build: remove setup.py and other build changes (#79)

* build: remove setup.py

* factor out test deps into pyproject.toml

* time to add uv to support dep groups

* playing with osx-arm64 support

* typo: missed an extension

* review: comments from Jennifer

Author: jandom

.dockerignore

@@ -6,7 +6,6 @@
 !LICENSE
 !pyproject.toml
 !README.md
-!setup.py
 
 # Allow specific directories
 !deepspeed_configs/**

.gitignore

@@ -13,3 +13,6 @@ cutlass/
 
 # User-specific claude settings
 .claude/
+
+# User-specific pre-commit settings
+.pre-commit-config.yaml

docker/DOCKER.md

@@ -1,16 +1,16 @@
 ## Generating and updating production.lock file
 
-While a conda env can be created from `environments/production.yml`, this causes the environment to be resolved from scratch everytime. 
+While a conda env can be created from `environments/production-linux-64.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.
 
-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.
+When you modify `environments/production-linux-64.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
+docker run -v $(pwd)/environments:/output --rm openfold3-update-reqs 
 
 # Commit the updated lock file
 git add environments/production-linux-64.lock

docker/Dockerfile

@@ -29,7 +29,7 @@ ENV PATH=/opt/conda/bin:$PATH
 # 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
+COPY environments/production-linux-64.yml /opt/openfold3/production-linux-64.yml
 
 # Install environment based on BUILD_MODE
 # - lock: uses conda-lock for exact reproducible builds (training/production)
@@ -38,7 +38,7 @@ 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; \
+         mamba env create -f /opt/openfold3/pproduction-linux-64 --name openfold3; \
        else \
          echo "Invalid BUILD_MODE: $BUILD_MODE. Use 'lock' or 'yaml'." && exit 1; \
        fi \
@@ -51,7 +51,6 @@ 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/
 COPY openfold3/__init__.py /opt/openfold3/openfold3/
 COPY scripts/ /opt/openfold3/scripts/
@@ -62,8 +61,7 @@ RUN /opt/openfold3/scripts/install_third_party_dependencies.sh
 
 # Install the package
 WORKDIR /opt/openfold3
-# even `pip install --no-build-isolation` not actually working here, needs investigation
-RUN python setup.py install
+RUN python -m uv pip install --editable --no-deps .
 
 # Set CUDA architecture for compilation (adjust based on your GPU)
 ENV TORCH_CUDA_ARCH_LIST="8.0;8.6;9.0"
@@ -130,8 +128,7 @@ WORKDIR /opt/openfold3
 # Test stage - build on devel layer with test dependencies
 FROM devel AS test
 
-COPY environments/requirements-test.txt /opt/openfold3/requirements-test.txt
-
 WORKDIR /opt/openfold3
-RUN pip install -r requirements-test.txt
-RUN pip install --no-deps --editable .
+# Only uv supports --dependency-groups from pyproject.toml
+RUN uv pip install --dependency-groups=test
+RUN uv pip install --no-deps --editable .

docker/Dockerfile.blackwell

@@ -17,7 +17,7 @@ RUN apt-get update && apt-get install -y \
 WORKDIR /opt
 RUN git clone https://github.com/aqlaboratory/openfold-3.git && \
     cd openfold-3 && \
-    cp -p environments/production.yml environments/production.yml.backup && \
+    cp -p environments/production-linux-64.yml environments/production.yml.backup && \
     grep -v "pytorch::pytorch" environments/production.yml > environments/production.yml.tmp && \
     mv environments/production.yml.tmp environments/production.yml
 
@@ -56,7 +56,7 @@ RUN git clone https://github.com/NVIDIA/cutlass --branch v3.6.0 --depth 1
 
 # Install OpenFold3 package itself (provides run_openfold command)
 WORKDIR /opt/openfold-3
-RUN python3 setup.py install
+RUN python3 -m pip install --editable --no-deps .
 
 # Set environment variables including CUDA architecture for Blackwell
 ENV PYTHONUNBUFFERED=1 \

docker/Dockerfile.update-reqs

@@ -15,16 +15,18 @@ RUN micromamba install -y -n base -c conda-forge conda-lock \
 
 USER $MAMBA_USER
 
-COPY --chown=$MAMBA_USER:$MAMBA_USER environments/production.yml /tmp/environment.yml
+COPY --chown=$MAMBA_USER:$MAMBA_USER environments/production-linux-64.yml /tmp/production-linux-64.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 \
+    --file /tmp/production-linux-64.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"]
+USER root
+CMD ["sh", "-c", "cp /tmp/production-*.lock /output/"]
+

environments/production-linux-64.lock

@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: c6c19afe77e0f661243e36155e1d001a14036561d4f5842ec9230565596b8060
+# input_hash: 12c5e0c7c920184c37043be6c44627092723a93293a4b6e68614446c10120d5d
 @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
@@ -67,12 +67,13 @@ https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-15.0.7-h0cdce71_0.co
 https://conda.anaconda.org/conda-forge/linux-64/opencl-headers-2025.06.13-h5888daf_0.conda#45c3d2c224002d6d0d7769142b29f986
 https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.47-haa7fec5_0.conda#7a3bff861a6583f1889021facefc08b1
 https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda#c01af13bdc553d1a8fbfff6e8db075f0
-https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
 https://conda.anaconda.org/conda-forge/linux-64/s2n-1.6.1-h23ded05_1.conda#d9f44253e28b48baee6e278d51ece70c
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda#86bc20552bf46075e3d92b67f089172d
+https://conda.anaconda.org/conda-forge/linux-64/uv-0.9.18-h76e24b7_0.conda#66a5d1348be63f1874f5a0dd0add29c2
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.6-he73a12e_0.conda#1c74ff8c35dcadf952a16f752ca5aa49
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda#c9f075ab2f33b3bbee9e62d4ad0a6cd8
-https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.2-h54a6638_0.conda#0faadd01896315ceea58bcc3479b1d21
+https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.2-hceb46e0_1.conda#40feea2979654ed579f1cda7c63ccb94
 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
 https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.23.3-had5c4f5_4.conda#a53c9f532e5c4a2b85d4b4c439ea5a5d
 https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hb03c661_1.conda#af39b9a8711d4a8d437b52c1d78eb6a1
@@ -137,7 +138,7 @@ https://conda.anaconda.org/conda-forge/noarch/distro-1.8.0-pyhd8ed1ab_0.conda#67
 https://conda.anaconda.org/conda-forge/linux-64/docutils-0.18.1-py312h7900ff3_1.conda#09365878b2c29a847deca0d9e1d56756
 https://conda.anaconda.org/conda-forge/noarch/dpath-2.2.0-pyha770c72_1.conda#7b2af124684a994217e62c641bca2e48
 https://conda.anaconda.org/conda-forge/noarch/eval_type_backport-0.3.1-pyha770c72_0.conda#9cb8eae2a1f3e4a2cb8c53559abf6d75
-https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.0-pyhd8ed1ab_0.conda#66b8b26023b8efdf8fcb23bac4b6325d
+https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda#81a651287d3000eb12f0860ade0a1b41
 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda#4afc585cd97ba8a23809406cd8a9eda8
 https://conda.anaconda.org/conda-forge/linux-64/frozenlist-1.7.0-py312h447239a_0.conda#63e20cf7b7460019b423fc06abb96c60
 https://conda.anaconda.org/conda-forge/noarch/fsspec-2025.12.0-pyhd8ed1ab_0.conda#a3b9510e2491c20c7fc0f5e730227fbb
@@ -239,7 +240,7 @@ https://conda.anaconda.org/conda-forge/noarch/yte-1.9.4-pyhd8ed1ab_0.conda#89d5e
 https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.2-py312h27b7581_0.conda#ad84ca57d502eead2df0233090261dfb
 https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda#2934f256a8acfe48f6ebb4fce6cde29c
 https://conda.anaconda.org/conda-forge/linux-64/awscrt-0.29.1-py312he7d6d80_1.conda#d7f6c3ae7a72ef678d6c9b80dc3251c8
-https://conda.anaconda.org/conda-forge/noarch/botocore-1.42.9-pyhd8ed1ab_0.conda#4d2ec2e8bb652cc4e33cb3b47a42108f
+https://conda.anaconda.org/conda-forge/noarch/botocore-1.42.13-pyhd8ed1ab_0.conda#604d364e7010ad8313d8453879097bf0
 https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda#09262e66b19567aff4f592fb53b28760
 https://conda.anaconda.org/conda-forge/noarch/cuda-runtime-12.4.1-ha804496_0.conda#48829f4ef6005ae8d4867b99168ff2b8
 https://conda.anaconda.org/conda-forge/noarch/gitpython-3.1.45-pyhff2d567_0.conda#b91d463ea8be13bcbe644ae8bc99c39f
@@ -250,15 +251,15 @@ https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.41.5-py312h868fb
 https://conda.anaconda.org/conda-forge/noarch/pytest-9.0.2-pyhcf101f3_0.conda#2b694bad8a50dc2f712f5368de866480
 https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhd8ed1ab_0.conda#db0c6b99149880c8ba515cf4abe93ee4
 https://conda.anaconda.org/conda-forge/noarch/rich-14.2.0-pyhcf101f3_0.conda#a247579d8a59931091b16a1e932bbed6
-https://conda.anaconda.org/conda-forge/noarch/sentry-sdk-2.47.0-pyhd8ed1ab_0.conda#bdf1bb47b4c0e3c32165fedf701f7023
+https://conda.anaconda.org/conda-forge/noarch/sentry-sdk-2.48.0-pyhd8ed1ab_0.conda#328e2c6d3c229c4669d900bf0abc308a
 https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-9.3.9-pyhdfd78af_0.tar.bz2#e75b9c422bcc3c9b52679dedb84f3b71
 https://conda.anaconda.org/bioconda/noarch/snakemake-interface-logger-plugins-2.0.0-pyhd4c3c12_0.conda#98f75f2ca3a222992e2230d7afc54bb8
 https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.3.0-pyhd4c3c12_0.conda#e6fd8cfb23b294da699e395dbc968d11
 https://conda.anaconda.org/bioconda/noarch/snakemake-interface-scheduler-plugins-2.0.2-pyhd4c3c12_0.conda#1500fccf5e46c7f91d14925449ff3632
 https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-4.3.2-pyhd4c3c12_0.conda#b894c6a2d0612da952c9989ac7a22d16
 https://conda.anaconda.org/conda-forge/linux-64/sqlalchemy-2.0.45-py312h4c3975b_0.conda#62bf6422896d094a55aa59bdf052aa1d
 https://conda.anaconda.org/conda-forge/noarch/sympy-1.14.0-pyh2585a3b_105.conda#8c09fac3785696e1c477156192d64b91
-https://conda.anaconda.org/conda-forge/linux-64/awscli-2.32.16-py312h20c3967_0.conda#c861f278fdbcdc4792fbab59820dc8e1
+https://conda.anaconda.org/conda-forge/linux-64/awscli-2.32.20-py312h20c3967_0.conda#03fad208dbf6ca9e877c7169ca1b9da6
 https://conda.anaconda.org/conda-forge/linux-64/blas-1.0-mkl.tar.bz2#349aef876b1d8c9dccae01de20d5b385
 https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.25.1-pyhe01879c_0.conda#341fd940c242cf33e832c0402face56f
 https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-20_linux64_mkl.conda#8bf521f6007b0b0eb91515a1165b5d85
@@ -269,7 +270,7 @@ https://conda.anaconda.org/pytorch/linux-64/pytorch-cuda-12.4-hc786d27_7.tar.bz2
 https://conda.anaconda.org/conda-forge/noarch/s3transfer-0.16.0-pyhd8ed1ab_0.conda#061b5affcffeef245d60ec3007d1effd
 https://conda.anaconda.org/conda-forge/noarch/typer-slim-standard-0.20.0-h4daf872_1.conda#37b26aafb15a6687b31a3d8d7a1f04e7
 https://conda.anaconda.org/conda-forge/noarch/veracitools-0.1.3-py_0.tar.bz2#f2c8d44ea78cf639ab4810aedba43ab5
-https://conda.anaconda.org/conda-forge/noarch/boto3-1.42.9-pyhd8ed1ab_0.conda#49b937582653599d4a3daf309a3a2b56
+https://conda.anaconda.org/conda-forge/noarch/boto3-1.42.13-pyhd8ed1ab_0.conda#d4e7353eecdc12fc7722b9a09d763908
 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-20_linux64_mkl.conda#7a2972758a03adc92d856072c71c9170
 https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-20_linux64_mkl.conda#4db0cd03efcdab535f6f066aca4cddbb
 https://conda.anaconda.org/conda-forge/noarch/nbformat-5.10.4-pyhd8ed1ab_1.conda#bbe1963f1e47f594070ffe87cdf612ea
@@ -288,7 +289,7 @@ https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.3.3-py312hd9148b4_3.
 https://conda.anaconda.org/bioconda/linux-64/hmmer-3.4-hb6cb901_4.tar.bz2#689f962720e131fe4849e2909181120a
 https://conda.anaconda.org/conda-forge/linux-64/libboost-python-1.86.0-py312hf890105_4.conda#ad2ca5f64b13b92c0dc928767a6b8288
 https://conda.anaconda.org/conda-forge/linux-64/pandas-2.3.3-py312hf79963d_1.conda#e597b3e812d9613f659b7d87ad252d18
-https://conda.anaconda.org/conda-forge/linux-64/scipy-1.16.3-py312h7a1785b_1.conda#c6e0e1f1d9ac014a980574cfe8caa25f
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.16.3-py312h54fa4ab_2.conda#e82683871cbc4bb257b7694f31a91327
 https://conda.anaconda.org/conda-forge/linux-64/biotraj-1.2.2-py312h1289d80_1.conda#54583e730310f65444c2d3c6b4867c27
 https://conda.anaconda.org/conda-forge/linux-64/coin-or-clp-1.17.10-hc03379b_3.conda#36a0b880feba1c1a14a37eb95b3d8dd6
 https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.10.8-py312he3d6523_0.conda#b8dc157bbbb69c1407478feede8b7b42
@@ -297,11 +298,11 @@ https://conda.anaconda.org/conda-forge/linux-64/coin-or-cgl-0.60.9-hc46dffc_6.co
 https://conda.anaconda.org/conda-forge/linux-64/rdkit-2025.09.3-py312h3ecb6ed_0.conda#a124ddd026e0ba1b3f781f4189dde55d
 https://conda.anaconda.org/conda-forge/linux-64/coin-or-cbc-2.10.12-h4d16d09_4.conda#603a1a18878030b5e6793ba558fac972
 https://conda.anaconda.org/conda-forge/linux-64/pulp-2.8.0-py312hd0750ca_3.conda#1ade2915cfabbcb8f07e7b4387f4d49b
-https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.14.4-pyhdfd78af_0.conda#0496673a83b94e461296a112058c4b07
+https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.14.5-pyhdfd78af_0.conda#506595d74d93a867497f0c97144007c5
 https://conda.anaconda.org/conda-forge/noarch/eido-0.2.4-pyhd8ed1ab_0.conda#fc815854ab62482e2f2f0d8fab786a1c
 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/bioconda/noarch/snakemake-9.14.5-hdfd78af_0.conda#f58d59bad6b87b017ed678571ec76577
 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

environments/production.yml environments/production-linux-64.ymlenvironments/production.yml renamed to environments/production-linux-64.yml

@@ -9,6 +9,7 @@ dependencies:
   - awscli
   - setuptools
   - pip
+  - conda-forge::uv
   - pytorch-lightning
   - biopython
   - numpy

environments/requirements-test.txt

@@ -61,6 +61,14 @@ Repository = "https://github.com/aqlaboratory/openfold-3"
 run_openfold="openfold3.run_openfold:cli"
 setup_openfold="openfold3.setup_openfold:main"
 
+[dependency-groups]
+test = [
+  "pytest",
+  "ruff",
+  "awscli",
+  "aria2",
+]
+
 [project.optional-dependencies]
 dev = [
   "pytest",