build: added environment.lock for 'stable' builds

.dockerignore

@@ -1,109 +1,17 @@
-# Git
-.git
-.gitignore
-.gitattributes
-
-# Documentation
-README.md
-*.md
-docs/
-*.rst
-
-# Python
-__pycache__/
-*.py[cod]
-*$py.class
-*.so
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# Testing
-.pytest_cache/
-.coverage
-htmlcov/
-.tox/
-.nox/
-coverage.xml
-*.cover
-.hypothesis/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# Environment
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# IDE
-.vscode/
-.idea/
-*.swp
-*.swo
-*~
-
-# OS
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-
-# Temporary files
-*.tmp
-*.temp
-*.log
-
-# Docker
-Dockerfile*
-docker-compose*
-.dockerignore
-
-# CI/CD
-.github/
-.gitlab-ci.yml
-.travis.yml
-.circleci/
-
-# Large data files (if any)
-*.h5
-*.hdf5
-*.pkl
-*.pickle
-*.npz
-*.npy
-data/
-datasets/
-
-# Model files (if any)
-models/
-checkpoints/
-*.ckpt
-*.pth
-*.pt
-
-# Results and outputs
-results/
-outputs/
-logs/ 
+# Exclude everything
+*
+
+# Allow specific files
+!CITATION.cff
+!LICENSE
+!pyproject.toml
+!README.md
+!setup.py
+
+# Allow specific directories
+!deepspeed_configs/**
+!devtools/**
+!environments/**
+!examples/**
+!openfold3/**
+!scripts/**

.github/workflows/ci-test-reusable.yml

@@ -4,6 +4,10 @@ on:
   # Can only be called by another workflow, not directly by the user
   workflow_call:
     inputs:
+      build_mode:
+        description: 'Build mode: "lock" for reproducible builds, "yaml" for flexible dev builds'
+        required: true
+        type: string
       cuda_base_image_tag:
         description: 'CUDA base image tag (e.g., 12.2.2-cudnn8-devel-ubuntu22.04)'
         required: true
@@ -68,6 +72,7 @@ jobs:
           push: true
           build-args: |
             CUDA_BASE_IMAGE_TAG=${{ inputs.cuda_base_image_tag }}
+            BUILD_MODE=${{ inputs.build_mode }}
           tags: |
             ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-${{ inputs.cuda_base_image_tag }}-${{ github.sha }}
           cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:cache-${{ inputs.cuda_base_image_tag }}

.github/workflows/ci-test.yml

@@ -23,10 +23,12 @@ jobs:
       matrix:
         include:
           - cuda_base_image_tag: "12.1.1-cudnn8-devel-ubuntu22.04"
+            build_mode: "yaml"
     concurrency:
       group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}-${{ matrix.cuda_base_image_tag }}
       cancel-in-progress: true
     uses: ./.github/workflows/ci-test-reusable.yml
     with:
       cuda_base_image_tag: ${{ matrix.cuda_base_image_tag }}
+      build_mode: ${{ matrix.build_mode }}
     secrets: inherit

docker/DOCKER.md

@@ -1,35 +1,75 @@
-## Production images
+## Updating the production.lock file
 
-TODO
+When you modify `environments/production.yml`, you need to regenerate the lock file to pin exact versions. This ensures reproducible builds, prevents conda from resolving the environment again. `environment/production.lock` is then used for 'stable' builds.
 
-For Blackwell image build, see [Build_instructions_blackwell.md](Build_instructions_blackwell.md)
+```bash
+# Build the lock file generator image
+docker build -f docker/Dockerfile.update-reqs -t openfold3-update-reqs .
+
+# Generate the lock file (linux-64 only for now)
+docker run --rm openfold3-update-reqs > environments/production.lock
+
+# Commit the updated lock file
+git add environments/production.lock
+git commit -m "Update production.lock"
+```
 
 ## Development images
 
 These images are the biggest but come with all the build tooling, needed to compile things at runtime (Deepspeed)
 
+```bash
+docker build \
+    -f docker/Dockerfile \
+    --target devel \
+    -t openfold-docker:devel-yaml .
 ```
+
+Or more explicitly
+
+```bash
 docker build \
     -f docker/Dockerfile \
+    --build-arg BUILD_MODE=yaml \
+    --build-arg CUDA_BASE_IMAGE_TAG=12.1.1-cudnn8-devel-ubuntu22.04 \
     --target devel \
-    -t openfold-docker:devel .
+    -t openfold-docker:devel-yaml .
 ```
 
 ## Test images
 
-Build the test image
-```
+Build the test image, with additional test-only dependencies
+
+```bash
 docker build \
-    -f docker/development/Dockerfile \
+    -f docker/Dockerfile \
     --target test \
     -t openfold-docker:test .
 ```
 
 Run the unit tests
-```
+
+```bash
 docker run \
     --rm \
     -v $(pwd -P):/opt/openfold3 \
     -t openfold-docker:test \
     pytest openfold3/tests -vvv
 ```
+
+## Production images
+
+Build a 'stable' image with all the dependancies exactly pinned (production.lock)
+
+```bash
+docker build \
+    -f docker/Dockerfile \
+    --build-arg BUILD_MODE=lock \
+    --build-arg CUDA_BASE_IMAGE_TAG=12.1.1-cudnn8-devel-ubuntu22.04 \
+    --target devel \
+    -t openfold-docker:devel-locked .
+```
+
+For Blackwell image build, see [Build_instructions_blackwell.md](Build_instructions_blackwell.md)
+
+

docker/Dockerfile

@@ -1,7 +1,10 @@
 # Full performance multi-stage build with complete CUDA toolchain
-ARG CUDA_BASE_IMAGE_TAG=12.2.2-cudnn8-devel-ubuntu22.04
+ARG CUDA_BASE_IMAGE_TAG=12.1.1-cudnn8-devel-ubuntu22.04
 FROM nvidia/cuda:${CUDA_BASE_IMAGE_TAG} AS builder
 
+# Environment mode: "lock" for reproducible builds, "yaml" for flexible dev builds
+ARG BUILD_MODE=lock
+
 # Install complete build dependencies including CUDA compiler tools
 RUN apt-get update && apt-get install -y \
     wget \
@@ -16,19 +19,37 @@ RUN apt-get update && apt-get install -y \
 # Install miniforge
 # FIXME this needs to be pinned, with more recent versions (25.11.0-1) the package resolution is stuck
 RUN wget -P /tmp \
-    "https://github.com/conda-forge/miniforge/releases/download/25.3.1-0/Miniforge3-Linux-x86_64.sh" \
+    "https://github.com/conda-forge/miniforge/releases/download/25.11.0-1/Miniforge3-Linux-x86_64.sh" \
     && bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda \
     && rm /tmp/Miniforge3-Linux-x86_64.sh
 
 ENV PATH=/opt/conda/bin:$PATH
-ENV CONDA_PREFIX=/opt/conda
 
-# Copy and install dependencies with aggressive cleanup
-COPY environments/production.yml /opt/openfold3/environment.yml
-RUN mamba env update -n base --file /opt/openfold3/environment.yml \
+# Copy environment files for both modes (small files, good for caching)
+# To regenerate the lock file, see docker/DOCKER.md
+# Use BUILD_MODE=lock (default) for reproducible builds, BUILD_MODE=yml for flexible dev builds
+COPY environments/production.lock /opt/openfold3/production.lock
+COPY environments/production.yml /opt/openfold3/production.yml
+
+# Install environment based on BUILD_MODE
+# - lock: uses conda-lock for exact reproducible builds (training/production)
+# - yaml: uses mamba env create for flexible version resolution (development/testing)
+RUN mamba install -n base -c conda-forge conda-lock --yes \
+    && if [ "$BUILD_MODE" = "lock" ]; then \
+         conda-lock install --name openfold3 /opt/openfold3/production.lock; \
+       elif [ "$BUILD_MODE" = "yaml" ]; then \
+         mamba env create -f /opt/openfold3/production.yml --name openfold3; \
+       else \
+         echo "Invalid BUILD_MODE: $BUILD_MODE. Use 'lock' or 'yaml'." && exit 1; \
+       fi \
     && mamba clean --all --yes \
     && conda clean --all --yes
 
+# Activate the openfold3 environment by default
+ENV PATH=/opt/conda/envs/openfold3/bin:$PATH
+ENV CONDA_PREFIX=/opt/conda/envs/openfold3
+ENV CONDA_DEFAULT_ENV=openfold3
+
 # Copy the minimal set of files needed to install the package
 COPY setup.py /opt/openfold3/
 COPY pyproject.toml /opt/openfold3/
@@ -52,7 +73,7 @@ ENV TORCH_CUDA_ARCH_LIST="8.0;8.6;9.0"
 #     python3 -c "import deepspeed; print('DeepSpeed ops loaded successfully')"
 
 # Devel stage - use devel image for full CUDA support
-ARG CUDA_BASE_IMAGE_TAG=12.2.2-cudnn8-devel-ubuntu22.04
+ARG CUDA_BASE_IMAGE_TAG=12.1.1-cudnn8-devel-ubuntu22.04
 FROM nvidia/cuda:${CUDA_BASE_IMAGE_TAG} AS devel
 
 # Install devel dependencies
@@ -82,16 +103,24 @@ RUN rm -rf /usr/local/cuda/doc \
 
 # Copy the entire conda environment
 COPY --from=builder /opt/conda /opt/conda
-ENV PATH=/opt/conda/bin:$PATH
 
 # Copy CUTLASS
 COPY --from=builder /opt/cutlass /opt/cutlass
 
+# Activate the openfold3 environment by default
+ENV PATH=/opt/conda/envs/openfold3/bin:/opt/conda/bin:$PATH
+ENV CONDA_PREFIX=/opt/conda/envs/openfold3
+ENV CONDA_DEFAULT_ENV=openfold3
+
+# Ensure interactive shells also activate openfold3
+RUN /opt/conda/bin/conda init bash \
+    && echo "conda activate openfold3" >> /root/.bashrc
+
 # Set environment variables
 ENV CUTLASS_PATH=/opt/cutlass
 ENV KMP_AFFINITY=none
-ENV LIBRARY_PATH=/opt/conda/lib:$LIBRARY_PATH
-ENV LD_LIBRARY_PATH=/opt/conda/lib:$LD_LIBRARY_PATH
+ENV LIBRARY_PATH=/opt/conda/envs/openfold3/lib:$LIBRARY_PATH
+ENV LD_LIBRARY_PATH=/opt/conda/envs/openfold3/lib:$LD_LIBRARY_PATH
 
 # Copy the entire source tree directly (at the very end for optimal caching)
 COPY . /opt/openfold3

docker/Dockerfile.update-reqs

@@ -0,0 +1,30 @@
+# Dockerfile for generating conda environment lock files
+# This produces a fully-pinned lock file for reproducible builds
+#
+# Usage:
+#   docker build -f docker/Dockerfile.update-reqs -t openfold3-update-reqs .
+#   docker run --rm openfold3-update-reqs > environments/production.lock
+
+FROM mambaorg/micromamba:1.5.10
+
+USER root
+
+# Install conda-lock
+RUN micromamba install -y -n base -c conda-forge conda-lock \
+    && micromamba clean --all --yes
+
+USER $MAMBA_USER
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER environments/production.yml /tmp/environment.yml
+
+# Generate explicit lock file for linux-64
+# The explicit format is directly consumable by mamba/conda
+RUN micromamba run -n base conda-lock lock \
+    --mamba \
+    --platform linux-64 \
+    --file /tmp/environment.yml \
+    --kind explicit \
+    --filename-template '/tmp/production-{platform}.lock'
+
+# Output the lock file to stdout when container runs
+CMD ["cat", "/tmp/production-linux-64.lock"]