rc-foundry 0.1.6__tar.gz → 0.1.9__tar.gz

rc_foundry-0.1.6/.github/workflows/lint_trunk.yaml → rc_foundry-0.1.9/.github/workflows/lint_production.yaml

@@ -1,10 +1,10 @@
-name: lint_trunk
+name: lint_production
 
 on:
   push:
-    branches: [main, trunk, wip/for-release, wip/remove-chemdata]
+    branches: [main, production, wip/for-release, wip/remove-chemdata]
   pull_request:
-    branches: [main, trunk, wip/for-release, wip/remove-chemdata]
+    branches: [main, production, wip/for-release, wip/remove-chemdata]
   pull_request_target:
     types: [ready_for_review]
   workflow_dispatch:
@@ -23,14 +23,15 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache: 'pip'
-      - name: Extract ruff version from requirements.txt
+      - name: Extract ruff version from pyproject.toml
         run: |
-          echo "RUFF_VERSION=$(grep 'ruff==' pyproject.toml | sed 's/.*ruff==\(.*\)/\1/')" >> $GITHUB_ENV
+          echo "RUFF_VERSION=$(grep 'ruff==' pyproject.toml \
+            | sed -E 's/.*ruff==([^",]+).*/\1/')" >> "$GITHUB_ENV"
       - name: Install ruff
         run: pip install ruff==${{ env.RUFF_VERSION }}
       - name: Ruff format
-        run: ruff format --diff src tests scripts notebooks
+        run: ruff format --diff src models tests
       - name: Ruff check
-        run: ruff check src tests scripts notebooks
+        run: ruff check src models tests

{rc_foundry-0.1.6 → rc_foundry-0.1.9}/.gitignore

@@ -1,4 +1,6 @@
 # For docs / outputs from example notebooks;
+demo/*/**.cif*
+demo/*/**.json
 examples/*.cif
 **.ckpt
 **.pt
@@ -187,7 +189,6 @@ dev.py
 *.benchmarks/
 
 # Images
-*.png
 *.pdf
 *.svg
 *.jpg

{rc_foundry-0.1.6 → rc_foundry-0.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rc-foundry
-Version: 0.1.6
+Version: 0.1.9
 Summary: Shared utilities and training infrastructure for biomolecular structure prediction models.
 Author-email: Institute for Protein Design <contact@ipd.uw.edu>
 License: BSD 3-Clause License
@@ -97,40 +97,45 @@ Foundry provides tooling and infrastructure for using and training all classes o
 
 All models within Foundry rely on [AtomWorks](https://github.com/RosettaCommons/atomworks) - a unified framework for manipulating and processing biomolecular structures - for both training and inference. 
 
+
+> [!NOTE]
+> We have a slack now! Join for updates and to get your questions answered [here](https://join.slack.com/t/proteinmodelfoundry/shared_invite/zt-3kpwru8c6-nrmTW6LNHnSE7h16GNnfLA).
+
 ## Getting Started
 ### Quickstart guide
 **Installation**
 ```bash
-pip install rc-foundry[all]
+pip install "rc-foundry[all]"
 ```
 
-**Downloading weights** All models can be downloaded to a target folder with:
-
+**Downloading weights** Models can be downloaded to a target folder with:
 ```
-foundry install all --checkpoint_dir <path/to/ckpt/dir>
+foundry install base-models --checkpoint-dir <path/to/ckpt/dir>
 ```
-This will download all the models supported (including multiple checkpoints of RF3) but as a beginner you can start with:
+where `checkpoint-dir` will be `~/.foundry/checkpoints` by default. Foundry always searches `~/.foundry/checkpoints` plus any colon-separated entries in `$FOUNDRY_CHECKPOINT_DIRS` during inference or subsequent commands to find checkpoints. `base-models` installs the latest RFD3, RF3 and MPNN variants - you can also download all of the models supported (including multiple checkpoints of RF3) with `all`, or by listing the models sequentially (e.g. `foundry install rfd3 rf3 ...`).
+To list the registry of available checkpoints:
 ```
-foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
+foundry list-available
 ```
+To check what you already have downloaded (searches `~/.foundry/checkpoints` plus `$FOUNDRY_CHECKPOINT_DIRS` if set):
+```
+foundry list-installed
+```
+
+>*See `examples/all.ipynb` for how to run each model and design proteins end-to-end in a notebook.*
 
->*See `examples/all.ipynb` for how to run each model in a notebook.*
+### Google Colab
+For an interactive Google Colab notebook walking through a basic design pipeline with RFD3, MPNN, and RF3, please see the [IPD Design Pipeline Tutorial](https://colab.research.google.com/drive/1ZwIMV3n9h0ZOnIXX0GyKUuoiahgifBxh?usp=sharing).
 
 ### RFdiffusion3 (RFD3)
 
 [RFdiffusion3](https://www.biorxiv.org/content/10.1101/2025.09.18.676967v2) is an all-atom generative model capable of designing protein structures under complex constraints. 
 
-> *See [models/rfd3/README.md](models/rfd3/README.md) for complete documentation.*
-
 <div align="center">
-  <img src="models/rfd3/docs/.assets/trajectory.png" alt="RFdiffusion3 generation trajectory." width="700">
+  <img src="docs/_static/cover.png" alt="RFdiffusion3 generation trajectory." width="700">
 </div>
 
-### ProteinMPNN
-[ProteinMPNN](https://www.science.org/doi/10.1126/science.add2187) and [LigandMPNN](https://www.nature.com/articles/s41592-025-02626-1) are lightweight inverse-folding models which can be use to design diverse sequences for backbones under constrained conditions.
-
-> *See [models/mpnn/README.md](models/mpnn/README.md) for complete documentation.*
-
+> *See [models/rfd3/README.md](models/rfd3/README.md) for complete documentation.*
 
 ### RosettaFold3 (RF3)
 
@@ -142,6 +147,11 @@ foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
 
 > *See [models/rf3/README.md](models/rf3/README.md) for complete documentation.*
 
+### ProteinMPNN
+[ProteinMPNN](https://www.science.org/doi/10.1126/science.add2187) and [LigandMPNN](https://www.nature.com/articles/s41592-025-02626-1) are lightweight inverse-folding models which can be use to design diverse sequences for backbones under constrained conditions.
+
+> *See [models/mpnn/README.md](models/mpnn/README.md) for complete documentation.*
+
 ---
 
 ## Development
@@ -159,11 +169,7 @@ foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
 Install both `foundry` and models in editable mode for development:
 
 ```bash
-# Install foundry and RF3 in editable mode
-uv pip install -e . -e ./models/rf3 -e ./models/rfd3 -e ./models/mpnn
-
-# Or install only foundry (no models)
-uv pip install -e .
+uv pip install -e '.[all,dev]'
 ```
 
 This approach allows you to:
@@ -171,6 +177,9 @@ This approach allows you to:
 - Work on specific models without installing all models
 - Add new models as independent packages in `models/`
 
+> [!NOTE]
+> Running tests is not currently supported, test files may be missing.
+
 ### Adding New Models
 
 To add a new model:

{rc_foundry-0.1.6 → rc_foundry-0.1.9}/README.md

@@ -4,40 +4,45 @@ Foundry provides tooling and infrastructure for using and training all classes o
 
 All models within Foundry rely on [AtomWorks](https://github.com/RosettaCommons/atomworks) - a unified framework for manipulating and processing biomolecular structures - for both training and inference. 
 
+
+> [!NOTE]
+> We have a slack now! Join for updates and to get your questions answered [here](https://join.slack.com/t/proteinmodelfoundry/shared_invite/zt-3kpwru8c6-nrmTW6LNHnSE7h16GNnfLA).
+
 ## Getting Started
 ### Quickstart guide
 **Installation**
 ```bash
-pip install rc-foundry[all]
+pip install "rc-foundry[all]"
 ```
 
-**Downloading weights** All models can be downloaded to a target folder with:
-
+**Downloading weights** Models can be downloaded to a target folder with:
 ```
-foundry install all --checkpoint_dir <path/to/ckpt/dir>
+foundry install base-models --checkpoint-dir <path/to/ckpt/dir>
 ```
-This will download all the models supported (including multiple checkpoints of RF3) but as a beginner you can start with:
+where `checkpoint-dir` will be `~/.foundry/checkpoints` by default. Foundry always searches `~/.foundry/checkpoints` plus any colon-separated entries in `$FOUNDRY_CHECKPOINT_DIRS` during inference or subsequent commands to find checkpoints. `base-models` installs the latest RFD3, RF3 and MPNN variants - you can also download all of the models supported (including multiple checkpoints of RF3) with `all`, or by listing the models sequentially (e.g. `foundry install rfd3 rf3 ...`).
+To list the registry of available checkpoints:
 ```
-foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
+foundry list-available
 ```
+To check what you already have downloaded (searches `~/.foundry/checkpoints` plus `$FOUNDRY_CHECKPOINT_DIRS` if set):
+```
+foundry list-installed
+```
+
+>*See `examples/all.ipynb` for how to run each model and design proteins end-to-end in a notebook.*
 
->*See `examples/all.ipynb` for how to run each model in a notebook.*
+### Google Colab
+For an interactive Google Colab notebook walking through a basic design pipeline with RFD3, MPNN, and RF3, please see the [IPD Design Pipeline Tutorial](https://colab.research.google.com/drive/1ZwIMV3n9h0ZOnIXX0GyKUuoiahgifBxh?usp=sharing).
 
 ### RFdiffusion3 (RFD3)
 
 [RFdiffusion3](https://www.biorxiv.org/content/10.1101/2025.09.18.676967v2) is an all-atom generative model capable of designing protein structures under complex constraints. 
 
-> *See [models/rfd3/README.md](models/rfd3/README.md) for complete documentation.*
-
 <div align="center">
-  <img src="models/rfd3/docs/.assets/trajectory.png" alt="RFdiffusion3 generation trajectory." width="700">
+  <img src="docs/_static/cover.png" alt="RFdiffusion3 generation trajectory." width="700">
 </div>
 
-### ProteinMPNN
-[ProteinMPNN](https://www.science.org/doi/10.1126/science.add2187) and [LigandMPNN](https://www.nature.com/articles/s41592-025-02626-1) are lightweight inverse-folding models which can be use to design diverse sequences for backbones under constrained conditions.
-
-> *See [models/mpnn/README.md](models/mpnn/README.md) for complete documentation.*
-
+> *See [models/rfd3/README.md](models/rfd3/README.md) for complete documentation.*
 
 ### RosettaFold3 (RF3)
 
@@ -49,6 +54,11 @@ foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
 
 > *See [models/rf3/README.md](models/rf3/README.md) for complete documentation.*
 
+### ProteinMPNN
+[ProteinMPNN](https://www.science.org/doi/10.1126/science.add2187) and [LigandMPNN](https://www.nature.com/articles/s41592-025-02626-1) are lightweight inverse-folding models which can be use to design diverse sequences for backbones under constrained conditions.
+
+> *See [models/mpnn/README.md](models/mpnn/README.md) for complete documentation.*
+
 ---
 
 ## Development
@@ -66,11 +76,7 @@ foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
 Install both `foundry` and models in editable mode for development:
 
 ```bash
-# Install foundry and RF3 in editable mode
-uv pip install -e . -e ./models/rf3 -e ./models/rfd3 -e ./models/mpnn
-
-# Or install only foundry (no models)
-uv pip install -e .
+uv pip install -e '.[all,dev]'
 ```
 
 This approach allows you to:
@@ -78,6 +84,9 @@ This approach allows you to:
 - Work on specific models without installing all models
 - Add new models as independent packages in `models/`
 
+> [!NOTE]
+> Running tests is not currently supported, test files may be missing.
+
 ### Adding New Models
 
 To add a new model:

{rc_foundry-0.1.6 → rc_foundry-0.1.9}/examples/all.ipynb

@@ -19,19 +19,34 @@
     "\n",
     "All models are unified through [AtomWorks](https://github.com/RosettaCommons/atomworks) (for both inference and training), relying on Biotite `AtomArray` objects.\n",
     "\n",
-    "Note: This notebook assumes you have the base checkpoints downloaded: `foundry install rfd3 ligandmpnn rf3`. You can also specify the paths directly yourself if you wish.\n",
+    "This notebook assumes you have the base checkpoints downloaded: `foundry install rfd3 ligandmpnn rf3`. You can also specify the paths directly yourself if you wish. You can register your foundry venv to jupyter with: `python -m ipykernel install --user --name=foundry --display-name \"foundry\"`.\n",
     "\n",
     "### Pipeline Flow\n",
     "```\n",
     "RFD3 (backbone) → MPNN (sequence) → RF3 (validation) → RMSD comparison\n",
     "```\n",
+    "---\n",
+    "\n",
+    "## Section 0: Installation\n",
+    "\n",
+    "Install the Foundry package (includes RFD3, MPNN, and RF3):\n",
+    "\n",
+    "```bash\n",
+    "pip install 'rc-foundry[all]'\n",
+    "```\n",
+    "\n",
+    "Download the model weights (~6GB total, takes a couple minutes):\n",
+    "\n",
+    "```bash\n",
+    "foundry install rfd3 ligandmpnn rf3\n",
+    "```\n",
     "\n",
     "---"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "id": "819e8193",
    "metadata": {},
    "outputs": [],
@@ -75,7 +90,8 @@
     "# Configure RFD3 inference\n",
     "config = RFD3InferenceConfig(\n",
     "    specification={\n",
-    "        'length': 15,  # Generate 80-residue proteins\n",
+    "        'length': 80,  # Generate 80-residue proteins\n",
+    "        'extra': {},  # We are not using any extra specifications here.\n",
     "    },\n",
     "    diffusion_batch_size=2,  # Generate 2 structures per batch\n",
     ")\n",
@@ -145,7 +161,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "d07ae413",
    "metadata": {},
    "outputs": [],
@@ -236,7 +252,7 @@
     "\n",
     "\n",
     "# Initialize RF3 inference engine\n",
-    "inference_engine = RF3InferenceEngine(ckpt_path='rf3_preprint_921', verbose=False)\n",
+    "inference_engine = RF3InferenceEngine(ckpt_path='rf3', verbose=False)\n",
     "\n",
     "# Create input from the MPNN-designed structure (first design)\n",
     "# This re-folds the sequence to validate it adopts the intended structure\n",
@@ -388,7 +404,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "modelworks",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },