diff --git a/.dockerignore b/.dockerignore
index 22ec6078..c8846126 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,109 +1,17 @@
-# Git
-.git
-.gitignore
-.gitattributes
-
-# Documentation
-README.md
-*.md
-docs/
-*.rst
-
-# Python
-__pycache__/
-*.py[cod]
-*$py.class
-*.so
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# Testing
-.pytest_cache/
-.coverage
-htmlcov/
-.tox/
-.nox/
-coverage.xml
-*.cover
-.hypothesis/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# Environment
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# IDE
-.vscode/
-.idea/
-*.swp
-*.swo
-*~
-
-# OS
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-
-# Temporary files
-*.tmp
-*.temp
-*.log
-
-# Docker
-Dockerfile*
-docker-compose*
-.dockerignore
-
-# CI/CD
-.github/
-.gitlab-ci.yml
-.travis.yml
-.circleci/
-
-# Large data files (if any)
-*.h5
-*.hdf5
-*.pkl
-*.pickle
-*.npz
-*.npy
-data/
-datasets/
-
-# Model files (if any)
-models/
-checkpoints/
-*.ckpt
-*.pth
-*.pt
-
-# Results and outputs
-results/
-outputs/
-logs/ 
+# Exclude everything
+*
+
+# Allow specific files
+!CITATION.cff
+!LICENSE
+!pyproject.toml
+!README.md
+!setup.py
+
+# Allow specific directories
+!deepspeed_configs/**
+!devtools/**
+!environments/**
+!examples/**
+!openfold3/**
+!scripts/**
\ No newline at end of file
diff --git a/.github/workflows/ci-test-reusable.yml b/.github/workflows/ci-test-reusable.yml
index 79f69b3c..2210acfd 100644
--- a/.github/workflows/ci-test-reusable.yml
+++ b/.github/workflows/ci-test-reusable.yml
@@ -4,6 +4,10 @@ on:
   # Can only be called by another workflow, not directly by the user
   workflow_call:
     inputs:
+      build_mode:
+        description: 'Build mode: "lock" for reproducible builds, "yaml" for flexible dev builds'
+        required: true
+        type: string
       cuda_base_image_tag:
         description: 'CUDA base image tag (e.g., 12.2.2-cudnn8-devel-ubuntu22.04)'
         required: true
@@ -68,6 +72,7 @@ jobs:
           push: true
           build-args: |
             CUDA_BASE_IMAGE_TAG=${{ 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 }}
diff --git a/.github/workflows/ci-test.yml b/.github/workflows/ci-test.yml
index 7fcf9e2b..2091b562 100644
--- a/.github/workflows/ci-test.yml
+++ b/.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
diff --git a/docker/DOCKER.md b/docker/DOCKER.md
index 46745847..2cc0f1ac 100644
--- a/docker/DOCKER.md
+++ b/docker/DOCKER.md
@@ -1,35 +1,78 @@
-## Production images
+## Generating and updating production.lock file
 
-TODO
+While a conda env can be created from `environments/production.yml`, this causes the environment to be resolved from scratch everytime. 
+For reproducible builds, one needs to generate a .lock file that exactly re-creates the environment.
 
-For Blackwell image build, see [Build_instructions_blackwell.md](Build_instructions_blackwell.md)
+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.
+
+```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-linux-64.lock
+
+# Commit the updated lock file
+git add environments/production-linux-64.lock
+git commit -m "Update production-linux-64.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 $(pwd -P):/opt/openfold3 \
     -t openfold-docker:test \
     pytest openfold3/tests -vvv
 ```
+
+## Production images
+
+Build a 'stable' image with all the dependancies exactly pinned (production.lock)
+
+```bash
+docker build \
+    -f docker/Dockerfile \
+    --build-arg BUILD_MODE=lock \
+    --build-arg CUDA_BASE_IMAGE_TAG=12.1.1-cudnn8-devel-ubuntu22.04 \
+    --target devel \
+    -t openfold-docker:devel-locked .
+```
+
+For Blackwell image build, see [Build_instructions_blackwell.md](Build_instructions_blackwell.md)
+
+
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 6b93f972..cd037175 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,7 +1,10 @@
 # Full performance multi-stage build with complete CUDA toolchain
-ARG CUDA_BASE_IMAGE_TAG=12.2.2-cudnn8-devel-ubuntu22.04
+ARG CUDA_BASE_IMAGE_TAG=12.1.1-cudnn8-devel-ubuntu22.04
 FROM nvidia/cuda:${CUDA_BASE_IMAGE_TAG} AS builder
 
+# Environment mode: "lock" for reproducible builds, "yaml" for flexible dev builds
+ARG BUILD_MODE=yaml
+
 # 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=yaml (default) for reproducible builds, BUILD_MODE=yml for flexible dev builds
+COPY environments/production-linux-64.lock /opt/openfold3/production-linux-64.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 [ "$BUILD_MODE" = "lock" ]; then \
+         conda-lock install --name openfold3 /opt/openfold3/production-linux-64.lock; \
+       elif [ "$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
diff --git a/docker/Dockerfile.update-reqs b/docker/Dockerfile.update-reqs
new file mode 100644
index 00000000..9eb87049
--- /dev/null
+++ b/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-linux64.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"]
diff --git a/environments/production-linux-64.lock b/environments/production-linux-64.lock
new file mode 100644
index 00000000..2b608beb
--- /dev/null
+++ b/environments/production-linux-64.lock
@@ -0,0 +1,316 @@
+# Generated by conda-lock.
+# platform: linux-64
+# input_hash: c6c19afe77e0f661243e36155e1d001a14036561d4f5842ec9230565596b8060
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/noarch/cuda-version-12.4-h3060b56_3.conda#c9a3fe8b957176e1a8452c6f3431b0d8
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7
+https://conda.anaconda.org/conda-forge/linux-64/mpi-1.0-openmpi.tar.bz2#1dcc49e16749ff79ba2194fa5d4ca5e7
+https://conda.anaconda.org/conda-forge/noarch/python_abi-3.12-8_cp312.conda#c3efd25ac4d74b1584d2f7a57195ddf1
+https://conda.anaconda.org/pytorch/noarch/pytorch-mutex-1.0-cuda.tar.bz2#a948316e36fb5b11223b3fcfa93f8358
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-h8577fbf_0.conda#338201218b54cadff2e774ac27733990
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda#f0991f0f84902f6b6009b4d2350a83aa
+https://conda.anaconda.org/conda-forge/noarch/cuda-cudart_linux-64-12.4.127-h85509e4_2.conda#329163110a96514802e9e64d971edf43
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda#26c46f90d0e727e95c6c9498a33a09f3
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda#887b70e1d607fba7957aa02f9ee0d939
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda#6d0363467e6ed84f11435eb309f2ff06
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda#e36ad70a7e0b48f091ed6902f04c23b8
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda#920bb03579f15389b9e512095ad995b7
+https://conda.anaconda.org/bioconda/linux-64/kalign2-2.04-h7b50bb2_8.tar.bz2#b8351c2fed8f377b6f7db3da31b966ff
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3
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+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.3-hecca717_0.conda#8b09ae86839581147ef2e5c5e229d164
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+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
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+https://conda.anaconda.org/conda-forge/linux-64/libntlm-1.8-hb9d3cd8_0.conda#7c7927b404672409d9917d49bff5f2d6
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_16.conda#68f68355000ec3f1d6f26ea13e8f525f
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+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835
+https://conda.anaconda.org/conda-forge/linux-64/libabseil-20250814.1-cxx17_hee66210_0.conda#a5a7729bb44d885d615560dd05e5d487
+https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.25.1-h3f43e3d_1.conda#3b0d184bc9404516d418d4509e418bdc
+https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.2.0-hb03c661_1.conda#366b40a69f0ad6072561c1d09301c886
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+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
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+https://conda.anaconda.org/conda-forge/linux-64/numpy-2.3.5-py312h33ff503_0.conda#1570db96376f9f01cf495afe203672e5
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+https://conda.anaconda.org/conda-forge/linux-64/biotite-1.2.0-py312h2ec8cdc_0.conda#dc41eec29177278e05f9440de7e023e6
+https://conda.anaconda.org/conda-forge/linux-64/coin-or-cgl-0.60.9-hc46dffc_6.conda#e98b685998df1badbaf1245f67b909a3
+https://conda.anaconda.org/conda-forge/linux-64/rdkit-2025.09.3-py312h3ecb6ed_0.conda#a124ddd026e0ba1b3f781f4189dde55d
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+https://conda.anaconda.org/conda-forge/linux-64/pulp-2.8.0-py312hd0750ca_3.conda#1ade2915cfabbcb8f07e7b4387f4d49b
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+https://conda.anaconda.org/conda-forge/noarch/pephubclient-0.4.4-pyhd8ed1ab_1.conda#08d92912686d87b05d53ce04f00142c8
+https://conda.anaconda.org/conda-forge/noarch/peppy-0.40.8-pyhd8ed1ab_0.conda#af8214b9b5fd6d49175958be2a4f5321
+https://conda.anaconda.org/bioconda/noarch/snakemake-9.14.4-hdfd78af_0.conda#ff4ac83ceb640f17c8b1191832ed9063
+https://conda.anaconda.org/pytorch/linux-64/pytorch-2.5.1-py3.12_cuda12.4_cudnn9.1.0_0.tar.bz2#42164c6ce8e563c20a542686a8b9b964
+https://conda.anaconda.org/conda-forge/noarch/torchmetrics-1.8.2-pyhd8ed1ab_0.conda#5d6e1558a945d0333ae7dc557add7201
+https://conda.anaconda.org/pytorch/linux-64/torchtriton-3.1.0-py312.tar.bz2#bb4b2d07cb6b9b476e78740c08ba69fe
+https://conda.anaconda.org/conda-forge/noarch/pytorch-lightning-2.6.0-pyhcf101f3_0.conda#8e15789d6cd57fd98f762c7475a59ded
+# pip einops @ https://files.pythonhosted.org/packages/87/62/9773de14fe6c45c23649e98b83231fffd7b9892b6cf863251dc2afa73643/einops-0.8.1-py3-none-any.whl#sha256=919387eb55330f5757c6bea9165c5ff5cfe63a642682ea788a6d472576d81737
+# pip gemmi @ https://files.pythonhosted.org/packages/17/23/60d1f411e2b5ee0a49b14f89261a8d1e594cfffa2863af00167dddab4ccf/gemmi-0.7.4-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl#sha256=535e25513e5674b9f11553e34bb3def8a223571bc2373c1854078e53f43b0a1a
+# pip hjson @ https://files.pythonhosted.org/packages/1f/7f/13cd798d180af4bf4c0ceddeefba2b864a63c71645abc0308b768d67bb81/hjson-3.1.0-py3-none-any.whl#sha256=65713cdcf13214fb554eb8b4ef803419733f4f5e551047c9b711098ab7186b89
+# pip ninja @ https://files.pythonhosted.org/packages/ed/de/0e6edf44d6a04dabd0318a519125ed0415ce437ad5a1ec9b9be03d9048cf/ninja-1.13.0-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl#sha256=fb46acf6b93b8dd0322adc3a4945452a4e774b75b91293bafcc7b7f8e6517dfa
+# pip py-cpuinfo @ https://files.pythonhosted.org/packages/e0/a9/023730ba63db1e494a271cb018dcd361bd2c917ba7004c3e49d5daf795a2/py_cpuinfo-9.0.0-py3-none-any.whl#sha256=859625bc251f64e21f077d099d4162689c762b5d6a4c3c97553d56241c9674d5
+# pip deepspeed @ https://files.pythonhosted.org/packages/1b/88/989a2346b7fd618695ad468f4e29a98656a053143fae5587c2924ddb34f8/deepspeed-0.18.3.tar.gz#sha256=0ee0002d8205667ee8463dab8461fb5914dac1583440fe1c48a3a385bb4130ea
+# pip pdbeccdutils @ https://files.pythonhosted.org/packages/5d/94/77773171d66dac29e59a22df87505e05faba30a2c4a1faceff5262228a10/pdbeccdutils-1.0.0-py3-none-any.whl#sha256=dcc6bcb363f9cb0f9be15c465abf2a56809926d8275ccdc50d4f8438ab776c7b
+# pip sympy @ https://files.pythonhosted.org/packages/b2/fe/81695a1aa331a842b582453b605175f419fe8540355886031328089d840a/sympy-1.13.1-py3-none-any.whl#sha256=db36cdc64bf61b9b24578b6f7bab1ecdd2452cf008f34faa33776680c26d66f8