Development: docker (and podman) by falkmielke · Pull Request #356 · inbo/tutorials · GitHub

Description

This tutorial summarizes initial steps in creating docker images.
Matter of fact, it is just an assembly of components and tutorials which I found helpful for applying docker in an INBO-environment.

Task list

My tutorial or article is placed in a subfolder of tutorials/content
The filename of my tutorial or article is index.md. In case of an Rmarkdown tutorial I have knitted my index.Rmd to index.md (both files are pushed to the repo).
I have included tags in the YAML header (see the tags listed in the tutorials website side bar for tags that have been used before)
I have added categories to the YAML header and my category tags are from the list of category tags
I have put images to the static folder.

(duplicate with branch `variograms`)

Site tested and ready for review. Thank you in advance!

While reviewing #356, the instructions of the PR template for reviewing seem to no longer work to render the site from the GHA artifact. With these changes, it seems to work again though, using python -m http.server 8887

Thanks for this guided tour! We can discuss some things live further. Some of my comments are an example and apply to more places.

Some questions.

Images are stored in different places between Docker and Podman:

$ podman images
REPOSITORY                TAG         IMAGE ID      CREATED      SIZE
docker.io/library/alpine  latest      b0c9d60fc5e3  4 weeks ago  8.13 MB
$ 
$ docker images
REPOSITORY                     TAG       IMAGE ID       CREATED         SIZE
test-mne                       latest    b711361627aa   2 days ago      5.47GB
nginx                          latest    97662d24417b   4 days ago      192MB
rocker/tidyverse               latest    0a2c0d551856   3 weeks ago     2.73GB
alpine                         latest    a606584aa9aa   7 months ago    7.8MB
geopython/geopython-workshop   latest    ed98940df343   20 months ago   1.05GB
ubuntu                         latest    99284ca6cea0   20 months ago   77.8MB
hello-world                    latest    d2c94e258dcb   21 months ago   13.3kB

Is it possible to let Podman run a container I installed or built with Docker in this setting?

Also, I'm hesitant to log into RStudio Server as root (Podman case): how should we look at this? What are the permissions of the rstudio user (Docker case)?

Is there a reason why the figures are not in a subdirectory of the tutorial directory? (Cf other tutorials)

Yes!
On all the other tutorials I saw, the images are generated by running the Rmd main file.
It makes nostalgic sense to keep them with the tutorial, but in fact they are subject to version control and change upon every re-render.

The images for this tutorial are screenshots, i.e. static images. In a hugo context, these are best stored in the static folder.

Both is possible. I would follow the opinion of the website maintainers (@damianooldoni ?)

Thanks for this guided tour! We can discuss some things live further. Some of my comments are an example and apply to more places.

Thank you for the thorough review! I will go through your comments and adjust.

Some questions.

Images are stored in different places between Docker and Podman:
[...]

Is it possible to let Podman run a container I installed or built with Docker in this setting?

I have not looked this up, but the chance is low. Pods work technically different from docker containers, and once you build or pull one, it is converted into a container of the respective system.
What you can do is

Use the same dockerfiles
mount the same volumes

so you can transfer the recipe's, not the outcome.
Generally, I think it is good practice to treat containers as volatile to keep them hostmachine-independent.

Also, I'm hesitant to log into RStudio Server as root (Podman case): how should we look at this? What are the permissions of the rstudio user (Docker case)?

The difference, as I understand it, is that a container with the unprivileged container user in the Docker case still requires privileged execution on the host system. To me, this brings the risk of privilege escalation in case of breakout to the root.
I do not know why RStudio requires a "root" user within the container; yet if that would escape, it would be far less dangerous. I think we could alternatively get a base-r container, non-root, but just terminal login.

I will double-check and try.

see #356

highlights: - general language and consistency - container permanence (`--rm`) - confusion with version control and virtual envs - rootless docker

@falkmielke I added some small comments for your latest changes.

The tutorial has considerable length compared to the average INBO tutorial. Perhaps you could consider splitting the tutorial into two or three tutorials (or an 'article' referring one or two tutorials, as here). It's just a thought, I'm not sure how well it would work here.

(I feel clumsy.)

Voila. Not one, not two, but four tutorials.
Some introductions and summaries added; please double check all crosslinks. The core content is exactly as it was before.

Thank you for another round of review @florisvdh @ThierryO !

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

While reviewing #356, the instructions of the PR template for reviewing seem to no longer work to render the site from the GHA artifact. With these changes, it seems to work again though, using python -m http.server 8887

falkmielke added 12 commits February 4, 2025 15:32

docker: docker build

697aae4

docker: extend rocker/rstudio for inbo

cc71aaf

docker: tested/run modified rstudio rocker

f5adca7

docker: podman

2a5c0fc

docker: rename folder

8bf932d

docker: the windows experience

db7d15a

docker: screenshots and wrapup V1

346f6de

docker: minor adjustments and additions

e349246

docker: installing private packages

2297c10

docker: minor adjustments

bcacce9

docker: render quarto -> md

1e1b862

docker: image references to static

0767adf

falkmielke added the proposal tutorial label Feb 4, 2025

falkmielke requested review from damianooldoni and florisvdh February 4, 2025 14:45

falkmielke added 2 commits February 4, 2025 15:48

docker: pasting in CSS for callout boxes

e09a382

(duplicate with branch `variograms`)

docker: hugo shortcode for callouts

3cd97b3

florisvdh reviewed Feb 10, 2025

View reviewed changes

Comment thread content/tutorials/development_docker/index.md Outdated

florisvdh mentioned this pull request Feb 10, 2025

Update pull_request_template.md #357

Merged

falkmielke added 7 commits February 10, 2025 18:13

docker (wip): review comments by @florisvdh

1367a8d

see #356

docker: review comments incorporated

2ec9d36

highlights: - general language and consistency - container permanence (`--rm`) - confusion with version control and virtual envs - rootless docker

docker: review changes to markdown

4a94915

docker: html anchors

581ef3a

docker: html anchors, attempt 2

7d14644

docker: html anchors, attempt 3

68568c1

docker: html anchors, attempt n+1

29b5ed8

falkmielke requested a review from florisvdh February 20, 2025 14:37

florisvdh reviewed Feb 20, 2025

View reviewed changes

Comment thread content/tutorials/development_docker/index.qmd Outdated

Comment thread content/tutorials/development_docker/index.qmd Outdated

falkmielke added 20 commits February 21, 2025 08:17

docker: pre-split changes (review suggestion)

b8fd9f0

docker: docker_run spin-off

4e5f527

docker: docker_build spin-off

950f02d

docker: containers_podman spin-off

52e9a22

docker: central node tutorial

990a04f

docker: rename for generalization

d4451e7

docker: link preparation and testing

8997b9a

docker: conversion to .md

32e0fef

docker: tutorial cluster interactions

580fb3a

docker: cherry - a catchy image for the overview

db380e3

docker: how to place a caption footnote

4a40f6e

docker: how to put colon in yaml title

28bc562

docker: that footnote again...

04821ee

docker: direct link to installation

b64f85a

docker: that footnote again :/

b862c61

docker: still no footnote

65e8d31

(I feel clumsy.)

docker: footnote (n'th attempt)

1057eea

docker: footnote hack in html

5b142cc

docker: adding a podman image

6626c0e

docker: changing notebook order (rename)

73cbcea

falkmielke requested a review from florisvdh February 21, 2025 11:40

falkmielke added 3 commits February 21, 2025 12:47

docker: crosslinks corrected

9c3fcb6

docker: markdown blocks / hugo clash

4c2cdcf

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

docker: typo performacne drop

df237da

falkmielke and others added 2 commits May 8, 2026 07:45

Merge branch 'master' into development_docker

90d4fea

development_docker: note on secrets ty @ThierryO

3db0887

Development: docker (and podman) by falkmielke · Pull Request #356 · inbo/tutorials · GitHub

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Development: docker (and podman) - #356

Development: docker (and podman)#356falkmielke wants to merge 53 commits intomasterinbo/tutorials:masterfrom development_dockerinbo/tutorials:development_dockerCopy head branch name to clipboard

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Development: docker (and podman)#356
falkmielke wants to merge 53 commits into
masterfrom
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falkmielke commented Feb 4, 2025 •
edited by bserrien
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