Merge main into docker - #20

Merged

andrewscouten merged 99 commits into

Mar 15, 2026

Commits on Jan 13, 2026

TCIA and Xena Browser Downloaders
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c8c717f
Add AMD GPU passthrough
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493fcd1
GPU configuration + PDC CLI
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66d926c
Update README to reflect GPU and downloader
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1de68d6
Create TCGA-BRCA.ipynb
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df1a54b
Add multiple dev containers
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3b77b81
Fix the PDC CLI download command
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2f58811
Enforce linux line endings
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66c08ef
Enforce linux line endings
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54282e6
Run proper service per dev container
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0240a6a
Merge branch 'feature-data-downloader' of https://github.com/collaborativebioinformatics/OncoLearn into feature-data-downloader
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b9979f8
Docker configurations
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fbd74ce
Correct line endings
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fdd1f80
Correct line endings
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f518219
More docker optimizations
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e24f0fd
buildpack-deps:jammy does not include unzip
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e807aed
Fix PDC CLI download
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5024ddf
Add UV arguemnts to Dockerfile
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bd08559
Update Docker CI workflow for multi-profile builds
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defd00d
Add cpu to dev containers & add toml extension
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9c28177
Merge pull request #7 from collaborativebioinformatics/feature-data-downloader
andrewscouten
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9215eef

Commits on Jan 14, 2026

Docker changes
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93720e6
Refactor downloader into API and CLI
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8fff185
CLI Updates & Removing emojis
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adcccdc

Commits on Jan 15, 2026

Correct TCGA configs, change docker, and flesh out CLI
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6210561
Remove unused dependencies
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d535be9
Add TCIA preprocessing to the CLI
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5448393
Merge pull request #6 from collaborativebioinformatics/feat/data-downloader
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9cb184e
Add submodules configuration
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d1c7a31
Properly add submodules
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76f013b
Merge pull request #10 from collaborativebioinformatics/fixt/submodules
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8989dd9
Updated wiki for API and CLI
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16cdb55
Merge pull request #12 from collaborativebioinformatics/docs/wiki
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e4bab64

Commits on Jan 21, 2026

Add linting arguments to dev containers
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22da50b

Commits on Jan 26, 2026

Delete notebooks/Transformer_RNABert_RESTRUCTURED.ipynb
QiyuYang-QYang
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47339d1
Add files via upload
QiyuYang-QYang
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fececdf

Commits on Feb 26, 2026

Commits on Feb 27, 2026

Fix uv header ordering
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ac3fa16

Commits on Feb 28, 2026

Commits on Mar 3, 2026

Remove outdated documentation
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3a5f0a1
Add cache files to .gitignore
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6d6df24
Better split project dependencies
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9acb06a
Dataset fixes
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b91d78a
Multimodal pipeline bugfixes
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6790c09
Update docs to reflect multimodal refactor
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82927cf
Create data/.gitignore and move relevant entries
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9dc3138
feat: Introduce config system & encoder registry.
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2e01993
Huggingface config replace with encoder config
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4426dc3

Commits on Mar 4, 2026

Working pipeline, now just need to run it
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a18bba5
Update docs based on working pipeline
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fbb14c8

Commits on Mar 5, 2026

Update code to be more accurate to original multimodal implementation
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e2e7eef
Make docker containers more readable
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2b1ceae
Update docker pipeline build
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17458c3

Commits on Mar 6, 2026

Add FM-BCMRI submodule. Necessary for a multimodal model checkpoint
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7d823f8

Commits on Mar 7, 2026

Commits on Mar 8, 2026

Commits on Mar 9, 2026

Move split files
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77f7920
cBioPortal API and CLI
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d3dd792
Refactor model training and configuration management
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7574af7

Commits on Mar 10, 2026

Commits on Mar 11, 2026

Commits on Mar 12, 2026

Commits on Mar 13, 2026

Commits on Mar 15, 2026