rc-foundry 0.1.1__tar.gz → 0.1.3__tar.gz

{rc_foundry-0.1.1 → rc_foundry-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rc-foundry
-Version: 0.1.1
+Version: 0.1.3
 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

{rc_foundry-0.1.1 → rc_foundry-0.1.3}/models/rf3/tests/data/ncaa/create_cif_with_ligand_as_ncaa.ipynb

@@ -7,10 +7,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from cifutils import parse\n",
-    "from cifutils.tools.inference import components_to_atom_array\n",
-    "from cifutils.utils.visualize import view\n",
-    "from cifutils.utils.io_utils import to_cif_file\n",
+    "from atomworks.io import parse\n",
+    "from atomwork.io.tools.inference import components_to_atom_array\n",
+    "from atomworks.io.utils.visualize import view\n",
+    "from atomworks.io.utils.io_utils import to_cif_file\n",
     "\n",
     "import os\n",
     "\n",

{rc_foundry-0.1.1 → rc_foundry-0.1.3}/models/rfd3/src/rfd3/testing/debug.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env -S /bin/sh -c '"$(dirname "$0")/../../../scripts/shebang/modelhub_exec.sh" "$0" "$@"'
 # JBs debugging file, please create your own and go crazy!
 import logging
 import os

{rc_foundry-0.1.1 → rc_foundry-0.1.3}/models/rfd3/src/rfd3/utils/vizualize.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env -S /bin/sh -c '"$(dirname "$0")/../../../scripts/shebang/modelhub_exec.sh" "$0" "$@"'
 """
 If you add the `/path/to/visualize.py` to your .bashrc/.zshrc like this:
 

{rc_foundry-0.1.1 → rc_foundry-0.1.3}/models/rfd3/tests/test_aa_design.py

@@ -1,9 +1,3 @@
-#!/usr/bin/env -S /bin/sh -c '"$(dirname "$0")/../../../scripts/shebang/modelhub_exec.sh" "$0" "$@"'
-# Usage:
-# >>> apptainer exec scripts/shebang/test_modelhub.sif pytest ./rfd3/tests/test_aa_design.py
-# To combine both make format and testing together you can use:
-# apptainer exec ./scripts/shebang/test_modelhub.sif make format || true && apptainer exec ./scripts/shebang/test_modelhub.sif pytest ./rfd3/tests/test_aa_design.py
-
 import contextlib
 import io
 import os

{rc_foundry-0.1.1 → rc_foundry-0.1.3}/src/foundry/version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.1'
-__version_tuple__ = version_tuple = (0, 1, 1)
+__version__ = version = '0.1.3'
+__version_tuple__ = version_tuple = (0, 1, 3)
 
 __commit_id__ = commit_id = None

{rc_foundry-0.1.1 → rc_foundry-0.1.3}/src/foundry_cli/download_checkpoints.py

@@ -24,7 +24,6 @@ from foundry.inference_engines.checkpoint_registry import (
     get_default_checkpoint_dir,
 )
 
-rootutils.setup_root(__file__, indicator=".project-root", pythonpath=True)
 load_dotenv(override=True)
 
 app = typer.Typer(help="Foundry model checkpoint installation utilities")
@@ -98,7 +97,7 @@ def install_model(
         raise typer.Exit(1)
 
     checkpoint_info = REGISTERED_CHECKPOINTS[model_name]
-    dest_path = checkpoint_dir / checkpoint_info["filename"]
+    dest_path = checkpoint_dir / checkpoint_info.filename
 
     # Check if already exists
     if dest_path.exists() and not force:
@@ -109,12 +108,12 @@ def install_model(
         return
 
     console.print(
-        f"[cyan]Installing {model_name}:[/cyan] {checkpoint_info['description']}"
+        f"[cyan]Installing {model_name}:[/cyan] {checkpoint_info.description}"
     )
 
     try:
         download_file(
-            checkpoint_info["url"], dest_path, checkpoint_info.get("sha256")
+            checkpoint_info.url, dest_path, checkpoint_info.sha256
         )
         console.print(
             f"[green]✓[/green] Successfully installed {model_name} to {dest_path}"
@@ -186,7 +185,7 @@ def list_models():
     """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']}")
+        console.print(f"  [cyan]{name:8}[/cyan] - {info.description}")
 
 
 @app.command()

rc_foundry-0.1.1/.ipd/apptainer/rf3-dev.def

@@ -1,114 +0,0 @@
-Bootstrap: localimage
-From: /net/software/containers/versions/modelhub/pytorch_25.06-py3.sif
-IncludeCmd: yes
-
-# RF3 Development Container - Dependencies only (excludes atomworks, which we expose through a submodule for development)
-
-# To build this Apptainer, from the project root, run:
-# apptainer build rf3-dev.sif .ipd/apptainer/rf3-dev.def
-
-%labels
-    Author Institute for Protein Design
-    Version 1.0-dev
-    Description RosettaFold3 - Dependencies only (for development and model training)
-
-%setup
-    # Create a directory in the container to bind the host's current working directory
-    mkdir ${APPTAINER_ROOTFS}/foundry_host
-    # ... for mounting `/projects` with --bind
-    mkdir ${APPTAINER_ROOTFS}/projects
-    # ... for mounting `/databases` with --bind
-    mkdir ${APPTAINER_ROOTFS}/net
-    # ... for mounting `/squash` with --bind
-    mkdir ${APPTAINER_ROOTFS}/squash
-
-%files
-    /etc/localtime
-    /etc/hosts
-    pyproject.toml /opt/core_pyproject.toml
-    models/rf3/pyproject.toml /opt/rf3_pyproject.toml
-    lib/atomworks/pyproject.toml /opt/atomworks_pyproject.toml
-
-%post
-    ## GENERAL SETUP
-
-    # Common symlinks (within container)
-    ln -s /net/databases /databases
-    ln -s /net/software /software
-    ln -s /home /mnt/home
-    ln -s /projects /mnt/projects
-    ln -s /net /mnt/net
-
-    # Update system and install essential packages
-    apt-get update && apt-get install -y \
-        build-essential \
-        git \
-        libxrender1 \
-        libxrender-dev \
-        libx11-6 \
-        libx11-dev \
-        libxext6 \
-        libxext-dev \
-        && rm -rf /var/lib/apt/lists/*
-
-    ## PYTHON DEPENDENCY INSTALLATION
-
-    # Upgrade pip
-    python -m pip install --upgrade pip
-
-    # Install uv for fast dependency resolution
-    pip install uv
-
-    # Auto-generate dependency lists for both core and RF3, with all extra dependencies
-    # (Core)
-    mv /opt/core_pyproject.toml /opt/pyproject.toml
-    uv pip compile /opt/pyproject.toml --output-file /opt/core_requirements.txt --all-extras
-    rm /opt/pyproject.toml
-
-    # (RF3)
-    mv /opt/rf3_pyproject.toml /opt/pyproject.toml
-    uv pip compile /opt/pyproject.toml --output-file /opt/rf3_requirements.txt --all-extras
-    rm /opt/pyproject.toml
-
-    # (AtomWorks)
-    mv /opt/atomworks_pyproject.toml /opt/pyproject.toml
-    uv pip compile /opt/pyproject.toml --output-file /opt/atomworks_requirements.txt --all-extras
-    rm /opt/pyproject.toml
-
-    # Merge and dedupe requirements, excluding packages we don't want
-    # (atomworks is mounted from host; torch/numpy/nvidia-* provided by base image)
-    # (pynvml/packaging/pandas/markdown-it-py/triton from NGC container to avoid conflicts)
-    # Deduplicate by package name (keeping first occurrence) to handle version conflicts
-    cat /opt/core_requirements.txt /opt/rf3_requirements.txt /opt/atomworks_requirements.txt | \
-        grep -vE "^(atomworks|torch(|vision|audio)|numpy|nvidia-.*|pynvml|packaging|pandas|markdown-it-py|triton)==" | \
-        awk -F'==' '!seen[$1]++' > /opt/combined_requirements.txt
-
-    # Print combined requirements for debugging
-    echo "=== Combined requirements to install ==="
-    cat /opt/combined_requirements.txt
-    echo "========================================"
-
-    # Install the cleaned, combined requirements (use uv for better resolver)
-    uv pip install --system --break-system-packages -r /opt/combined_requirements.txt
-
-    # Clean up to minimize container size
-    uv cache clean
-    pip cache purge
-    apt-get clean
-    rm -rf /var/lib/apt/lists/* 2>/dev/null || true
-    rm -rf /root/.cache 2>/dev/null || true
-    rm -rf /opt/*.txt 2>/dev/null || true
-
-%environment
-    # (Flag to increase accessible GPU memory)
-    export PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True
-
-    # (Turn off NVLink)
-    export NCCL_P2P_DISABLE=1
-
-%runscript
-   # NOTE: The %runscript is invoked when the container is run without specifying a different command.
-   exec python "$@"
-
-%help
-    RosettaFold3 (RF3) development container with dependencies only.

rc_foundry-0.1.1/.ipd/apptainer/rf3-full.def

@@ -1,81 +0,0 @@
-Bootstrap: localimage
-From: .ipd/apptainer/rf3-dev.sif
-IncludeCmd: yes
-
-# RF3 Full Production Container - Includes foundry, rf3, and atomworks packages installed
-
-# To build this Apptainer, from the project root, run:
-# apptainer build rf3-full.sif .ipd/apptainer/rf3-full.def
-
-%labels
-    Author Institute for Protein Design
-    Version 1.0.0
-    Description RosettaFold3 - Full production container with all packages installed
-
-%setup
-    # Copy entire repository to container
-    echo "Copying repository..."
-
-    # Create base directory
-    mkdir -p ${APPTAINER_ROOTFS}/opt/foundry
-
-    # Copy everything except large/unnecessary files
-    rsync -av --info=progress2 \
-        --exclude='.venv' \
-        --exclude='__pycache__' \
-        --exclude='*.pyc' \
-        --exclude='.pytest_cache' \
-        --exclude='*.egg-info' \
-        --exclude='.ruff_cache' \
-        --exclude='outputs' \
-        --exclude='logs' \
-        --exclude='*.sif' \
-        --exclude='distillation' \
-        --exclude='benchmarks' \
-        --exclude='**/slurm_logs' \
-        ./ ${APPTAINER_ROOTFS}/opt/foundry/
-
-    echo "Repository copied successfully."
-
-%post
-    echo "Installing packages into container..."
-
-    # Do editable installs so everything works as in development
-    cd /opt/foundry
-
-    # Install foundry (editable, no dependencies - already in base image)
-    echo "Installing foundry..."
-    uv pip install --system --break-system-packages --no-deps -e .
-
-    # Install rf3 (editable, no dependencies - already in base image)
-    echo "Installing rf3..."
-    cd /opt/foundry/models/rf3
-    uv pip install --system --break-system-packages --no-deps -e .
-
-    # Install atomworks (editable, no dependencies - already in base image)
-    echo "Installing atomworks..."
-    cd /opt/foundry/lib/atomworks
-    uv pip install --system --break-system-packages --no-deps -e .
-
-    # Cleanup caches only
-    echo "Cleaning up caches..."
-    uv cache clean
-    pip cache purge
-    apt-get clean
-    rm -rf /var/lib/apt/lists/* 2>/dev/null || true
-    rm -rf /root/.cache 2>/dev/null || true
-
-    echo "Package installation complete."
-
-%runscript
-    # Simple runscript - just run Python with any arguments
-    exec python "$@"
-
-%help
-    RosettaFold3 (RF3) full production container.
-
-    Contains foundry, rf3, and atomworks packages installed in site-packages.
-    All dependencies are included from the base rf3-dev container.
-
-    Usage:
-        apptainer exec --nvccli rf3-full.sif rf3 fold inputs="example.json"

rc_foundry-0.1.1/.ipd/apptainer/rfd3-full.def

@@ -1,81 +0,0 @@
-Bootstrap: localimage
-From: .ipd/apptainer/rf3-dev.sif
-IncludeCmd: yes
-
-# RFD3 Full Production Container - Includes foundry, rfd3, and atomworks packages installed
-
-# To build this Apptainer, from the project root, run:
-# apptainer build rfd3-full.sif .ipd/apptainer/rfd3-full.def
-
-%labels
-    Author Institute for Protein Design
-    Version 1.0.0
-    Description RFDiffusion3 - Full production container with all packages installed
-
-%setup
-    # Copy entire repository to container
-    echo "Copying repository..."
-
-    # Create base directory
-    mkdir -p ${APPTAINER_ROOTFS}/opt/foundry
-
-    # Copy everything except large/unnecessary files
-    rsync -av --info=progress2 \
-        --exclude='.venv' \
-        --exclude='__pycache__' \
-        --exclude='*.pyc' \
-        --exclude='.pytest_cache' \
-        --exclude='*.egg-info' \
-        --exclude='.ruff_cache' \
-        --exclude='outputs' \
-        --exclude='logs' \
-        --exclude='*.sif' \
-        --exclude='distillation' \
-        --exclude='benchmarks' \
-        --exclude='**/slurm_logs' \
-        ./ ${APPTAINER_ROOTFS}/opt/foundry/
-
-    echo "Repository copied successfully."
-
-%post
-    echo "Installing packages into container..."
-
-    # Do editable installs so everything works as in development
-    cd /opt/foundry
-
-    # Install foundry (editable, no dependencies - already in base image)
-    echo "Installing foundry..."
-    uv pip install --system --break-system-packages --no-deps -e .[all]
-
-    # Install rfd3 (editable, no dependencies - already in base image)
-    echo "Installing rfd3..."
-    cd /opt/foundry/models/rfd3
-    uv pip install --system --break-system-packages --no-deps -e .
-
-    # Install atomworks (editable, no dependencies - already in base image)
-    echo "Installing atomworks..."
-    cd /opt/foundry/lib/atomworks
-    uv pip install --system --break-system-packages --no-deps -e .
-
-    # Cleanup caches only
-    echo "Cleaning up caches..."
-    uv cache clean
-    pip cache purge
-    apt-get clean
-    rm -rf /var/lib/apt/lists/* 2>/dev/null || true
-    rm -rf /root/.cache 2>/dev/null || true
-
-    echo "Package installation complete."
-
-%runscript
-    # Simple runscript - just run Python with any arguments
-    exec python "$@"
-
-%help
-    RFDiffusion3 (RFD3) full production container.
-
-    Contains foundry, rfd3, and atomworks packages installed in site-packages.
-    All dependencies are included from the base rf3-dev container.
-
-    Usage:
-        apptainer exec --nvccli rfd3-full.sif rfd3 run_inference inputs="example.json"

rc_foundry-0.1.1/.ipd/shebang/README.md

@@ -1,6 +0,0 @@
-This directory contains scripts that are not to be run directly by the user. 
-They are [SHEBANG scripts](https://en.wikipedia.org/wiki/Shebang_(Unix)) that are used to run the appropriate apptainer container.
-
-For example, the script `rf3_exec.sh` is used to run the RF3 apptainer container with the latest apptainer image stored locally or at the IPD.
-
-The shebang lines (`#!/bin/bash` ...) at the top of entry point scripts like `train.py` redirect the system to here to find the correct apptainer container.

rc_foundry-0.1.1/.ipd/shebang/mpnn_exec.sh

@@ -1,129 +0,0 @@
-#!/usr/bin/bash
-
-###################
-# You can add the path to this file as the shebang line in your python script. 
-# Then by default, the python script will be executed with the python interpreter
-# in the SIF_PATH container. Here, we launch the container with nvidia gpu and slurm support.
-#
-# Example shebang: #!/usr/bin/env -S /bin/sh -c '"$(dirname "$0")/.ipd/shebang/mpnn_exec.sh" "$0" "$@"'
-###################
-
-# Let the user know this script is setting things up behind the scene
-SCRIPT_PATH=$(realpath $0)
-SCRIPT_DIR=$(dirname $SCRIPT_PATH)
-echo '################## Start shebang info ##################'
-echo "The file $SCRIPT_PATH is being run as a shebang executable.
-    It will...
-
-    1. Add 'src/foundry', 'models/mpnn/src', and 'lib/atomworks/src' to your PYTHONPATH.
-    2. Run your python script from the right container, which contains all dependencies.
-    3. Launch the container with slurm and nvidia gpu support."
-
-# Extract the path to the Python script from the arguments
-PYTHON_SCRIPT=$(realpath "$1")
-shift
-
-# Find repository root by looking for .project-root file
-find_repo_root() {
-    local current_dir="$1"
-    while [ "$current_dir" != "/" ]; do
-        if [ -f "$current_dir/.project-root" ]; then
-            echo "$current_dir"
-            return 0
-        fi
-        current_dir="$(dirname "$current_dir")"
-    done
-    return 1
-}
-
-echo
-echo "Searching for repository root directory..."
-REPO_ROOT=$(find_repo_root "$(dirname "$PYTHON_SCRIPT")")
-if [ -z "$REPO_ROOT" ]; then
-    echo "Error: Could not find .project-root file in any parent directory"
-    exit 1
-else
-    echo "... found repository root at '$REPO_ROOT'"
-fi
-
-# Function to add a directory to PYTHONPATH if it's not already included
-add_to_pythonpath() {
-    local dir_path="$1"
-    if [[ ":$PYTHONPATH:" != *":$dir_path:"* ]]; then
-        export PYTHONPATH="$dir_path:$PYTHONPATH"
-        echo "Added '$dir_path' to PYTHONPATH."
-    else
-        echo "'$dir_path' is already in PYTHONPATH."
-    fi
-}
-
-# Add foundry, mpnn, and atomworks to PYTHONPATH
-echo
-echo "Adding foundry, MPNN, and atomworks to PYTHONPATH..."
-FOUNDRY_PATH="$REPO_ROOT/src"
-MPNN_PATH="$REPO_ROOT/models/mpnn/src"
-ATOMWORKS_PATH="$REPO_ROOT/lib/atomworks/src"
-add_to_pythonpath "$FOUNDRY_PATH"
-add_to_pythonpath "$MPNN_PATH"
-add_to_pythonpath "$ATOMWORKS_PATH"
-
-echo
-echo "Fetching the appropriate apptainer image..."
-
-SIF_PATH="$REPO_ROOT/.ipd/apptainer/rf3-dev.sif"
-
-echo "... looking for a local apptainer image at '$SIF_PATH'"
-if [ ! -f "$SIF_PATH" ]; then
-    echo "... apptainer not found. To build it, run: apptainer build .ipd/apptainer/rf3-dev.sif .ipd/apptainer/rf3-dev.def"
-    echo "Attempting to run $PYTHON_SCRIPT with $(which python)"
-    SIF_PATH=""
-fi
-
-# Function to print debug=mode warning
-print_debug_warning() {
-    echo
-    echo "###############################################################################"
-    echo "#                                                                             #"
-    echo "#                               ⚠️  WARNING ⚠️                                  #"
-    echo "#                     RUNNING WITH DEBUGPY ON PORT $DEBUG_PORT                       #"
-    echo "#                      DON'T FORGET TO ATTACH A DEBUGGER                      #"
-    echo "#                                                                             #"
-    echo "###############################################################################"
-    echo
-}
-
-if [ -n "$DEBUG_PORT" ]; then
-    print_debug_warning
-    python_cmd="python -m debugpy --listen $DEBUG_PORT --wait-for-client"
-else
-    python_cmd="python"
-    echo
-fi
-
-if [ ! -z $SIF_PATH ]; then
-    echo "Running $PYTHON_SCRIPT with apptainer: $SIF_PATH."
-
-    # Determine GPU binding method: prefer --nvccli, fallback to --nv, then no GPU
-    GPU_FLAG=""
-    if command -v nvidia-container-cli &> /dev/null && [ -c /dev/nvidiactl ] 2>/dev/null; then
-        GPU_FLAG="--nvccli"
-        echo "Using --nvccli for GPU support"
-    elif [ -c /dev/nvidiactl ] 2>/dev/null; then
-        GPU_FLAG="--nv"
-        echo "Using --nv for GPU support"
-    else
-        echo "No GPU detected, running without GPU support"
-    fi
-
-    echo '################## End shebang info ####################'
-    echo
-    /usr/bin/apptainer exec $GPU_FLAG --slurm \
-        --bind "$REPO_ROOT:$REPO_ROOT" \
-        --env PYTHONPATH="\$PYTHONPATH:$PYTHONPATH" \
-        $SIF_PATH $python_cmd "$PYTHON_SCRIPT" "$@"
-else
-    echo "Running $PYTHON_SCRIPT with python: $(which python)"
-    echo '################## End shebang info ####################'
-    echo
-    $python_cmd "$PYTHON_SCRIPT" "$@"
-fi

rc_foundry-0.1.1/.ipd/shebang/rf3_exec.sh

@@ -1,129 +0,0 @@
-#!/usr/bin/bash
-
-###################
-# You can add the path to this file as the shebang line in your python script. 
-# Then by default, the python script will be executed with the python interpreter
-# in the SIF_PATH container. Here, we launch the container with nvidia gpu and slurm support.
-#
-# Example shebang: #!/usr/bin/env -S /bin/sh -c '"$(dirname "$0")/.ipd/shebang/rf3_exec.sh" "$0" "$@"'
-###################
-
-# Let the user know this script is setting things up behind the scene
-SCRIPT_PATH=$(realpath $0)
-SCRIPT_DIR=$(dirname $SCRIPT_PATH)
-echo '################## Start shebang info ##################'
-echo "The file $SCRIPT_PATH is being run as a shebang executable.
-    It will...
-
-    1. Add 'src/foundry', 'models/rf3/src', and 'lib/atomworks/src' to your PYTHONPATH.
-    2. Run your python script from the right container, which contains all dependencies.
-    3. Launch the container with slurm and nvidia gpu support."
-
-# Extract the path to the Python script from the arguments
-PYTHON_SCRIPT=$(realpath "$1")
-shift
-
-# Find repository root by looking for .project-root file
-find_repo_root() {
-    local current_dir="$1"
-    while [ "$current_dir" != "/" ]; do
-        if [ -f "$current_dir/.project-root" ]; then
-            echo "$current_dir"
-            return 0
-        fi
-        current_dir="$(dirname "$current_dir")"
-    done
-    return 1
-}
-
-echo
-echo "Searching for repository root directory..."
-REPO_ROOT=$(find_repo_root "$(dirname "$PYTHON_SCRIPT")")
-if [ -z "$REPO_ROOT" ]; then
-    echo "Error: Could not find .project-root file in any parent directory"
-    exit 1
-else
-    echo "... found repository root at '$REPO_ROOT'"
-fi
-
-# Function to add a directory to PYTHONPATH if it's not already included
-add_to_pythonpath() {
-    local dir_path="$1"
-    if [[ ":$PYTHONPATH:" != *":$dir_path:"* ]]; then
-        export PYTHONPATH="$dir_path:$PYTHONPATH"
-        echo "Added '$dir_path' to PYTHONPATH."
-    else
-        echo "'$dir_path' is already in PYTHONPATH."
-    fi
-}
-
-# Add foundry, rf3, and atomworks to PYTHONPATH
-echo
-echo "Adding foundry, RF3, and atomworks to PYTHONPATH..."
-FOUNDRY_PATH="$REPO_ROOT/src"
-RF3_PATH="$REPO_ROOT/models/rf3/src"
-ATOMWORKS_PATH="$REPO_ROOT/lib/atomworks/src"
-add_to_pythonpath "$FOUNDRY_PATH"
-add_to_pythonpath "$RF3_PATH"
-add_to_pythonpath "$ATOMWORKS_PATH"
-
-echo
-echo "Fetching the appropriate apptainer image..."
-
-SIF_PATH="$REPO_ROOT/.ipd/apptainer/rf3-dev.sif"
-
-echo "... looking for a local apptainer image at '$SIF_PATH'"
-if [ ! -f "$SIF_PATH" ]; then
-    echo "... apptainer not found. To build it, run: apptainer build .ipd/apptainer/rf3-dev.sif .ipd/apptainer/rf3-dev.def"
-    echo "Attempting to run $PYTHON_SCRIPT with $(which python)"
-    SIF_PATH=""
-fi
-
-# Function to print debug=mode warning
-print_debug_warning() {
-    echo
-    echo "###############################################################################"
-    echo "#                                                                             #"
-    echo "#                               ⚠️  WARNING ⚠️                                  #"
-    echo "#                     RUNNING WITH DEBUGPY ON PORT $DEBUG_PORT                       #"
-    echo "#                      DON'T FORGET TO ATTACH A DEBUGGER                      #"
-    echo "#                                                                             #"
-    echo "###############################################################################"
-    echo
-}
-
-if [ -n "$DEBUG_PORT" ]; then
-    print_debug_warning
-    python_cmd="python -m debugpy --listen $DEBUG_PORT --wait-for-client"
-else
-    python_cmd="python"
-    echo
-fi
-
-if [ ! -z $SIF_PATH ]; then
-    echo "Running $PYTHON_SCRIPT with apptainer: $SIF_PATH."
-
-    # Determine GPU binding method: prefer --nvccli, fallback to --nv, then no GPU
-    GPU_FLAG=""
-    if command -v nvidia-container-cli &> /dev/null && [ -c /dev/nvidiactl ] 2>/dev/null; then
-        GPU_FLAG="--nvccli"
-        echo "Using --nvccli for GPU support"
-    elif [ -c /dev/nvidiactl ] 2>/dev/null; then
-        GPU_FLAG="--nv"
-        echo "Using --nv for GPU support"
-    else
-        echo "No GPU detected, running without GPU support"
-    fi
-
-    echo '################## End shebang info ####################'
-    echo
-    /usr/bin/apptainer exec $GPU_FLAG --slurm \
-        --bind "$REPO_ROOT:$REPO_ROOT" \
-        --env PYTHONPATH="\$PYTHONPATH:$PYTHONPATH" \
-        $SIF_PATH $python_cmd "$PYTHON_SCRIPT" "$@"
-else
-    echo "Running $PYTHON_SCRIPT with python: $(which python)"
-    echo '################## End shebang info ####################'
-    echo
-    $python_cmd "$PYTHON_SCRIPT" "$@"
-fi