rbio migration cleanup

[davidsmejia]

Issue Number

#3572

Purpose/Implementation Notes

Every entry in scripts/ now has a replacement landed earlier in this stack (rbio commands, install/*.sh helpers, or relocated to infrastructure/). This PR ports the last script (calculate_ram_hours.py) to a Django management command, trims the last code-side dependency on scripts/common.sh, then deletes the directory and refreshes the READMEs to match.

Commits

This PR is split into four commits so reviewers can step through them independently:

1. foreman: add calculate_ram_hours management command Ports scripts/calculate_ram_hours.py to a Django management command in foreman. Replaces pyrefinebio HTTP queries with direct ORM access via Sample.get_downloader_jobs() / get_processor_jobs(). Invocation: rbio compose:manage foreman calculate_ram_hours <accession> locally, or docker exec dr_foreman python3 manage.py calculate_ram_hours <accession> on the prod foreman EC2.

2. infra/format_batch_with_env.sh: drop dead common.sh source + unused exports The script sourced ../scripts/common.sh solely to call get_docker_db_ip_address, which on the deploy box (no drdb container) returned an empty string. The exported DB_HOST_IP and EXTRA_HOSTS values are never substituted into any *.tpl.json template (verified by grep). Dead exports kept alive by a dead source. Removes the last code-side dependency on scripts/common.sh.

3. remove scripts/ and obsolete shell wrappers; rbio --help is the entry point The big delete: 18 files. Every deletion has a landed replacement (or, in the case of foreman/test_survey.sh, is confirmed dead via grep of @tag("manual") across foreman tests).

4. docs: refresh READMEs to point at rbio commands Walks README.md and foreman/README.md and replaces every reference to a deleted script with its rbio equivalent. Touches the Quick Start, Installation (manual + automatic), Postgres helpers, Testing, Surveyor commands, Downloader/Processor Job examples, Development Helpers, Docker Images, and Terraform sections.

Deletes in commit 3

scripts/ (12 files):

Deleted	Replacement
calculate_ram_hours.py	foreman/.../management/commands/calculate_ram_hours.py (added in commit 1)
common.sh	callers inlined what they used; helpers either dead or replaced by --network refinebio_default
create_virtualenv.sh	install/setup_venv.sh + rbio install:venv
install_all.sh	install/install_deps.sh + rbio install:deps
kill_all_jobs.{py,sh}	rbio ops:kill-jobs
prepare_image.sh	rbio build <target>
run_all_tests.sh	rbio test:all
run_full_pipeline.py	rbio dev:pipeline
run_manage.sh	rbio compose:manage <service> <args>
run_shell.sh	rbio compose:manage <service> shell
update_docker_images.sh	rbio build --push <group>

Other deletes (6 files):

Deleted	Replacement
.github/scripts/run_terraform.sh	inlined into remote_deploy.sh; final SSH calls rbio deploy:up
foreman/run_management_command.sh	rbio compose:manage foreman <args>
workers/run_command.sh	rbio compose:manage <worker> <args>
foreman/test_survey.sh	dead (no @tag("manual") tests exist); the --exclude-tag=manual default in test:foreman is a tracked follow-up
workers/run_job.sh	rbio dev:job <image> <subcommand> [args]
workers/run_janitor.sh	rbio dev:janitor

What is NOT affected

The metasra README and the prod foreman EC2 user-data template reference a different run_management_command.sh that lives on the prod foreman instance (generated by user-data on that box). Those references are correct and intentionally unchanged.

Methods

N/A

Types of changes

• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Functional tests

N/A

Checklist

• Lint and unit tests pass locally with my changes
• I have added necessary documentation (if appropriate)

Screenshots

N/A