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docs: update RFD3 README (#714)

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* Added more explanation and fixed small issues in demo commands in RFD3 README

* fix github actions grepping ruff

---------

Co-authored-by: Rohith Krishna <rohith@localhost>
This commit is contained in:
Rachel Clune
2025-12-02 16:42:04 -08:00
committed by GitHub
parent 050390fd67
commit 76e61e0c2d
2 changed files with 21 additions and 5 deletions
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2
.github/workflows/lint_trunk.yaml vendored
View File

@@ -27,7 +27,7 @@ jobs:
cache: 'pip'
- name: Extract ruff version from requirements.txt
run: |
echo "RUFF_VERSION=$(grep 'ruff==' requirements.txt | sed 's/.*ruff==\(.*\)/\1/')" >> $GITHUB_ENV
echo "RUFF_VERSION=$(grep 'ruff==' pyproject.toml | sed 's/.*ruff==\(.*\)/\1/')" >> $GITHUB_ENV
- name: Install ruff
run: pip install ruff==${{ env.RUFF_VERSION }}
- name: Ruff format

24
models/rfd3/README.md
View File

@@ -15,10 +15,11 @@ git clone https://github.com/RosettaCommons/foundry.git \
&& source .venv/bin/activate \
&& uv pip install -e ".[rfd3]"
```
<!--
> [!IMPORTANT]
> You must install `foundry` (the root package) with `-e` first, then install `rfd3`. This ensures both packages are in editable mode for proper development workflow.
-->
> [!NOTE]
> optionally make installed venv available as ipynb kernel (helpful for running examples in `examples/all.ipynb`)
`python -m ipykernel install --user --name=foundry --display-name "foundry"`
@@ -26,10 +27,18 @@ git clone https://github.com/RosettaCommons/foundry.git \
```bash
wget http://files.ipd.uw.edu/pub/rfd3/rfd3_foundry_2025_12_01.ckpt
```
*You can store these weights anywhere you would like,
but if you do not store them in the root directory
you will need to change the `cur_ckpt` variable discussed
later on.*
**Setup**
```bash
export PROJECT_PATH="$(pwd)/models/rfd3/src:$(pwd)/src:$(pwd)/lib/atomworks/src"
```
If your virtual environment is not already active you will
also need to run:
```
source .venv/bin/activate
```
@@ -45,12 +54,19 @@ cur_ckpt=rfd3_foundry_2025_12_01.ckpt
To run inference
```bash
python ./src/foundry/inference.py out_dir=logs/inference_outs/demo/0 ckpt_path=$cur_ckpt inputs=models/rfd3/docs/demo.json print_config=True dump_trajectories=True
python ./models/rfd3/src/rfd3/run_inference.py out_dir=logs/inference_outs/demo/0 ckpt_path=$cur_ckpt inputs=./models/rfd3/docs/demo.json verbose=True dump_trajectories=True
```
> [!NOTE]
> This demo will take a very long amount of time if run on a
> CPU instead of a GPU. On a GPU, this should take on the
> order of 10 minutes.
Additional args here are added for verbosity, aligning trajectory structures, printing the config and dumping trajectories are turned off by default.
For full details on how to specify inputs, see the [input specification documentation](./docs/input.md).
The output directory will automatically be created.
For full details on how to specify inputs, see the [input specification documentation](./docs/input.md). You can also see `models/rfd3/configs/inference_engine/rfdiffusion3.yaml`.
## Further example jsons for different applications