ipSAE ranking, Dockerfile upgrade, nipah Glycoprotein G design support

.gitignore

@@ -210,3 +210,4 @@ data/test_set
 visualization_data_designed_only
 visualization_results_designed_only
 similarity.ipynb
+/test

Dockerfile

@@ -1,62 +1,88 @@
-# syntax=docker/dockerfile:1
+# Lightweight Docker container for Boltzgen
+# Provides a standardized Linux environment for testing and inference with torch.compile support
 
-FROM nvidia/cuda:12.2.2-cudnn8-devel-ubuntu22.04
+# CUDA / cuDNN base with no Python
+FROM nvidia/cuda:12.8.0-cudnn-devel-ubuntu24.04
 
+# System prerequisites + Python 3.12
 ENV DEBIAN_FRONTEND=noninteractive \
-    PIP_NO_CACHE_DIR=1 \
-    PYTHONDONTWRITEBYTECODE=1 \
-    PYTHONUNBUFFERED=1 \
-    CUDA_HOME=/usr/local/cuda \
-    PIP_EXTRA_INDEX_URL=https://download.pytorch.org/whl/cu121 \
-    HF_HOME=/cache
-
+    PYTHON_VERSION=3.12.7 \
+    PATH=/usr/local/bin:$PATH \
+    TF_CPP_MIN_LOG_LEVEL=2 \
+    TF_ENABLE_ONEDNN_OPTS=0 \
+    TOKENIZERS_PARALLELISM=true
+
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-    python3.10 \
-    python3.10-dev \
-    python3-pip \
-    python3-venv \
-    python3-wheel \
-    build-essential \
-    git \
-    cmake \
-    pkg-config \
-    libffi-dev \
-    libssl-dev \
-    libxml2-dev \
-    libxslt-dev \
-    libgl1 \
-    libhdf5-dev \
-    libboost-all-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.10 1 && \
-    update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 1 && \
-    python -m pip install --upgrade pip setuptools setuptools_scm wheel
+        build-essential curl git ca-certificates wget \
+        libssl-dev zlib1g-dev libbz2-dev libreadline-dev \
+        libsqlite3-dev libncursesw5-dev xz-utils tk-dev \
+        libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev \
+        ninja-build && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN curl -fsSLO https://www.python.org/ftp/python/${PYTHON_VERSION}/Python-${PYTHON_VERSION}.tgz && \
+    tar -xzf Python-${PYTHON_VERSION}.tgz && \
+    cd Python-${PYTHON_VERSION} && \
+    ./configure --enable-optimizations && \
+    make -j"$(nproc)" && \
+    make altinstall && \
+    cd .. && rm -rf Python-${PYTHON_VERSION}* && \
+    ln -s /usr/local/bin/python3.12 /usr/local/bin/python && \
+    ln -s /usr/local/bin/pip3.12 /usr/local/bin/pip
 
+# Location of project code (inside image) – NOT shared with host
 WORKDIR /app
 
-COPY . /app
+# Copy project files first for layer caching
+COPY pyproject.toml ./
+COPY src/ ./src/
+
+# Install packages
+# Order is important
+# 1. Upgrade pip/setuptools
+# 2. Install this repo
+# 3. Reinstall torch/torchvision with CUDA 12.8, so we have the most up to date version
+# 4. Reinstall numpy, numpy > 2.0 fails with scipy and some other packages, so we manually revert to 1.26.4
+RUN pip install --upgrade pip setuptools && \
+    pip install --no-cache-dir -e /app && \
+    pip install torch torchvision --index-url https://download.pytorch.org/whl/cu128 -U && \
+    pip install numpy==1.26.4
+
+# Copy the rest of the source (examples, tests, etc.)
+COPY . .
 
-RUN pip install --no-cache-dir -e /app
+# ──────────────────────────────────────────────────────────────────────────────
+# Single persistent host volume (/workspace) for *all* artefacts & caches
+# Bind-mount it when you run the container:  -v ${PWD}:/workspace
+# ──────────────────────────────────────────────────────────────────────────────
+ENV PROJECT_ROOT=/workspace \
+    PYTHONPATH=/app \
+    CHAI_DOWNLOADS_DIR=/workspace/models/chai1 \
+    HF_HUB_ENABLE_HF_TRANSFER=1 \
+    DISABLE_PANDERA_IMPORT_WARNING=True \
+    HF_HOME=/workspace/.cache/huggingface \
+    TORCH_HOME=/workspace/.cache/torch \
+    XDG_CACHE_HOME=/workspace/.cache \
+    WANDB_DIR=/workspace/logs \
+    TQDM_CACHE=/workspace/.cache/tqdm
+
+RUN mkdir -p \
+      /workspace/.cache/huggingface \
+      /workspace/.cache/torch \
+      /workspace/.cache/tqdm \
+      /workspace/logs \
+      /workspace/data \
+      /workspace/results
 
 ARG DOWNLOAD_WEIGHTS=false
 RUN mkdir -p "${HF_HOME}" && \
     if [ "${DOWNLOAD_WEIGHTS}" = "true" ]; then \
         boltzgen download all --cache "${HF_HOME}" --force_download; \
     fi
 
-ARG USERNAME=boltzgen
-ARG USER_UID=1000
-ARG USER_GID=1000
-
-RUN groupadd --gid ${USER_GID} ${USERNAME} && \
-    useradd --uid ${USER_UID} --gid ${USER_GID} --create-home --shell /bin/bash ${USERNAME}
-
-RUN mkdir -p "${HF_HOME}" && chown -R ${USER_UID}:${USER_GID} "${HF_HOME}"
-
-USER ${USERNAME}
-WORKDIR /workspace
+# Declare the volume so other developers know it's intended to persist
+VOLUME ["/workspace"]
 
-ENTRYPOINT ["boltzgen"]
-CMD ["--help"]
+# Default command – override in `docker run … python ...`
+CMD ["bash"]