Fix installation

.env

@@ -62,3 +62,4 @@ COLABFOLD_LOCAL_DB_PATH_CPU=
 # Network access (fallback; may cause IO-related issues)
 COLABFOLD_NET_DB_PATH_GPU=
 COLABFOLD_NET_DB_PATH_CPU=
+FOUNDRY_CHECKPOINTS_DIR='/home/jbutch/.foundry/checkpoints'

.gitignore

@@ -1,4 +1,6 @@
 # For docs / outputs from example notebooks;
+demo/*/**.cif*
+demo/*/**.json
 examples/*.cif
 **.ckpt
 **.pt

README.md

@@ -21,6 +21,15 @@ This will download all the models supported (including multiple checkpoints of R
 foundry install rfd3 ligandmpnn rf3 --checkpoint-dir  <path/to/ckpt/dir>
 ```
 
+List the registry of available checkpoints with:
+```
+foundry list-available
+```
+Check what you already have downloaded (defaults to `$FOUNDRY_CHECKPOINTS_DIR` if set) with:
+```
+foundry list-installed --checkpoint-dir <path/to/ckpt/dir>
+```
+
 >*See `examples/all.ipynb` for how to run each model in a notebook.*
 
 ### Google Colab

models/rfd3/README.md

@@ -10,7 +10,7 @@ both are described in more detail below.
   <img src="docs/.assets/overview.png" alt="All-atom design with RFD3">
 </p>
 
-## Get Started
+## Getting Started
 1. Install RFdiffusion3. See [Main README](../../README.md) for instructions how to install all models to run full pipeline (recommended). If you have already installed all the models skip [here](#run-inference). 
 ```bash
 pip install rc-foundry[rfd3]
@@ -21,7 +21,7 @@ foundry install rfd3 --checkpoint-dir /path/to/ckpt/dir
 ```
 This sets `FOUNDRY_CHECKPOINTS_DIR` and will in future look for checkpoints in that directory, allowing you to run inference without supplying the checkpoint path. The checkpoint directory is optional, defaulting to `~/.foundry/checkpoints` if unset.
 
-## Run Inference
+## Running Inference
 
 To run inference (with foundry installed in your environment, or RFD3 & Foundry src in PYTHONPATH):
 ```bash
@@ -54,15 +54,6 @@ that you are running the examples from the `foundry/models/rfd3/docs`
 directory. If you would like to run RFD3 from a different location, 
 you will need to change the path in the `.json` file(s) before running.
 
-### Install HBPLUS for hydrogen bond conditioning:
-One of the examples shows how to incorporate hydrogen bond conditioning 
-into your designs. To make use of this feature, you will need to 
-additionally complete the following steps:
-
-1. Download hbplus from here: https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/download.html (available for free)
-2. Follow the installation instruction here: https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/install.html
-3. Update `HBPLUS_PATH` in `foundry/.env` file with the path to your `hbplus` executable.
-
 <table>
   <tr>
     <td align="center">
@@ -90,7 +81,7 @@ additionally complete the following steps:
   </tr>
 </table>
 
-## Training:
+## Training and Fine-Tuning
 
 We make available to the community not only the weights to run RFdiffusion3 but also the complete training code, easily extendable to additional use cases. Any AtomWorks-compatible dataset (and thus, any collection of structure files) can be readily incorporated and used for training or fine-tuning.
 
@@ -112,9 +103,10 @@ RFdiffusion3 supports arbitrary datasets of structure files for training and fin
 
 After setting up Hydra configs, launch a training run:
 ```bash
-uv run python models/rfd3/src/rfd3/train.py experiment=pretrain
+uv run python models/rfd3/src/rfd3/train.py experiment=pretrain ckpt_path=<path/to/ckpt>
 ```
 
+Supplying `ckpt_path=null` (default) will start with fresh weights.
 See the [path configs](/models/rfd3/configs/paths/) to customize data input and log output directories.
 
 ### Logging Configuration
@@ -162,6 +154,17 @@ In `models/rfd3/configs/datasets/design_base.yaml` there's the shared configs fo
 
 **Training with WandB:** We strongly recommend tracking your runs via wandb. To use it, simply have your WANDB_API_KEY set and use the wandb logger. For more details see [here](wandb.ai)
 
+# Appendix
+
+## Install HBPLUS for hydrogen bond conditioning:
+One of the examples shows how to incorporate hydrogen bond conditioning 
+into your designs. To make use of this feature, you will need to 
+additionally complete the following steps:
+
+1. Download hbplus from here: https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/download.html (available for free)
+2. Follow the installation instruction here: https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/install.html
+3. Update `HBPLUS_PATH` in `foundry/.env` file with the path to your `hbplus` executable.
+
 ## Citation
 
 If you use this code or data in your work, please consider citing:

src/foundry_cli/download_checkpoints.py

@@ -29,6 +29,13 @@ app = typer.Typer(help="Foundry model checkpoint installation utilities")
 console = Console()
 
 
+def _resolve_checkpoint_dir(checkpoint_dir: Optional[Path]) -> Path:
+    """Return user-specified checkpoint dir or fall back to default."""
+    return (
+        checkpoint_dir if checkpoint_dir is not None else get_default_checkpoint_dir()
+    )
+
+
 def download_file(url: str, dest: Path, verify_hash: Optional[str] = None) -> None:
     """Download a file with progress bar and optional hash verification.
 
@@ -123,7 +130,7 @@ def install_model(model_name: str, checkpoint_dir: Path, force: bool = False) ->
 def install(
     models: list[str] = typer.Argument(
         ...,
-        help="Models to install: 'all', 'rfd3', 'rf3', 'mpnn', or combination",
+        help="Models to install: 'all', 'rfd3', 'rf3', 'mpnn', or a combination thereof",
     ),
     checkpoint_dir: Optional[Path] = typer.Option(
         None,
@@ -136,18 +143,12 @@ def install(
     ),
 ):
     """Install model checkpoints for foundry.
-
     Examples:
-
         foundry install all
-
-        foundry install rfd3 rf3
-
         foundry install proteinmpnn --checkpoint-dir ./checkpoints
     """
     # Determine checkpoint directory
-    if checkpoint_dir is None:
-        checkpoint_dir = get_default_checkpoint_dir()
+    checkpoint_dir = _resolve_checkpoint_dir(checkpoint_dir)
 
     console.print(f"[bold]Checkpoint directory:[/bold] {checkpoint_dir}")
     console.print()
@@ -177,26 +178,18 @@ def install(
     console.print("[bold green]Installation complete![/bold green]")
 
 
-@app.command(name="list")
-def list_models():
+@app.command(name="list-available")
+def list_available():
     """List available model checkpoints."""
     console.print("[bold]Available models:[/bold]\n")
     for name, info in REGISTERED_CHECKPOINTS.items():
         console.print(f"  [cyan]{name:8}[/cyan] - {info.description}")
 
 
-@app.command()
-def show(
-    checkpoint_dir: Optional[Path] = typer.Option(
-        None,
-        "--checkpoint-dir",
-        "-d",
-        help="Checkpoint directory to show",
-    ),
-):
-    """Show installed checkpoints."""
-    if checkpoint_dir is None:
-        checkpoint_dir = get_default_checkpoint_dir()
+@app.command(name="list-installed")
+def list_installed():
+    """List installed checkpoints and their sizes."""
+    checkpoint_dir = _resolve_checkpoint_dir(None)
 
     if not checkpoint_dir.exists():
         console.print(
@@ -219,21 +212,14 @@ def show(
     console.print(f"\n[bold]Total:[/bold] {total_size:.2f} GB")
 
 
-@app.command()
+@app.command(name="clean")
 def clean(
-    checkpoint_dir: Optional[Path] = typer.Option(
-        None,
-        "--checkpoint-dir",
-        "-d",
-        help="Checkpoint directory to clean",
-    ),
     confirm: bool = typer.Option(
         True, "--confirm/--no-confirm", help="Ask for confirmation before deleting"
     ),
 ):
     """Remove all downloaded checkpoints."""
-    if checkpoint_dir is None:
-        checkpoint_dir = get_default_checkpoint_dir()
+    checkpoint_dir = _resolve_checkpoint_dir(None)
 
     if not checkpoint_dir.exists():
         console.print(f"[yellow]No checkpoints found at {checkpoint_dir}[/yellow]")