Release: Add Amelie's fork of Chai-1

apps/chai-amelie/Dockerfile

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+FROM docker.io/library/python:3.12-slim-bookworm
+
+LABEL \
+  maintainer="Liana64" \
+  org.opencontainers.image.source="https://github.com/amelie-iska/chai-lab"
+
+ARG TARGETPLATFORM
+ARG VERSION
+ARG CHANNEL
+ARG DEBIAN_FRONTEND=noninteractive
+
+ENV \
+  NVIDIA_DRIVER_CAPABILITIES="compute,video,utility,graphics" \
+  PATH="/opt/venv/bin:$PATH" \
+  UMASK="0002" \
+  LANG=C.UTF-8 \
+  TZ="Etc/UTC" \
+  USERNAME=rare \
+  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
+
+USER root
+WORKDIR /app
+
+RUN \
+  groupadd --gid ${GID} ${USERNAME} \
+  && useradd --uid ${UID} --gid ${GID} --create-home --shell /bin/bash ${USERNAME} \
+  && apt-get update && apt-get install -y --no-install-recommends \
+  curl unzip build-essential catatonit jq \
+  gnupg ca-certificates lsb-release \
+  nano vim tree git \
+  # -----------------------------------
+  # TODO: Build images with extras
+  # -----------------------------------
+  # htop tmux psmisc \
+  # socat rsync aria2 openssh-server \
+  # -----------------------------------
+  # TODO: Build images with RDMA & InfiniBand
+  # -----------------------------------
+  # libibverbs1 librdmacm1 \
+  # -----------------------------------
+  && git clone https://github.com/amelie-iska/chai-lab.git /tmp/chai \
+  && cp -R /tmp/chai/LICENSE /app \
+  && cp -R /tmp/chai/assets /app \
+  && cp -R /tmp/chai/examples /app \
+  && cp -R /tmp/chai/tests /app \
+  && printf "UpdateMethod=docker\nBranch=master\nPackageVersion=%s\nPackageAuthor=[RareCompute](https://github.com/RareCompute)\n" "${VERSION}" > /app/package_info \
+  && chown -R ${UID}:${GID} /app && chmod -R 755 /app \
+  && curl -LsSf https://astral.sh/uv/0.5.6/install.sh | sh \
+  && . $HOME/.local/bin/env \
+  && uv venv --no-python-downloads /opt/venv \
+  && . /opt/venv/bin/activate \
+  && cd /tmp/chai \
+  && uv pip install -r /tmp/chai/requirements.in \
+  && uv pip install . \
+  && chown -R ${UID}:${GID} /opt/venv && chmod -R 755 /opt/venv \
+  && apt-get purge -y build-essential \
+  && 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/chai/entrypoint.sh /entrypoint.sh
+RUN chmod -R 755 /entrypoint.sh
+
+USER ${USERNAME}
+WORKDIR /app
+
+ENTRYPOINT ["/usr/bin/catatonit", "--", "/entrypoint.sh"]

apps/chai-amelie/README.md

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+# Chai
+
+Amelie's fork of Chai-1, from the [upstream repository](https://github.com/amelie-iska/chai-lab):
+
+> Chai-1 is a multi-modal foundation model for molecular structure prediction that performs at the state-of-the-art across a variety of benchmarks. Chai-1 enables unified prediction of proteins, small molecules, DNA, RNA, glycosylations, and more.
+
+## 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                           |
+| `CHAI_DOWNLOADS_DIR` | N/A                | `PATH`    | `/tmp/downloads` | The path where downloads will be cached.        |
+| `USE_MSA_SERVER`     | `--use-msa-server` | `BOOLEAN` | `False`          | Whether to use the MSA server to generate MSAs. |
+| `MSA_SERVER_URL`     | `--msa-server-url` | `STR`     | N/A              | Use a custom MSA server                         |

apps/chai-amelie/ci/goss.yaml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/goss-org/goss/master/docs/schema.yaml
+file:
+  /opt/venv/bin/chai:
+    exists: true
+  /app/LICENSE:
+    exists: true

apps/chai-amelie/ci/latest.sh

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+#!/usr/bin/env bash
+git clone --quiet https://github.com/amelie-iska/chai-lab.git /tmp/chai
+pushd /tmp/chai > /dev/null || exit
+version=$(git rev-list --count --first-parent HEAD)
+popd > /dev/null || exit
+rm -rf /tmp/chai
+printf "1.0.%d" "${version}"

apps/chai-amelie/entrypoint.sh

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+#!/usr/bin/env bash
+
+EXTRA_FLAGS=""
+declare -A FLAG_MAP=(
+    [USE_MSA_SERVER]="--use-msa-server"
+    [MSA_SERVER_URL]="--msa-server-url"
+)
+
+for VAR in "${!FLAG_MAP[@]}"; do
+    if [ -n "${!VAR}" ]; then
+        VALUE_LOWER=$(echo "${!VAR}" | tr '[:upper:]' '[:lower:]')
+        if [[ "$VALUE_LOWER" == "true" ]]; then
+            EXTRA_FLAGS+=" ${FLAG_MAP[$VAR]}"
+        elif [[ "$VALUE_LOWER" != "false" ]]; then
+            EXTRA_FLAGS+=" ${FLAG_MAP[$VAR]} ${!VAR}"
+        fi
+    fi
+done
+
+exec \
+  chai \
+  "$@" \
+  $EXTRA_FLAGS

apps/chai-amelie/metadata.yaml

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+---
+#yamllint disable
+app: chai-amelie
+semver: true
+channels:
+  - name: stable
+    platforms: ["linux/amd64", "linux/arm64"]
+    stable: true
+    tests:
+      enabled: false
+      type: cli