docker: markdown blocks / hugo clash

curly brackets did not go well with the hugo update
#359

Author: falkmielke

content/tutorials/development_containers1/index.md

@@ -138,7 +138,7 @@ Either way, note that you need to run the docker app or docker in a terminal *as
 More info about the installation on your specific Linux operation systems [can be found here](https://docs.docker.com/engine/install).
 The procedure for Debian or Ubuntu-based distributions involves trusting dockers gpg keys and adding an extra repository, [some caution is warranted](https://wiki.debian.org/DontBreakDebian).
 
-``` {sh}
+``` sh
 #| eval: false
 sudo apt update && sudo apt install docker-ce docker-buildx-plugin # debian-based
 # sudo pacman -Sy docker docker-buildx # Arch Linux
@@ -151,7 +151,7 @@ Many features which you would take for granted in this kind of software (securit
 For users to be able to use Docker, they must be in the "docker" group.
 (Insert your username at `<your-username>`.)
 
-``` {sh}
+``` sh
 #| eval: false
 sudo usermod -a -G docker <your-username>
 ```
@@ -165,7 +165,7 @@ However, due to [diverse](https://docs.docker.com/engine/security) [security](ht
 
 On a `systemd` system, you can start and stop Docker on demand via the following commands (those will ask you for `sudo` authentification if necessary).
 
-``` {sh}
+``` sh
 #| eval: false
 systemctl start docker
 
@@ -179,7 +179,7 @@ For aficionados: docker actually runs multiple services: the docker service, the
 
 You can check the Docker installation by confirming the version at which the service is running.
 
-``` {sh}
+``` sh
 #| eval: false
 docker --version
 ```
@@ -296,14 +296,16 @@ In this (and only this) situation, the simple solution is to copy a clone of the
 The `git clone` should reside within the Dockerfile folder.
 Then the Dockerfile section can look like the following:
 
-    # copy the repo
-    COPY my_private_repo /opt/my_private_repo
+```
+# copy the repo
+COPY my_private_repo /opt/my_private_repo
 
-    # manually install dependencies
-    RUN R -q -e 'install.packages("remotes", dependencies = TRUE)'
+# manually install dependencies
+RUN R -q -e 'install.packages("remotes", dependencies = TRUE)'
 
-    # install package from folder
-    RUN R -q -e 'install.packages("/opt/my_private_repo", repos = NULL, type = "source", dependencies = TRUE)'
+# install package from folder
+RUN R -q -e 'install.packages("/opt/my_private_repo", repos = NULL, type = "source", dependencies = TRUE)'
+```
 
 This way of handling private repositories [seems to be good practice](https://stackoverflow.com/questions/23391839/clone-private-git-repo-with-dockerfile/55761914#55761914), for being simple, secure, and generally most feasible.
 

content/tutorials/development_containers1/index.qmd

@@ -147,7 +147,7 @@ Either way, note that you need to run the docker app or docker in a terminal *as
 More info about the installation on your specific Linux operation systems [can be found here](https://docs.docker.com/engine/install).
 The procedure for Debian or Ubuntu-based distributions involves trusting dockers gpg keys and adding an extra repository, [some caution is warranted](https://wiki.debian.org/DontBreakDebian).
 
-```{sh}
+```sh
 #| eval: false
 sudo apt update && sudo apt install docker-ce docker-buildx-plugin # debian-based
 # sudo pacman -Sy docker docker-buildx # Arch Linux
@@ -162,7 +162,7 @@ Many features which you would take for granted in this kind of software (securit
 For users to be able to use Docker, they must be in the "docker" group.
 (Insert your username at `<your-username>`.)
 
-```{sh}
+```sh
 #| eval: false
 sudo usermod -a -G docker <your-username>
 ```
@@ -178,7 +178,7 @@ However, due to [diverse](https://docs.docker.com/engine/security) [security](ht
 
 On a `systemd` system, you can start and stop Docker on demand via the following commands (those will ask you for `sudo` authentification if necessary).
 
-```{sh}
+```sh
 #| eval: false
 systemctl start docker
 
@@ -195,7 +195,7 @@ For aficionados: docker actually runs multiple services: the docker service, the
 
 You can check the Docker installation by confirming the version at which the service is running.
 
-```{sh}
+```sh
 #| eval: false
 docker --version
 ```
@@ -328,7 +328,7 @@ In this (and only this) situation, the simple solution is to copy a clone of the
 The `git clone` should reside within the Dockerfile folder.
 Then the Dockerfile section can look like the following:
 
-```{}
+```
 # copy the repo
 COPY my_private_repo /opt/my_private_repo
 

content/tutorials/development_containers2_run/index.qmd

@@ -157,14 +157,14 @@ benchmark(test())
 
 In the terminal:
 
-```{}
+```
     test replications elapsed relative user.self sys.self user.child sys.child
 1 test()          100  22.391        1    83.961   65.291          0         0
 ```
 
 In the container:
 
-```{}
+```
     test replications elapsed relative user.self sys.self user.child sys.child
 1 test()          100  26.076        1   102.494   153.89          0         0
 ```

content/tutorials/development_containers3_build/index.md

@@ -104,20 +104,22 @@ The Dockerfile resides in your working folder (yet it also defines a [`WORKDIR`]
 
 <!-- -->
 
-    # Use the official Python image (Alpine Linux, Python 3)
-    FROM python:3-alpine
+```
+# Use the official Python image (Alpine Linux, Python 3)
+FROM python:3-alpine
 
-    # install app dependencies
-    RUN apk update && apk add --no-cache python3 py3-pip
-    RUN pip install flask
+# install app dependencies
+RUN apk update && apk add --no-cache python3 py3-pip
+RUN pip install flask
 
-    # install app
-    COPY hello.py /
+# install app
+COPY hello.py /
 
-    # final configuration
-    ENV FLASK_APP=hello
-    EXPOSE 8000
-    CMD ["flask", "run", "--host", "0.0.0.0", "--port", "8000"]
+# final configuration
+ENV FLASK_APP=hello
+EXPOSE 8000
+CMD ["flask", "run", "--host", "0.0.0.0", "--port", "8000"]
+```
 
 Note that the following `hello.py` file needs to be present in your working directory (you will be reminded by a friendly error message):
 
@@ -132,7 +134,7 @@ def hello():
 
 With the `Dockerfile` and `hello.py` in place, you can build the container [^2].
 
-``` {sh}
+``` sh
 #| eval: false
 # on Windows, you are already in an administrator terminal
 docker build --pull -t my-flask .
@@ -156,7 +158,7 @@ You should now see a `python` image, which is the base alpine image we built upo
 There is also a `my-flask`.
 Try it!
 
-``` {sh}
+``` sh
 #| eval: false
 docker run my-flask
 ```
@@ -208,36 +210,38 @@ They prepared quite [a lot of useful images](https://hub.docker.com/u/rocker), i
 
 Note the syntax in `FROM`: it is `rocker/<image>:<version>`.
 
-    FROM rocker/rstudio:latest
-    # (Use the rocker rstudio image)
+```
+FROM rocker/rstudio:latest
+# (Use the rocker rstudio image)
 
-    # update the system packages
-    RUN apt update \
-        && apt upgrade --yes
+# update the system packages
+RUN apt update \
+    && apt upgrade --yes
 
-    # git2rdata requires git
-    RUN  apt-get update \
-      && apt-get install -y --no-install-recommends \
-        git libgit2-dev\
-      && apt-get clean
+# git2rdata requires git
+RUN  apt-get update \
+  && apt-get install -y --no-install-recommends \
+    git libgit2-dev\
+  && apt-get clean
 
-    # update pre-installed R packages
-    # RUN Rscript -e 'update.packages(ask=FALSE)'
+# update pre-installed R packages
+# RUN Rscript -e 'update.packages(ask=FALSE)'
 
-    # copy a `.Rprofile` to the container
-    # available here: https://tutorials.inbo.be/installation/administrator/admin_install_r/Rprofile.site
-    COPY docker/.Rprofile $R_HOME/etc/Rprofile.site
+# copy a `.Rprofile` to the container
+# available here: https://tutorials.inbo.be/installation/administrator/admin_install_r/Rprofile.site
+COPY docker/.Rprofile $R_HOME/etc/Rprofile.site
 
-    # install package via an R command (`R -q -e` or `Rscript -e`)
-    # (a) from pre-configured repositories
-    RUN Rscript -e 'install.packages("git2rdata")'
+# install package via an R command (`R -q -e` or `Rscript -e`)
+# (a) from pre-configured repositories
+RUN Rscript -e 'install.packages("git2rdata")'
 
-    # (b) via r-universe
-    RUN R -q -e 'install.packages("watina", repos = c(inbo = "https://inbo.r-universe.dev", CRAN = "https://cloud.r-project.org"))'
+# (b) via r-universe
+RUN R -q -e 'install.packages("watina", repos = c(inbo = "https://inbo.r-universe.dev", CRAN = "https://cloud.r-project.org"))'
 
-    # (b) from github
-    RUN R -q -e 'install.packages("remotes")'
-    RUN R -q -e 'remotes::install_github("inbo/INBOmd", dependencies = TRUE)'
+# (b) from github
+RUN R -q -e 'install.packages("remotes")'
+RUN R -q -e 'remotes::install_github("inbo/INBOmd", dependencies = TRUE)'
+```
 
 It takes some puzzle work to get the dependencies right, e.g. with the `libgit2` dependency (try commenting out that line to get a feeling for build failure).
 However, there is hope: (i) the error output is quite instructive (at least for Linux users), (ii) building is incremental, so you can add successively.
@@ -255,14 +259,14 @@ More here: <https://docs.docker.com/build/building/best-practices>
 
 Test the image:
 
-``` {sh}
+``` sh
 #| eval: false
 docker build -t test-rstudio .
 ```
 
 Run it, as before:
 
-``` {sh}
+``` sh
 #| eval: false
 docker run --rm -p 8787:8787 -e PASSWORD=YOURNEWPASSWORD test-rstudio
 ```

content/tutorials/development_containers3_build/index.qmd

@@ -113,7 +113,7 @@ The Dockerfile resides in your working folder (yet it also defines a [`WORKDIR`]
 - Edit the file in your favorite text editor (`vim Dockerfile`; Windows users probably use "notepad"). 
 - Paste and optionally modify the content below.
 
-```{}
+```
 # Use the official Python image (Alpine Linux, Python 3)
 FROM python:3-alpine
 
@@ -133,7 +133,7 @@ CMD ["flask", "run", "--host", "0.0.0.0", "--port", "8000"]
 
 Note that the following `hello.py` file needs to be present in your working directory (you will be reminded by a friendly error message):
 
-```{python}
+```python
 #| eval: false
 from flask import Flask
 app = Flask(__name__)
@@ -146,7 +146,7 @@ def hello():
 
 With the `Dockerfile` and `hello.py` in place, you can build the container [^4].
 
-```{sh}
+```sh
 #| eval: false
 # on Windows, you are already in an administrator terminal
 docker build --pull -t my-flask .
@@ -171,7 +171,7 @@ You should now see a `python` image, which is the base alpine image we built upo
 There is also a `my-flask`. 
 Try it!
 
-```{sh}
+```sh
 #| eval: false
 docker run my-flask
 ```
@@ -229,7 +229,7 @@ They prepared quite [a lot of useful images](https://hub.docker.com/u/rocker), i
 
 Note the syntax in `FROM`: it is `rocker/<image>:<version>`.
 
-```{}
+```
 FROM rocker/rstudio:latest
 # (Use the rocker rstudio image)
 
@@ -280,15 +280,15 @@ More here: <https://docs.docker.com/build/building/best-practices>
 
 Test the image:
 
-```{sh}
+```sh
 #| eval: false
 docker build -t test-rstudio .
 ```
 
 
 Run it, as before:
 
-```{sh}
+```sh
 #| eval: false
 docker run --rm -p 8787:8787 -e PASSWORD=YOURNEWPASSWORD test-rstudio
 ```

content/tutorials/development_containers4_podman/index.md

@@ -73,7 +73,7 @@ I follow the `podman` installation instructions for Arch Linux, to set up a **ro
 
 Installation:
 
-``` {sh}
+``` sh
 #| eval: false
 pacman -Sy podman podman-docker passt
 ```
@@ -87,23 +87,23 @@ Just to be safe, I briefly list the major configuration steps.
 
 The first step is to confirm a required kernel module: check that `unpriviledged_users_clone` is set to one.
 
-``` {sh}
+``` sh
 #| eval: false
 sysctl kernel.unprivileged_userns_clone
 ```
 
 Then, configure "subordinate user IDs".
 There are detail differences in each Linux distribution; with some luck, your username is already present in these lists:
 
-``` {sh}
+``` sh
 #| eval: false
 cat /etc/subuid
 cat /etc/subgid
 ```
 
 If not, you can be admitted to the club of subordinates with the command:
 
-``` {sh}
+``` sh
 #| eval: false
 usermod --add-subuids 100000-165535 --add-subgids 100000-165535 <username>
 podman system migrate
@@ -112,7 +112,7 @@ podman system migrate
 We note some useful commands on the way: `podman system ...` and `podman info`.
 You might immediately check "native rootless overlays" (has something to do with mounting filesystems in the container):
 
-``` {sh}
+``` sh
 #| eval: false
 podman info | grep -i overlay
 ```
@@ -127,7 +127,7 @@ You can use images from `docker.io` with Podman.
 The only difference from Docker is the explicit mention of the source, `docker.io`.
 For example:
 
-``` {sh}
+``` sh
 #| eval: false
 podman search docker.io/alpine
 podman pull docker.io/alpine # download a machine
@@ -141,7 +141,7 @@ Except for the prefix, everything you [can read in our `docker run` tutorial](..
 
 Note that at least some `docker.io` images will not work: I actually experienced issues with the "rootless Docker image":
 
-``` {sh}
+``` sh
 #| eval: false
 # podman run --rm -it docker.io/docker:25.0-dind-rootless
 ```
@@ -162,7 +162,7 @@ Any Dockerfile should work, with the mentioned mini-adjustment to `FROM`.
 And you can use any Docker image; `docker.io/rocker/rstudio` [is available](https://rocker-project.org/use/rootless-podman.html) (don't forget to specify the port).
 You may even write `docker` in the terminal: it will alias to `podman` (via the `podman-docker` package on Linux, or an alias).
 
-``` {sh}
+``` sh
 #| eval: false
 podman run --rm -p 8787:8787 -e PASSWORD=YOURNEWPASSWORD -v /data/git/coding-club:/root/coding-club docker.io/rocker/rstudio
 ```