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Fix incorrect types for WandbConfig #410

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merged 71 commits into from
Nov 8, 2024
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23ff3fe
Bump NeMo/Mcore
skothenhill-nv Aug 29, 2024
597d8c1
Merge branch 'v2-main' of github.com:NVIDIA/bionemo-fw-ea into hillst…
skothenhill-nv Sep 4, 2024
ef671c8
Working nemo run example for geneformer pretraining.
skothenhill-nv Sep 10, 2024
ef9f4ea
added readme
skothenhill-nv Sep 10, 2024
14e4bbd
adding files for nemo run
skothenhill-nv Sep 11, 2024
28ddc6b
Added entrypoint for launching experiment with a local executor and e…
skothenhill-nv Sep 11, 2024
71a9570
Merge branch 'v2-main' of github.com:NVIDIA/bionemo-fw-ea into hillst…
skothenhill-nv Sep 16, 2024
1be8678
updating repo
skothenhill-nv Sep 23, 2024
df1eb38
Merge branch 'main' of github.com:NVIDIA/bionemo-fw-ea into hillst/ne…
skothenhill-nv Sep 23, 2024
a3ce991
updating
skothenhill-nv Sep 24, 2024
bd85253
expose launcher
skothenhill-nv Sep 24, 2024
a1e9458
update type signature on entrypoint to avoid the | operator
skothenhill-nv Sep 24, 2024
8924a84
wrapping in distributed guards
skothenhill-nv Sep 24, 2024
748cc22
fixed
skothenhill-nv Sep 24, 2024
758aaec
update
skothenhill-nv Sep 24, 2024
254e46f
updates
skothenhill-nv Sep 24, 2024
07e2963
adding slurm run example
skothenhill-nv Sep 25, 2024
3c5fba5
Intermediate convert that moves toward a pydantic based validation
skothenhill-nv Oct 2, 2024
f61911b
cleansup modified files
skothenhill-nv Oct 2, 2024
ac9a13f
Updated design to match discussion with JSJ:
skothenhill-nv Oct 4, 2024
ba43c41
Merge branch 'main' of github.com:NVIDIA/bionemo-fw-ea into hillst/py…
skothenhill-nv Oct 4, 2024
467cb22
Adds entrypoints for bionemo-geneformer-train and bionemo-geneformer-…
skothenhill-nv Oct 4, 2024
4393fc4
add the bionemo.llm config and train files
skothenhill-nv Oct 4, 2024
69ae0e9
Merge branch 'main' of github.com:NVIDIA/bionemo-fw-ea into hillst/py…
skothenhill-nv Oct 4, 2024
ec7587c
Fixes the default config for geneformer to use the non-finetuning one.
skothenhill-nv Oct 4, 2024
6cd633d
exposes initial_ckpt_path to the recipe maker
skothenhill-nv Oct 4, 2024
b05be9b
fix default factory for finetuning in the exposed geneformer configs
skothenhill-nv Oct 4, 2024
ae88b15
checkpointing current work on ux
skothenhill-nv Oct 8, 2024
1100906
saving work
skothenhill-nv Oct 8, 2024
e74ae7b
Adds supporting tests for the pydantic CLI interface.
skothenhill-nv Oct 16, 2024
5924097
backing up
skothenhill-nv Oct 17, 2024
de517f1
- adds esm2 configs with pydantic
skothenhill-nv Oct 22, 2024
c7f679c
add the missing recipes and init file
skothenhill-nv Oct 22, 2024
cec010d
add missing configs
skothenhill-nv Oct 22, 2024
08ef41f
saving work to merge from main
skothenhill-nv Oct 28, 2024
fefff70
Merge branch 'main' of github.com:NVIDIA/bionemo-fw-ea into hillst/py…
skothenhill-nv Oct 28, 2024
80fa0ff
Merge branch 'main' of github.com:NVIDIA/bionemo-fw-ea into hillst/py…
skothenhill-nv Oct 29, 2024
8a377ea
backing up work before creating a repro example of the weirdness with…
skothenhill-nv Oct 30, 2024
26e76f5
starting with a fresh repo
skothenhill-nv Oct 30, 2024
5127dc9
missing files with the correct paths
skothenhill-nv Oct 30, 2024
090e1d8
fixed recipe
skothenhill-nv Oct 30, 2024
82ae551
Adds recipes for 8m, 650m, 3b parameter models. Adds docstrings for
skothenhill-nv Nov 4, 2024
1d88386
Fixes a typo in the ESM2 readme, adds geneformer pydantic section to
skothenhill-nv Nov 4, 2024
3b5c769
formatting
skothenhill-nv Nov 4, 2024
0306f94
formatting
skothenhill-nv Nov 4, 2024
a361c8b
formatting
skothenhill-nv Nov 4, 2024
48a448f
Merge branch 'main' of github.com:NVIDIA/bionemo-framework into hills…
skothenhill-nv Nov 4, 2024
a4d0870
refactor train to match new lightning module workflow
skothenhill-nv Nov 4, 2024
bca9c8d
Fixes bug where we are using the wrong BioBertLightningModule method
skothenhill-nv Nov 4, 2024
f5e096c
Formatting
skothenhill-nv Nov 4, 2024
48c02c3
Update README.md
skothenhill-nv Nov 5, 2024
9b2bc43
Update sub-packages/bionemo-esm2/src/bionemo/esm2/run/main.py
skothenhill-nv Nov 5, 2024
0566901
Apply suggestions from code review
skothenhill-nv Nov 5, 2024
99d796b
Addressed comments on PR
skothenhill-nv Nov 5, 2024
13d56c2
formatting
skothenhill-nv Nov 5, 2024
bfcb2c9
Merge branch 'hillst/pydantic-ux' of github.com:NVIDIA/bionemo-framew…
skothenhill-nv Nov 5, 2024
79381a9
moved esm2 scheduler into llm
skothenhill-nv Nov 5, 2024
c4eff16
addressed comments
skothenhill-nv Nov 5, 2024
67d83c3
added missing recipe argument for get_attention_mask_from_fusion
skothenhill-nv Nov 5, 2024
0bdbff1
removed hanging exception
skothenhill-nv Nov 6, 2024
3d50ad3
missing refactor from certain tests
skothenhill-nv Nov 6, 2024
12133df
last one
skothenhill-nv Nov 6, 2024
0421bce
format
skothenhill-nv Nov 6, 2024
958e037
remove validation check that wasx erronious
skothenhill-nv Nov 6, 2024
f699b26
formatting
skothenhill-nv Nov 6, 2024
5340b34
Merge branch 'main' of https://github.com/NVIDIA/bionemo-framework in…
skothenhill-nv Nov 6, 2024
cfd397b
Merge branch 'main' of https://github.com/NVIDIA/bionemo-framework in…
skothenhill-nv Nov 7, 2024
1768b0f
fix incorrect types for WandbConfig
skothenhill-nv Nov 7, 2024
cacffaf
Merge branch 'main' of https://github.com/NVIDIA/bionemo-framework in…
skothenhill-nv Nov 7, 2024
3fb021d
fmt
skothenhill-nv Nov 7, 2024
5d96e89
Merge branch 'main' into hillst/wandbconfig_fix
skothenhill-nv Nov 8, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -42,14 +42,14 @@ class WandbConfig(BaseModel):
anonymous: Enables or explicitly disables anonymous logging.
""" # noqa: D205

entity: str # The team posting this run (default: your username or your default team)
entity: str | None # The team posting this run (default: your username or your default team)
project: str # The name of the project to which this run will belong.
# name: #Display name for the run. "This is handled by NeMoLogger"
# save_dir: #Path where data is saved. "This is handled by NeMoLogger"
tags: List[str] # Tags associated with this run.
group: str # A unique string shared by all runs in a given group
tags: List[str] | None # Tags associated with this run.
group: str | None # A unique string shared by all runs in a given group
offline: bool # Run offline (data can be streamed later to wandb servers).
id: str # Sets the version, mainly used to resume a previous run.
id: str | None # Sets the version, mainly used to resume a previous run.
anonymous: bool # Enables or explicitly disables anonymous logging.
log_model: bool # Save checkpoints in wandb dir to upload on W&B servers.

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