ["Open Science Ambassadors Day 2021"](https://osambassadors.mpdl.mpg.de/) | [Max Planck PhDnet](https://www.phdnet.mpg.de/home) and the [Max Planck Digital Library](https://www.mpdl.mpg.de/en/) |
@@ -33,20 +34,40 @@ Note, that this does not render the RMarkdown in the Docker container but your l
 
 After updating the [Dockerfile](Dockerfile), I use the following command to push the newest image to [dockerhub](https://hub.docker.com/r/lennartwittkuhn/talk-rdm):
 
+### Login
+
 ```bash
 docker login
 ```
 
+### Build
+
+```bash
+docker build --platform linux/amd64 -t lennartwittkuhn/talk-rdm:amd64 .
+```
+
+### Push
+
+```bash
+docker push lennartwittkuhn/talk-rdm:amd64
+```
+
+### Pull
+
 ```bash
-docker build -t  lennartwittkuhn/talk-rdm:latest .
+docker image pull lennartwittkuhn/talk-rdm:amd64
 ```
 
+### Run
+
 ```bash
-docker push lennartwittkuhn/talk-rdm:latest
+docker run --rm --platform linux/amd64 -v $PWD:/home lennartwittkuhn/talk-rdm:amd64 /bin/sh -c "cd /home; make all"
 ```
 
+### Run interactively
+
 ```bash
-docker run --rm -v $PWD:/home lennartwittkuhn/talk-rdm /bin/sh -c "cd /home; make all"
+docker run -it --rm --platform linux/amd64 -v $PWD:/home lennartwittkuhn/talk-rdm:amd64 /bin/sh
 ```
 
 ## Make PDF

diff --git a/archive/20211018-osambassadors/talk-rdm.Rmd b/archive/20211018-osambassadors/talk-rdm.Rmd
@@ -153,7 +153,7 @@ knitr::include_graphics("https://the-turing-way.netlify.app/_images/reproducible
 # Challenges: Many stages in the research cycle
 
 ```{r, echo=FALSE, fig.align="center", out.width="58%", fig.retina=1, fig.cap='<a href="https://zenodo.org/record/4906004" target="_blank"><sup>by Scriberia for The Turing Way community (CC-BY 4.0)</sup></a>'}
-knitr::include_graphics("https://the-turing-way.netlify.app/_images/research-cycle.jpg") 
+knitr::include_graphics("https://keeper.mpdl.mpg.de/f/3a1863ac2c2e40809c5f/?dl=1")
 ```
 
 ---

diff --git a/archive/20211020-lndg/talk-rdm.Rmd b/archive/20211020-lndg/talk-rdm.Rmd
@@ -1256,7 +1256,7 @@ knitr::include_graphics("https://the-turing-way.netlify.app/_images/reproducible
 # Challenges: Many stages in the research cycle
 
 ```{r, echo=FALSE, fig.align="center", out.width="58%", fig.retina=1, fig.cap='<a href="https://zenodo.org/record/4906004" target="_blank"><sup>by Scriberia for The Turing Way community (CC-BY 4.0)</sup></a>'}
-knitr::include_graphics("https://the-turing-way.netlify.app/_images/research-cycle.jpg") 
+knitr::include_graphics("https://keeper.mpdl.mpg.de/f/3a1863ac2c2e40809c5f/?dl=1")
 ```
 
 ---

diff --git a/archive/20220913-mpg-fdm-workshop/talk-rdm.Rmd b/archive/20220913-mpg-fdm-workshop/talk-rdm.Rmd
@@ -178,7 +178,7 @@ knitr::include_graphics("https://the-turing-way.netlify.app/_images/reproducible
 # Challenge: Many stages in the research cycle
 
 ```{r, echo=FALSE, fig.align="center", out.width="58%", fig.retina=1, fig.cap='<a href="https://zenodo.org/record/4906004" target="_blank"><sup>by Scriberia for The Turing Way community (CC-BY 4.0)</sup></a>'}
-knitr::include_graphics("https://the-turing-way.netlify.app/_images/research-cycle.jpg") 
+knitr::include_graphics("https://keeper.mpdl.mpg.de/f/3a1863ac2c2e40809c5f/?dl=1")
 ```
 
 ???
@@ -1662,7 +1662,7 @@ knitr::include_graphics("https://the-turing-way.netlify.app/_images/reproducible
 # Challenges: Many stages in the research cycle
 
 ```{r, echo=FALSE, fig.align="center", out.width="58%", fig.retina=1, fig.cap='<a href="https://zenodo.org/record/4906004" target="_blank"><sup>by Scriberia for The Turing Way community (CC-BY 4.0)</sup></a>'}
-knitr::include_graphics("https://the-turing-way.netlify.app/_images/research-cycle.jpg") 
+knitr::include_graphics("https://keeper.mpdl.mpg.de/f/3a1863ac2c2e40809c5f/?dl=1")
 ```
 
 ---