Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / NVIDIA/bionemo-framework issues and pull requests

#180 - NeMo1 -> NeMo2 checkpoint conversion

Pull Request - State: open - Opened by jstjohn 2 months ago - 11 comments
Labels: NOT_related_to_v24.10

#178 - use importlib resources for files

Pull Request - State: closed - Opened by pstjohn 2 months ago - 4 comments

#174 - multi-epoch dataset resamplers

Pull Request - State: closed - Opened by pstjohn 2 months ago - 5 comments

#169 - add tokenization test

Pull Request - State: closed - Opened by pstjohn 2 months ago - 1 comment

#161 - add dependabot file

Pull Request - State: closed - Opened by pstjohn 2 months ago - 6 comments

#154 - edits to make tests more amenable to being run against an installed package

Pull Request - State: closed - Opened by pstjohn 2 months ago - 6 comments

#151 - Add example for how we can do distributed inference

Pull Request - State: closed - Opened by jstjohn 2 months ago - 3 comments
Labels: NOT_related_to_v24.10

#135 - streamline python packaging with uv

Pull Request - State: closed - Opened by pstjohn 3 months ago - 14 comments

#117 - refactor the docs structure a bit

Pull Request - State: closed - Opened by pstjohn 3 months ago

#100 - LightningDataModule for webdataset

Pull Request - State: closed - Opened by DejunL 3 months ago - 11 comments

#99 - Handle special tokens in the bert masking function

Pull Request - State: closed - Opened by pstjohn 3 months ago - 2 comments

#98 - adding github action for docs deployment

Pull Request - State: closed - Opened by pstjohn 3 months ago - 3 comments

#96 - Bump 3rdparty/Megatron-LM from `104d864` to `cf0f9b2`

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#95 - Update dependabot.yml

Pull Request - State: closed - Opened by pstjohn 3 months ago - 1 comment

#94 - Create dependabot.yml

Pull Request - State: closed - Opened by pstjohn 3 months ago - 2 comments

#93 - ESM2 pretrain and loss test

Pull Request - State: closed - Opened by farhadrgh 3 months ago - 9 comments

#92 - Upgrade nemo and megatron, and fix configs to reflect the change

Pull Request - State: closed - Opened by jstjohn 3 months ago - 2 comments

#91 - WIP add finetuning head as a ModelTransform callback

Pull Request - State: closed - Opened by gwarmstrong 3 months ago - 1 comment

#90 - fixing version issue

Pull Request - State: closed - Opened by polinabinder1 4 months ago - 4 comments

#89 - version not working in scdl

Issue - State: closed - Opened by jstjohn 4 months ago - 1 comment
Labels: bug

#88 - fix post-create command

Pull Request - State: closed - Opened by pstjohn 4 months ago - 3 comments

#87 - Fix NeMo TOT

Issue - State: closed - Opened by jstjohn 4 months ago - 2 comments
Labels: bug

#86 - Pin ptl to <2.4.0 to fix nemo bug

Pull Request - State: closed - Opened by pstjohn 4 months ago - 4 comments

#85 - ESM2 Golden Value Testing

Pull Request - State: closed - Opened by farhadrgh 4 months ago - 8 comments

#84 - [Draft] Bump NeMo commit to point to @farhadr's fix

Pull Request - State: closed - Opened by jstjohn 4 months ago - 2 comments

#83 - Add DCO sign-off enforcement to repo

Issue - State: open - Opened by jstjohn 4 months ago

#82 - Add a `pip-licenses` test

Issue - State: open - Opened by jstjohn 4 months ago

#81 - adding some additional docstrings

Pull Request - State: closed - Opened by pstjohn 4 months ago - 1 comment

#80 - testing signoff

Pull Request - State: closed - Opened by skothenhill-nv 4 months ago - 1 comment

#79 - adding disclaimer to dockerfile.arm

Pull Request - State: open - Opened by yzhang123 4 months ago

#78 - Add ESM2 Dataset and Datamodule

Pull Request - State: closed - Opened by pstjohn 4 months ago - 1 comment

#77 - Updates to devcontainer

Pull Request - State: closed - Opened by skothenhill-nv 4 months ago - 2 comments

#76 - Pbinder/move scdl

Pull Request - State: closed - Opened by polinabinder1 4 months ago - 9 comments

#75 - Add dsmbind sbdd esm1 esm2 esm2_lora testing data

Pull Request - State: closed - Opened by ohadmo 4 months ago - 2 comments

#74 - Adding license, and contributing guidelines from #72 and #65

Pull Request - State: closed - Opened by jstjohn 4 months ago - 4 comments

#73 - trigger blossom on merge-group

Pull Request - State: closed - Opened by pstjohn 4 months ago - 6 comments

#72 - Copy over bionemo1 3p license file into global LICENCE folder.

Issue - State: open - Opened by jstjohn 4 months ago
Labels: bug

#71 - adding merge_group to existing actions

Pull Request - State: closed - Opened by pstjohn 4 months ago - 1 comment

#70 - add devcontainer prebuild action

Pull Request - State: closed - Opened by pstjohn 4 months ago - 1 comment

#69 - [do not merge] pulling out masking and adding test

Pull Request - State: closed - Opened by pstjohn 4 months ago - 3 comments

#68 - Add license-check to pre-commit hook

Pull Request - State: closed - Opened by ohadmo 4 months ago

#67 - Split out the lightning example tutorial

Pull Request - State: closed - Opened by jstjohn 4 months ago - 3 comments

#66 - Clean up src vs test mirroring rule violations.

Pull Request - State: closed - Opened by jstjohn 4 months ago - 3 comments

#65 - Adding DCO contributor signoff to CONTRIBUTING.md files

Issue - State: open - Opened by jstjohn 4 months ago
Labels: bug

#64 - fixing devcontainer target

Pull Request - State: closed - Opened by pstjohn 4 months ago - 3 comments

#63 - Reconfigure the pre-commit workflow

Pull Request - State: closed - Opened by pstjohn 4 months ago - 2 comments

#62 - Update devcontainer for new package structure

Pull Request - State: closed - Opened by pstjohn 4 months ago - 1 comment

#61 - Tell pytest to ignore 3rdparty/{NeMo,MegatronLM}

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago - 3 comments

#60 - Revert "Add some additional ruff checks, ignoring existing violations"

Pull Request - State: closed - Opened by pstjohn 4 months ago - 4 comments

#58 - convert root_directory to a field with default_factory

Pull Request - State: closed - Opened by pstjohn 4 months ago - 4 comments

#57 - Fix `RUF009` violation in `data/preprocess.py`

Issue - State: open - Opened by pstjohn 4 months ago

#56 - Add some additional ruff checks, ignoring existing violations

Pull Request - State: closed - Opened by pstjohn 4 months ago - 5 comments

#55 - Add BERT-style masking function

Pull Request - State: closed - Opened by pstjohn 4 months ago - 4 comments

#54 - Add a CLI option to restore training from a nemo1 checkpoint

Pull Request - State: closed - Opened by jstjohn 4 months ago - 2 comments

#53 - Pbinder/add scdl

Pull Request - State: closed - Opened by polinabinder1 4 months ago - 1 comment

#52 - Add NeMo and Megatron-LM as git submodules

Pull Request - State: closed - Opened by pstjohn 4 months ago - 7 comments

#51 - Reorganize bionemo-contrib into namespace packages

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago - 12 comments

#50 - small MR - change to sc data download

Pull Request - State: closed - Opened by camirr-nv 4 months ago - 1 comment

#49 - Add ESM2 Data Module

Pull Request - State: closed - Opened by pstjohn 4 months ago

#48 - add docstring format config

Pull Request - State: closed - Opened by pstjohn 4 months ago

#47 - Test merge into main

Pull Request - State: closed - Opened by broland-hat 4 months ago - 2 comments

#46 - Cherry-pick pstjohn md5sum check into main

Pull Request - State: closed - Opened by ohadmo 4 months ago - 2 comments

#45 - Add trufflehog as a github action check

Pull Request - State: closed - Opened by pstjohn 4 months ago - 3 comments

#44 - Add mamba as a dependency in the dockerfile

Pull Request - State: closed - Opened by pstjohn 4 months ago - 4 comments

#43 - Add future TE support and mixed precision support to biobert test

Pull Request - State: closed - Opened by jstjohn 4 months ago - 3 comments

#42 - Use github runners to run pre-commit hooks

Pull Request - State: closed - Opened by pstjohn 4 months ago - 4 comments

#41 - Make artifact downloads more robust

Pull Request - State: closed - Opened by pstjohn 4 months ago - 6 comments

#40 - Add documentation build system for BioNeMo v2

Pull Request - State: closed - Opened by pstjohn 4 months ago - 5 comments
Labels: documentation

#39 - Update dependency tags to match PR #36, and try to fix test failure

Pull Request - State: closed - Opened by jstjohn 4 months ago - 6 comments

#38 - A dummy PR to test CI without cache

Pull Request - State: closed - Opened by pstjohn 4 months ago - 2 comments

#37 - Test checkpoint IO loss is close to expected.

Pull Request - State: closed - Opened by jstjohn 4 months ago - 3 comments

#36 - Update pinned versions of bionemo dependencies

Pull Request - State: closed - Opened by pstjohn 4 months ago - 3 comments

#35 - Use precision lowest value instead of -torch.inf

Pull Request - State: closed - Opened by farhadrgh 4 months ago - 4 comments

#34 - Add final apporval action

Pull Request - State: closed - Opened by trvachov 4 months ago - 2 comments

#33 - Add licence check utility

Pull Request - State: closed - Opened by trvachov 4 months ago - 1 comment

#32 - trivial merge request 2

Pull Request - State: closed - Opened by polinabinder1 4 months ago - 1 comment

#31 - trivial pull request

Pull Request - State: closed - Opened by polinabinder1 4 months ago

#29 - Update dependency commits for v2-main

Issue - State: closed - Opened by pstjohn 4 months ago - 2 comments

#28 - ESM2 implementation

Pull Request - State: closed - Opened by farhadrgh 4 months ago - 7 comments

#27 - Add pstjohn as authorized user for pull request CI

Pull Request - State: closed - Opened by pstjohn 4 months ago - 2 comments

#26 - Add pstjohn as authorized user for pull request CI

Pull Request - State: closed - Opened by pstjohn 4 months ago - 1 comment

#25 - Add back the removed bionemo-core sub-package

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago - 5 comments

#24 - Checkpointing example with Geneformer

Pull Request - State: closed - Opened by skothenhill-nv 4 months ago - 8 comments

#23 - brings over single cell dataset unit tests

Pull Request - State: open - Opened by skothenhill-nv 4 months ago - 3 comments

#22 - Add license check to pre-commit hook

Pull Request - State: closed - Opened by ohadmo 4 months ago - 4 comments

#21 - places the ptl artifacts ignore lines to the root directory only.

Pull Request - State: closed - Opened by skothenhill-nv 4 months ago - 4 comments

#20 - Change to gelu default from relu which is what we actually used before

Pull Request - State: closed - Opened by jstjohn 4 months ago - 7 comments

#19 - trivial commit to bionemo2

Pull Request - State: closed - Opened by broland-hat 4 months ago - 5 comments

#18 - trivial commit to bionemo1

Pull Request - State: closed - Opened by broland-hat 4 months ago - 1 comment

#17 - Jstjohn/fix geneformer multinode

Pull Request - State: closed - Opened by jstjohn 4 months ago - 2 comments

#15 - Updated CODEOWNERS

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago - 3 comments

#14 - Updated CODEOWNERS

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago

#13 - Update pre-commit hooks to latest.

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago - 5 comments

#12 - Update pre-commit hooks to latest

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago

#11 - Adds CONTRIBUTING, CODE-REVIEW guides and pull request template

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago - 1 comment
Labels: documentation

#10 - Adds CONTRIBUTING, CODE-REVIEW guides and pull request template

Pull Request - State: closed - Opened by malcolmgreaves 4 months ago - 8 comments
Labels: documentation