Merge branch 'main' into renovate/jinja2-3.x

README.md

@@ -110,6 +110,8 @@ Container | Channel | Image
 [ligandmpnn](https://github.com/RareCompute/containers/pkgs/container/ligandmpnn) | stable | ghcr.io/RareCompute/ligandmpnn
 [protenix](https://github.com/RareCompute/containers/pkgs/container/protenix) | stable | ghcr.io/RareCompute/protenix
 [protenix-develop](https://github.com/RareCompute/containers/pkgs/container/protenix-develop) | develop | ghcr.io/RareCompute/protenix-develop
+[rfdiffusion](https://github.com/RareCompute/containers/pkgs/container/rfdiffusion) | stable | ghcr.io/RareCompute/rfdiffusion
+[rfdiffusion-develop](https://github.com/RareCompute/containers/pkgs/container/rfdiffusion-develop) | develop | ghcr.io/RareCompute/rfdiffusion-develop
 
 
 ## Deprecations

apps/rfdiffusion/Dockerfile

@@ -0,0 +1,81 @@
+FROM docker.io/library/python:3.9-slim-bookworm
+
+LABEL \
+  maintainer="Liana64" \
+  org.opencontainers.image.source="https://github.com/RosettaCommons/RFdiffusion"
+
+ARG TARGETPLATFORM
+ARG VERSION
+ARG CHANNEL
+ARG DEBIAN_FRONTEND=noninteractive
+
+ENV \
+  NVIDIA_DRIVER_CAPABILITIES="compute,video,utility,graphics" \
+  UMASK="0002" \
+  LANG=C.UTF-8 \
+  TZ="Etc/UTC" \
+  USERNAME=rare \
+  DEBUG=0 \
+  UID=900 \
+  GID=900 \
+  PYTHONDONTWRITEBYTECODE=1 \
+  PYTHONUNBUFFERED=1 \
+  PYTHONFAULTHANDLER=1 \
+  PIP_ROOT_USER_ACTION=ignore \
+  PIP_NO_CACHE_DIR=1 \
+  PIP_DISABLE_PIP_VERSION_CHECK=1 \
+  PIP_BREAK_SYSTEM_PACKAGES=1 \
+  UV_HTTP_TIMEOUT=1000 \
+  DGLBACKEND="pytorch"
+
+USER root
+WORKDIR /app
+
+RUN \
+  groupadd --gid ${GID} ${USERNAME} \
+  && useradd --uid ${UID} --gid ${GID} --create-home --shell /bin/bash ${USERNAME} \
+  && apt-get update && apt-get install -y --no-install-recommends \
+  curl unzip catatonit \
+  nano vim tree git \
+  && curl -LsSf https://astral.sh/uv/0.5.6/install.sh | sh \
+  && . $HOME/.local/bin/env \
+  && case "${CHANNEL}" in \
+  'stable') \
+  curl -fsSL -o /tmp/app.zip "https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags/v${VERSION}.zip" \
+  && unzip -q /tmp/app.zip -d /tmp/app \
+  && cp -R /tmp/app/RFdiffusion-${VERSION}/* /app \
+  ;; \
+  'develop') \
+  git clone https://github.com/amelie-iska/RFdiffusion.git /app \
+  ;; \
+  esac \
+  && cd /app \
+  && uv pip install --system \
+  dgl==1.0.2+cu116 -f "https://data.dgl.ai/wheels/cu116/repo.html" \
+  torch==1.12.1+cu116 --extra-index-url "https://download.pytorch.org/whl/cu116" \
+  e3nn==0.3.3 \
+  wandb==0.12.0 \
+  pynvml==11.0.0 \
+  git+https://github.com/NVIDIA/dllogger#egg=dllogger \
+  decorator==5.1.0 \
+  hydra-core==1.3.2 \
+  pyrsistent==0.19.3 \
+  /app/env/SE3Transformer \
+  && printf "UpdateMethod=docker\nBranch=master\nPackageVersion=%s\nPackageAuthor=[RareCompute](https://github.com/RareCompute)\n" "${VERSION}" > /app/package_info \
+  && chown -R ${UID}:${GID} /app && chmod -R 755 /app \
+  && uv pip install --no-deps --system /app \
+  && apt-get autoremove -y \
+  && apt-get clean \
+  && rm -rf /root/.cache /var/lib/apt/lists/* /tmp/* /var/tmp/* \
+  && chsh -s /bin/bash
+
+COPY --chown=${UID}:${GID} ./apps/rfdiffusion/entrypoint.sh /entrypoint.sh
+RUN chmod -R 755 /entrypoint.sh
+
+WORKDIR /models
+VOLUME ["/models"]
+
+USER ${USERNAME}
+WORKDIR /app
+
+ENTRYPOINT ["/usr/bin/catatonit", "--", "/entrypoint.sh"]

apps/rfdiffusion/README.md

@@ -0,0 +1,24 @@
+# Chai
+
+From the [upstream repository](https://github.com/RosettaCommons/RFdiffusion)
+
+> RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper.
+>
+> Things Diffusion can do
+>
+> Motif Scaffolding
+> Unconditional protein generation
+> Symmetric unconditional generation (cyclic, dihedral and tetrahedral symmetries currently implemented, more coming!)
+> Symmetric motif scaffolding
+> Binder design
+> Design diversification ("partial diffusion", sampling around a design)
+
+## Environment variables
+
+You can configure the docker image using the below environment variables
+
+| Environment Variable | CLI Flag | Type      | Default Value | Description                |
+| -------------------- | -------- | --------- | ------------- | -------------------------- |
+| `USERNAME`           | N/A      | `STR`     | `rare`        | Username for the container |
+| `UID`                | N/A      | `INTEGER` | `900`         | UID for the container      |
+| `GID`                | N/A      | `INTEGER` | `900`         | GID for the container      |

apps/rfdiffusion/ci/goss.yaml

@@ -0,0 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/goss-org/goss/master/docs/schema.yaml
+file:
+  /app/LICENSE:
+    exists: true

apps/rfdiffusion/ci/latest.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+channel=$1
+
+if [[ "${channel}" == "stable" ]]; then
+  version=$(curl -sX GET "https://api.github.com/repos/RosettaCommons/RFdiffusion/releases/latest" | jq --raw-output '.tag_name' 2>/dev/null)
+  version="${version#*v}"
+  version="${version#*release-}"
+  printf "%s" "${version}"
+fi
+
+if [[ "${channel}" == "develop" ]]; then
+  git clone --quiet https://github.com/amelie-iska/RFdiffusion.git /tmp/rfdiffusion
+  pushd /tmp/rfdiffusion > /dev/null || exit
+  version=$(git rev-list --count --first-parent HEAD)
+  popd > /dev/null || exit
+  rm -rf /tmp/rfdiffusion
+  printf "%s" "${version}"
+fi

apps/rfdiffusion/entrypoint.sh

@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+
+MODELS_PATH="/models"
+BASE_URL="http://files.ipd.uw.edu/pub/RFdiffusion"
+
+DOWNLOAD_ALL=$(echo "$DOWNLOAD_ALL" | tr '[:upper:]' '[:lower:]')
+DOWNLOAD_COMPLEX_BETA=$(echo "$DOWNLOAD_COMPLEX_BETA" | tr '[:upper:]' '[:lower:]')
+DOWNLOAD_STRUCTURE_PREDICTION_WEIGHTS=$(echo "$DOWNLOAD_STRUCTURE_PREDICTION_WEIGHTS" | tr '[:upper:]' '[:lower:]')
+
+declare -A downloads=(
+  ["Base_ckpt.pt"]="$BASE_URL/6f5902ac237024bdd0c176cb93063dc4/Base_ckpt.pt"
+  ["Complex_base_ckpt.pt"]="$BASE_URL/e29311f6f1bf1af907f9ef9f44b8328b/Complex_base_ckpt.pt"
+  ["Complex_Fold_base_ckpt.pt"]="$BASE_URL/60f09a193fb5e5ccdc4980417708dbab/Complex_Fold_base_ckpt.pt"
+  ["InpaintSeq_ckpt.pt"]="$BASE_URL/74f51cfb8b440f50d70878e05361d8f0/InpaintSeq_ckpt.pt"
+  ["InpaintSeq_Fold_ckpt.pt"]="$BASE_URL/76d00716416567174cdb7ca96e208296/InpaintSeq_Fold_ckpt.pt"
+  ["ActiveSite_ckpt.pt"]="$BASE_URL/5532d2e1f3a4738decd58b19d633b3c3/ActiveSite_ckpt.pt"
+  ["Base_epoch8_ckpt.pt"]="$BASE_URL/12fc204edeae5b57713c5ad7dcb97d39/Base_epoch8_ckpt.pt"
+)
+
+if [ "$DOWNLOAD_COMPLEX_BETA" == "true" ] || [ "$DOWNLOAD_ALL" == "true" ]; then
+  files["Complex_beta_ckpt.pt"]="$BASE_URL/f572d396fae9206628714fb2ce00f72e/Complex_beta_ckpt.pt"
+fi
+
+if [ "$DOWNLOAD_STRUCTURE_PREDICTION_WEIGHTS" == "true" ] || [ "$DOWNLOAD_ALL" == "true" ]; then
+  files["RF_structure_prediction_weights.pt"]="$BASE_URL/1befcb9b28e2f778f53d47f18b7597fa/RF_structure_prediction_weights.pt"
+fi
+
+for filename in "${!files[@]}"; do
+  filepath="$MODELS_PATH/$filename"
+  if [ ! -f "$filepath" ]; then
+    echo "Downloading $filename..."
+    wget -q -P $MODELS_PATH --timestamping "${files[$filename]}"
+  else
+    if [ $DEBUG -ne 0 ]; then
+      echo "Skipping $filename since it already exists"
+    fi
+  fi
+done
+
+exec \
+  python \
+  /app/scripts/run_inference.py \
+  "$@"

apps/rfdiffusion/metadata.yaml

@@ -0,0 +1,17 @@
+---
+#yamllint disable
+app: rfdiffusion
+semver: true
+channels:
+  - name: stable
+    platforms: ["linux/amd64"]
+    stable: true
+    tests:
+      enabled: false
+      type: cli
+  - name: develop
+    platforms: ["linux/amd64"]
+    stable: false
+    tests:
+      enabled: false
+      type: cli