Code

Adding Apptainer/Singularity support#134

Code

Merged

chainsawriot merged 33 commits intogesistsa:v0.3gesistsa/rang:v0.3from e-kotov:singularitye-kotov/rang:singularityCopy head branch name to clipboardApr 17, 2023

+1,339-59

Commits

Commits on Apr 14, 2023

• move and update .insert_materials_dir() in preparation for support for apptainer/singularity

  e-kotov

  committed
  0c5309c

• move and rename .write_dockerfile() to .write_container_file() in preparation for Apptainer/Singularity container support

  e-kotov

  committed
  7c10b0c

• add Apptainer/Singularity container support (no tests yet)

  e-kotov

  committed
  f713979

• add Apptainer/Singularity helper functions

  e-kotov

  committed
  6c89cab

• rename singularity.def to more neutral container.def container definition file name

  e-kotov

  committed
  177e5c1

• fixes to 'from scratch' debian. needs to be tested

  e-kotov

  committed
  7454aad

• fix missing Apptainer/Singularity definition keywords/sections

  e-kotov

  committed
  9e33460

• adapt formal tests from dockerize() to apptainerise()

  e-kotov

  committed
  a69d95b

• add space before and after Apptainer/Singularity definition sections

  e-kotov

  committed
  8b64c4a

• remove debian image cache for apptainer, no easy way to do it, better to bootrstrap from docker image

  e-kotov

  committed
  cc919e8

• fix tests for apptainer with custom post install

  e-kotov

  committed
  d46449e

• Update README and FAQ vignette with info about Apptainer/Singularity

  e-kotov

  committed
  2aa5b85

• fix typos in error and warnings messages

  e-kotov

  committed
  045a848

• add tests for new version of .insert_materials_dir

  e-kotov

  committed
  d5ef076

• add missing newline at end of file

  e-kotov

  committed
  c421162

• add reference to apptainerize() in export_rang() docs

  e-kotov

  committed
  913fdfd

• update readme, remove HPC references

  e-kotov

  committed
  b734f49

• (1) make 4 spaces indent; (2) rewrite .generate_docker_readme() to generate_container_readme() to work with both types of containers; (3) apptainerize() inherits duplicate params from dockerize()

  e-kotov

  committed
  b30a4d2

• update docs

  e-kotov

  committed
  5ffc556

• rename docker readme template, apptainer readme will be added as a separate file

  e-kotov

  committed
  cf5a53d

• create Rproj file with deafult for 4 spaces for tab

  e-kotov

  committed
  fa3df34

Commits on Apr 17, 2023

• Add Apptainer/Singularity README template

  e-kotov

  committed
  033d541

• fix Apptainer/Singularity startscript, as /init uses s6 overlay seemingly incompatible with Apptainer/Singularity

  e-kotov

  committed
  e1ddbea

• Update README.md/Rmd and faq.Rmd with correct instructions to start RStudio IDE in Apptainer/Singularity

  e-kotov

  committed
  e6e7da4

• remove deprecated purrr::prepend()

  e-kotov

  committed
  0edf289

• add info that Apptainer/Singularity containers with RStudio IDE cannot be started using root user

  e-kotov

  committed
  94d748d

• update README: (1) compatibility with old RStudio IDE (<4.0) that requires binding .rstudio to the container (2) add default port parameter so that it is obvious how to change it

  e-kotov

  committed
  2d476a3

• Fix RStudio Apptainer/Singularity instance start. Add ENV variables that are needed for start of the instance, but not the install process

  e-kotov

  committed
  17959e4

• Update README, readme template for Apptainer/Singularity and FAQ with instructions in running containers

  e-kotov

  committed
  a73ad9c

• Update test for correct Apptainer/Singularity container for RStudio image

  e-kotov

  committed
  670c166

• CACHE_PATH should be available during container build, not in the enviroment of a running container

  e-kotov

  committed
  b636b5a

• fix typos

  e-kotov

  committed
  b546f78

• remove tests from test_appteinerize.R that have nothing to do with appteinerize() and are carbon copies of tests in tests_dockerize.R

  e-kotov

  committed
  f5cdc3e