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feature/rbio scripts migration - #3598

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davidsmejia merged 51 commits into
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feature/rbio-scripts-migration
Jun 16, 2026
Merged

feature/rbio scripts migration#3598
davidsmejia merged 51 commits into
devfrom
feature/rbio-scripts-migration

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@davidsmejia

@davidsmejia davidsmejia commented Jun 16, 2026

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Issue Number

N/A

Purpose/Implementation Notes

Merges in the rbio script migration feature and the compendia instance changes.

Methods

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Types of changes

  • Bugfix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)

Functional tests

N/A

Checklist

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

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davidsmejia added 30 commits May 26, 2026 14:00
@davidsmejia
rbio: add @requires decorator + mtime-gated common sdist rebuild
15608d1
@davidsmejia
rbio: add compose:* + new dev:* + test:all (local dev surface)
f679022
@davidsmejia
rbio: add deploy:* ops:* install:* (cloud surface)
0b0548e
@davidsmejia
rbio: add debug:* diagnostics (env, deps, venv)
c948622
@davidsmejia
infra: relocate format_batch_with_env.sh into infrastructure/
0401025
@davidsmejia
api: migrate serve scripts to rbio build + refinebio_default network
87d4ad8
@davidsmejia
infra/deploy.sh: drop scripts/common.sh source, inline its consumers
1e13b3a
@davidsmejia
ci: switch deploy to rbio commands, inline branch resolution, rename …
61d89fc 
…CI_* → DEPLOY_*
@davidsmejia
foreman: add calculate_ram_hours management command
7c9ed58
@davidsmejia
infra/format_batch_with_env.sh: drop dead common.sh source + unused e…
e829e77 
…xports
@davidsmejia
remove scripts/ and obsolete shell wrappers; rbio --help is the entry…
280117a 
… point
@davidsmejia
docs: refresh READMEs to point at rbio commands
253fe71
@davidsmejia
ci: rename dev:up → compose:up in test job preflight steps
9be60c3
@davidsmejia
Merge branch 'davidsmejia/3572-02-rbio-local-dev' into davidsmejia/35…
230e495 
…72-03-rbio-cloud
@davidsmejia
Merge branch 'davidsmejia/3572-03-rbio-cloud' into davidsmejia/3572-0…
4b0167b 
…4-rbio-diagnostics
@davidsmejia
Merge branch 'davidsmejia/3572-04-rbio-diagnostics' into davidsmejia/…
c5b7e97 
…3572-05-relocate-format-batch
@davidsmejia
Merge branch 'davidsmejia/3572-05-relocate-format-batch' into davidsm…
9c8f4e9 
…ejia/3572-06-app-shell-callers
@davidsmejia
Merge branch 'davidsmejia/3572-06-app-shell-callers' into davidsmejia…
fa24bea 
…/3572-07-infrastructure-callers
@davidsmejia
Merge branch 'davidsmejia/3572-07-infrastructure-callers' into davids…
b75a719 
…mejia/3572-08-ci-workflow
@davidsmejia
Merge branch 'davidsmejia/3572-08-ci-workflow' into davidsmejia/3572-…
47648d6 
…09-cleanup
@davidsmejia
docker: upgrade base image from Ubuntu 18.04 to 22.04
a0edc34
@davidsmejia
docker: widen common sdist COPY glob to accept dash or underscore
a64568b
@davidsmejia
requirements: drop backports-zoneinfo for Python 3.10
eac54cc
@davidsmejia
drop RVM curl + gpg + source; replace with single gem install aspera…
5e01c1d 
…-cli -v 4.10.0
@davidsmejia
register /usr/local/lib/R/lib with ldconfig
e17b407
@davidsmejia
docker: make R 3.4.4 + rpy2 usable on jammy's runtime
47f228c
@davidsmejia
workers: use PATH-based Rscript, capture R version via cmd_line
ebbe1d1
@davidsmejia
foreman: bump pandas + numpy pins to Python 3.10-compatible versions
1f2c1ef
@davidsmejia
test: chmod only container-owned files in coverage_command
eac2245
@davidsmejia
docker: pre-install testthat with patched Catch.h for glibc 2.34+ compat
a3bcc0b
davidsmejia added 21 commits June 4, 2026 17:41
@davidsmejia
docker/deps: fix testthat compile, urllib3/vcrpy, and Py3.10 test imp…
95c7f3f 
…orts on jammy
@davidsmejia
replace loop with if
73d5a5d
@davidsmejia
docker: restore unzip on jammy base + set -e in worker download blocks
da918ef
@davidsmejia
docker: drop unsupported --break-system-packages from base pip install
90bcf51
@davidsmejia
docker: constrain cffi<2 so rpy2 3.4.5 builds against its expected ABI
9c7ada8
@davidsmejia
docker: prebuild rpy2 wheel in base so downstream skips the broken sd…
b29a55b 
…ist build
@davidsmejia
foreman: skip live-API ArrayExpress metadata test
00a7ef3
@davidsmejia
compendia: remove visualization deps and phantomjs code path
16f231c
@davidsmejia
compendia: move off nvidia/cuda base onto dr_base
7f3e16c
@davidsmejia
compendia: install fancySVD --no-deps, drop redundant compendia.txt
f88b4af
@davidsmejia
Merge pull request #3583 from AlexsLemonade/davidsmejia/3572-01-rbio-…
4fa6670 
…foundation

rbio: add @requires decorator + mtime-gated common sdist rebuild
@davidsmejia
Merge pull request #3584 from AlexsLemonade/davidsmejia/3572-02-rbio-…
7d6572e 
…local-dev

rbio: add compose:* + new dev:* + test:all (local dev surface)
@davidsmejia
Merge pull request #3585 from AlexsLemonade/davidsmejia/3572-03-rbio-…
d60f2d2 
…cloud

rbio: add deploy:* ops:* install:* (cloud surface)
@davidsmejia
Merge pull request #3586 from AlexsLemonade/davidsmejia/3572-04-rbio-…
0e3bd98 
…diagnostics

rbio: add debug:* diagnostics (env, deps, venv)
@davidsmejia
Merge pull request #3587 from AlexsLemonade/davidsmejia/3572-05-reloc…
c0ab332 
…ate-format-batch

relocate format_batch_with_env.sh into infrastructure/
@davidsmejia
Merge pull request #3588 from AlexsLemonade/davidsmejia/3572-06-app-s…
5271312 
…hell-callers

api: migrate serve scripts to rbio build + refinebio_default network
@davidsmejia
Merge pull request #3589 from AlexsLemonade/davidsmejia/3572-07-infra…
1ba4262 
…structure-callers

infra/deploy.sh: drop scripts/common.sh source, inline its consumers
@davidsmejia
Merge pull request #3590 from AlexsLemonade/davidsmejia/3572-08-ci-wo…
9b90c8b 
…rkflow

ci: switch deploy to rbio commands, inline branch resolution, rename CI_* -> DEPLOY_*
@davidsmejia
Merge pull request #3591 from AlexsLemonade/davidsmejia/3572-09-cleanup
8140d2e 
rbio migration cleanup
@davidsmejia
Merge pull request #3592 from AlexsLemonade/davidsmejia/3573-base-ubu…
2f37714 
…ntu-22

upgrade base ubuntu 22 + common sdist output file name fix
@davidsmejia
Merge pull request #3593 from AlexsLemonade/davidsmejia/3574-un-nvidi…
7ec93f6 
…a-compendia

Move compendia off of nvidia cuda image and onto base
avrohomgottlieb
avrohomgottlieb approved these changes Jun 16, 2026
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@avrohomgottlieb avrohomgottlieb left a comment

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👍

@davidsmejia
davidsmejia merged commit 7dd8862 into dev Jun 16, 2026
38 of 39 checks passed
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@avrohomgottlieb avrohomgottlieb avrohomgottlieb approved these changes
@nozomione nozomione Awaiting requested review from nozomione

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@davidsmejia @avrohomgottlieb