28  Install Language Package Layer

This notebook installs R and Python project packages after Spack and R have already been validated.

Note that from here on out, you should be binding your fake $HOME directory to CONTAINER_HOME, and your fake $TMP directory to CONTAINER_TMP, so that R and Python package installations can write to a writable home and tmp directory.

import submitit
from rse_workbench.helpers import show_submitit_job
from rse_workbench.build_install import install_in_container

executor = submitit.AutoExecutor(folder=str(project_contract.submitit_dir / "%j"))
executor.update_parameters(
    timeout_min=project_contract.slurm_build_hours * 60,
    slurm_partition=project_contract.slurm_build_partition,
    mem_gb=float(project_contract.slurm_build_mem.rstrip("G")),
    cpus_per_task=project_contract.slurm_build_cpus,
    slurm_job_name=f"install-langs-{project_contract.project_name}",
    mail_user=project_contract.slurm_email,
)

LANGUAGE_INSTALL_COMMAND = r'''
set -euo pipefail

source /work/env/activate.sh

which R
which Rscript
which rv
which python3
which uv

rv init
rv sync
rv summary

uv sync || true

echo LANGUAGE_INSTALL_DONE
'''

job = executor.submit(
    install_in_container,
    project_dir=project_contract.project_dir,
    SINGULARITY_IMAGE=project_contract.singularity_image,
    runtime_command=LANGUAGE_INSTALL_COMMAND,
)
job.job_id

result = show_submitit_job(job)
if result is not None:
    print(''.join(result['message']))

show_spython(
    spython_exec(
        command=r"""
set -euo pipefail

source /work/env/activate.sh
cd /work

rv sync

Rscript -e '
cat("R.home(): ", R.home(), "\n\n")
cat(".libPaths():\n")
print(.libPaths())
cat("\nknitr:\n")
print(find.package("knitr"))
cat("\nrmarkdown:\n")
print(find.package("rmarkdown"))
'

quarto check knitr
""",
        image=project_contract.singularity_image,
        options=[
            "--home", f"{project_contract.container_home}:/home/rse",
            "--bind", f"{project_contract.container_tmp}:/tmp",
        ],
        bind_project=project_contract.project_dir,
    ),
    tail=240,
)

Stop here until language package installation succeeds.