targeting new containers

[j-i-l]

The r-containers were updated to adhere to the naming convention used by r-hub (https://github.com/furrer-lab/r-containers)

[j-i-l]

We have a large amount of linting warnings:
https://github.com/furrer-lab/abn/actions/runs/24606127666/job/71952550479

this could be managed easily with an agent but it would lead to non-functional changes all over the code-base which is something we should do in a single isolated step.

@matteodelucchi: My suggestion would be to ignore the linting "errors" for now and address this in a later step.

[j-i-l]

Regarding the memory management tests, we have quite a few warnings and errors: https://github.com/furrer-lab/abn/actions/runs/24609036222
Some of these will not be related directly to our code-base but rather the dependencies.
It might make sense to go through these errors once an categorize them into "internal" and "external" one, declassifying the 'external' ones to warning.

These errors might also be interesting to @mariaderrico

[j-i-l]

@matteodelucchi: This turned into quite the update for the ci/cd workflows, but we should have recovered a functioning state now (the release workflow is not tested yet.)

My suggestion: after merging #243 we bump to 3.2.0 (with JSON IO as new feature + others(?)). What do you think?

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Changelog for new-containers branch (vs main)

CI / Workflows — Container path migration

• Updated all container image references from os/compiler/r-version format (e.g. debian/gcc/release) to flat format (e.g. debian-gcc-release) to match the new r-containers naming scheme
• Fixed default container in development_run.yml: debian/clang/devel → debian-clang-devel
• Replaced os/compiler/r-version matrix strategy in onlabel_CRAN_checks.yml and onlabel_rebuild_vignettes.yml with explicit container list, removing the exclude rules
• Added valgrind-gcc-devel container to memory checks matrix; conditional valgrind install (skip if container already has it)

CI / Workflows — renv handling

• Replaced all renv::deactivate() Rscript steps with RENV_CONFIG_AUTOLOADER_ENABLED: 'false' env var across 10 workflows (Fedora, MacOS, Ubuntu, Windows setup, development_run, CRAN checks, linting, memory checks, rebuild vignettes, publish enforce/merging)

CI / Workflows — Compatibility fixes

• onlabel_lintingPlus.yml: lintr::with_defaults() → lintr::linters_with_defaults() (removed in recent lintr)
• onlabel_memory_checks.yml: devtools::install(upgrade='never') → devtools::install(upgrade=FALSE) (new devtools rejects string values)

pkgdown

• Added new "Import / Export" section with export_abnFit
• Added as.data.frame.abnDag to "Miscellaneous" section

Vignettes

• Updated data_simulation.Rmd: version string bump (3.1.9 → 3.1.13), removed factorial masking message, updated INLA version string
• Updated multiprocessing.Rmd: added lme4 S3 method overwrite message in output
• Recompiled vignette PNG figures (4 binary files changed)

Build

• Added ^Meta$ to .Rbuildignore

[j-i-l]

mostly changes to workflows, only _pkgcdown.yml includes previously missing sections now

[matteodelucchi]

We have a large amount of linting warnings: https://github.com/furrer-lab/abn/actions/runs/24606127666/job/71952550479

this could be managed easily with an agent but it would lead to non-functional changes all over the code-base which is something we should do in a single isolated step.

@matteodelucchi: My suggestion would be to ignore the linting "errors" for now and address this in a later step.

Agree, it should be addressed either on its own or it might even age away if parts of the code base change significantly

[matteodelucchi]

@matteodelucchi: This turned into quite the update for the ci/cd workflows, but we should have recovered a functioning state now (the release workflow is not tested yet.)

Awesome!

My suggestion: after merging #243 we bump to 3.2.0 (with JSON IO as new feature + others(?)). What do you think?

Agree, let's do a minor version upgrade after #243!