Zarr Archive Format for Inference Traces (Issue #39)

.gitignore

@@ -6,6 +6,7 @@ build
 dist
 
 # files from script downloads
+data
 openfold/resources/
 tests/test_data/
 cutlass/

archive/environment.yml

@@ -0,0 +1,64 @@
+name: vip-zarr-vizfold
+channels:
+  - pytorch
+  - nvidia
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - python=3.10
+  - setuptools=59.5.0
+  - pip
+
+  # Core scientific stack
+  - numpy
+  - pandas
+  - scipy
+  - matplotlib
+  - pillow
+  - tqdm
+  - psutil
+  - PyYAML
+  - typing-extensions
+  - requests
+  - biopython
+
+  # Notebook / interactive workflow
+  - jupyterlab
+  - ipykernel
+
+  # PyTorch with CUDA 12.4
+  # CPU-only alternative: comment out the three lines below and uncomment these:
+  #   - pytorch
+  #   - torchvision
+  #   - cpuonly
+  - pytorch::pytorch=2.5
+  - pytorch::torchvision
+  - pytorch::pytorch-cuda=12.4
+
+  # OpenFold / VizFold runtime dependencies
+  # Note: cuda package provides nvcc + headers for compiling attn_core_inplace_cuda via setup.py
+  # Note: gcc=12.4 is Linux-only; on Windows use MSVC (Visual Studio Build Tools with C++ workload)
+  - cuda
+  - openmm
+  - pdbfixer
+  - pytorch-lightning
+  - ml-collections
+  - mkl
+
+  # Zarr archive stack
+  - zarr=2.16
+  - numcodecs
+  - fsspec
+
+  - pip:
+      # OpenFold extras
+      - dm-tree==0.1.6
+      - modelcif==0.7
+      # NOTE: do NOT put "-e .." here.
+      # setup.py imports torch at the top level, so pip's isolated build
+      # subprocess fails with ModuleNotFoundError before torch is installed.
+      # After activating this env, install openfold manually from the repo root:
+      #   cd ..
+      #   pip install -e .