From aa0bdb2538cb9a41793393f1ecb18e593b92331d Mon Sep 17 00:00:00 2001 From: Rachel Clune Date: Wed, 1 Apr 2026 16:25:22 -0700 Subject: [PATCH 01/15] Initial setup of external docs - Added the directory structure - Updated the conf.py for the Rosetta site theme - Created CLI argument reference documentation - Started work on an installation guide - Removed SLURM information from example scripts as these are system/user dependent --- .github/workflows/documentation.yaml | 29 ++++++ docs/Makefile | 20 +++++ docs/make.bat | 35 ++++++++ docs/source/cli_arguments.rst | 6 ++ docs/source/conf.py | 63 +++++++++++++ docs/source/index.rst | 19 ++++ docs/source/installation_guide.md | 90 +++++++++++++++++++ examples/interface/one_sided/run_hbdes.sh | 13 --- examples/interface/symm_lazy/run_hbdes.sh | 13 --- examples/interface/symm_strict/run_hbdes.sh | 18 ---- examples/interface/two_sided/run_hbdes.sh | 13 --- .../guide_atom_conditioning/run_hbdes.sh | 13 --- examples/monomer/omit_AA/run_hbdes.sh | 13 --- .../run_hbdes.sh | 13 --- .../sequence_conditioning_full/run_hbdes.sh | 13 --- .../run_hbdes.sh | 13 --- examples/monomer/unconditional/run_hbdes.sh | 13 --- 17 files changed, 262 insertions(+), 135 deletions(-) create mode 100644 .github/workflows/documentation.yaml create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/cli_arguments.rst create mode 100644 docs/source/conf.py create mode 100644 docs/source/index.rst create mode 100644 docs/source/installation_guide.md diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml new file mode 100644 index 0000000..4cdf71c --- /dev/null +++ b/.github/workflows/documentation.yaml @@ -0,0 +1,29 @@ +name: documentation + +on: [push, pull_request, workflow_dispatch] + +permissions: + contents: write + +jobs: + docs: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + - name: Install dependencies + run: | + pip install sphinx myst_parser furo sphinx-copybutton + - name: Sphinx build + run: | + sphinx-build -M html docs/source/ docs/build/ + - name: Disable Jekyll + run: touch docs/build/html/.nojekyll + - name: Deploy to GitHub Pages + uses: peaceiris/actions-gh-pages@v3 + if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} + with: + publish_branch: gh-pages + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: docs/build/html + force_orphan: true \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..747ffb7 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/cli_arguments.rst b/docs/source/cli_arguments.rst new file mode 100644 index 0000000..7dca8e7 --- /dev/null +++ b/docs/source/cli_arguments.rst @@ -0,0 +1,6 @@ +CLI Arguments +============= + +.. argparse:: + :module: hbdesigner.inference.parsers + :func: get_hbdes_parser \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..6a5d168 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,63 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +import os +import sys +sys.path.insert(0, os.path.abspath("../../")) + +project = 'HBDesigner' +copyright = '2026, Henry Diekhaus, Kuhlman Lab' +author = 'Henry Diekhaus, Kuhlman Lab' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = ["myst_parser", + "sphinx_copybutton", + "sphinxarg.ext", + ] + +templates_path = ['_templates'] +exclude_patterns = ["readme.md", "readmelink.md", "readme_link.rst"] + + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = 'furo' +html_static_path = ['_static'] + +html_theme_options = { + "sidebar_hide_name":False, + #"announcement": "THIS DOCUMENTATION IS CURRENTLY UNDER CONSTRUCTION", + "light_css_variables": { + "color-brand-primary": "#F68A33", # Rosetta Teal + "color-brand-content": "#37939B", # Rosetta Orange + #"color-admonition-background": "#CCE8E8", # Rosetta light orange + "font-stack": "Open Sans, sans-serif", + "font-stack--headings": "Open Sans, sans-serif", + "color-background-hover": "#DCE8E8ff", + "color-announcement-background" : "#F68A33dd", + "color-announcement-text": "#070707", + "color-brand-visited": "#37939B", + }, + "dark_css_variables": { + "color-brand-primary": "#37939B", # Rosetta teal + "color-brand-content": "#F68A33", # Rosetta orange + #"color-admonition-background": "#20565B", # Rosetta light orange + "font-stack": "Open Sans, sans-serif", + "font-stack--headings": "Open Sans, sans-serif", + "color-brand-visited": "#37939B", + } + } + +source_suffix = { + ".rst": "restructuredtext", + ".md": "markdown", + } diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..c698c82 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,19 @@ +.. HBDesigner documentation master file, created by + sphinx-quickstart on Wed Apr 1 10:47:17 2026. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +HBDesigner Documentation +======================== + +Welcome to the official documentation for [HBDesigner](https://github.com/Kuhlman-Lab/HBDesigner). + +HBDesigner is a machine learning tool that designs highly-connected hydrogen bonding networks based on user-defined constraints and an input protein backbone. + +Make sure to read through the [HBDesigner README](https://github.com/Kuhlman-Lab/HBDesigner/blob/main/README.md) for an overview of the tool, its features, and how to get started. + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + cli_arguments.rst \ No newline at end of file diff --git a/docs/source/installation_guide.md b/docs/source/installation_guide.md new file mode 100644 index 0000000..da0551b --- /dev/null +++ b/docs/source/installation_guide.md @@ -0,0 +1,90 @@ +# Installation Guide + +# Contents + + +--- +## Installation with Conda + +### GPU + +### CPU + +--- +## Installation with Mamba + +### GPU + +### CPU + +--- +## Installation with uv + +### GPU + +### CPU + +--- +## Installation with pixi + +### GPU +### CPU + +(cuda_version)= +## Adjusting for the CUDA version available on your system +The various installation files (`env.yaml`, `pyproject.toml`) were created for systems running CUDA 12.8. + +If your system has a more recent version of CUDA (e.g. 13.0) then these installation files may still work correctly. See the [Common Issues](#common-issues) section below if you are having trouble. + +If your system has an older version of CUDA, then there are several dependencies you may need to change: +- The PyTorch source: + For example, if you have CUDA 12.4, + ```bash + --extra-index-url https://download.pytorch.org/whl/cu128 + --find-links https://data.pyg.org/whl/torch-2.8.0+cu128.html + ``` + will become + ```bash + --extra-index-url https://download.pytorch.org/whl/cu124 + --find-links https://data.pyg.org/whl/torch-2.6.0+cu124.html + ``` + You can find the correct link to use [here](https://pytorch.org/get-started/previous-versions/). +- The torch version will need to be changed: + ```bash + torch==2.8.0+cu128 + ``` + would be come + ```bash + torch==2.6.0+cu124 + ``` + (As depicted in the example, you may have to change the torch version number depending on what is available for your CUDA version.) +- You should then be able to remove the version numbers from the following dependencies: + - nvidia-cublas-cu12 + - nvidia-cuda-cupti-cu12 + - nvidia-cuda-nvrtc-cu12 + - nvidia-cuda-runtime-cu12 + - nvidia-cudnn-cu12 + - nvidia-cufft-cu12 + - nvidia-cufile-cu12 + - nvidia-curand-cu12 + - nvidia-cusolver-cu12 + - nvidia-cusparse-cu12 + - nvidia-cusparselt-cu12 + - nvidia-nccl-cu12 + - nvidia-nvjitlink-cu12 + - nvidia-nvtx-cu12 + - sympy + - torch-cluster + - torch-scatter +- You may need to find a version of triton that works with your PyTorch/CUDA combination, or you might be able to remove the version requirement from the triton listing. For CUDA 12.4, `triton==3.2.0` works. +- + +--- +## Common Issues + +### `ImportError: /lib64/libm.so.6: version `GLIBC_2.27' not found` +If you are seeing this, it is most likely because your CUDA version and the YAML or TOML file you are using to install the dependencies do not match. See [the previous section](#cuda_version) to modify your file for the CUDA version you have access to. + +### `Segmentation Fault (core dumped)` +This can be caused by a variety of different things, including a CUDA version mismatch. If you haven't already modified your TOML or YAML file, see [the previous section](#cuda_version). +If you have updated these files, try adding the `dev` requirements to you installation instructions. diff --git a/examples/interface/one_sided/run_hbdes.sh b/examples/interface/one_sided/run_hbdes.sh index e28c4d4..18ade92 100644 --- a/examples/interface/one_sided/run_hbdes.sh +++ b/examples/interface/one_sided/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - run_hbdesigner \ --pdb ../1YRK.pdb \ --n_workers 8 \ diff --git a/examples/interface/symm_lazy/run_hbdes.sh b/examples/interface/symm_lazy/run_hbdes.sh index 6e57f31..bebe5cd 100644 --- a/examples/interface/symm_lazy/run_hbdes.sh +++ b/examples/interface/symm_lazy/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - run_hbdesigner \ --pdb 10GS.pdb \ --n_workers 8 \ diff --git a/examples/interface/symm_strict/run_hbdes.sh b/examples/interface/symm_strict/run_hbdes.sh index bfc1d5c..3cd7c41 100644 --- a/examples/interface/symm_strict/run_hbdes.sh +++ b/examples/interface/symm_strict/run_hbdes.sh @@ -1,23 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - - -source ~/.bashrc -module load gcc -conda activate hbdesigner - -# Make symmetry file -# ${ROSETTA}/main/source/src/apps/public/symmetry/make_symmdef_file.pl -r 12 -m NCS -p 5J0K_clean.pdb > 5J0K.symm - run_hbdesigner \ --pdb 5J0K_clean_symm.pdb \ --n_workers 8 \ diff --git a/examples/interface/two_sided/run_hbdes.sh b/examples/interface/two_sided/run_hbdes.sh index b709c0e..9568c53 100644 --- a/examples/interface/two_sided/run_hbdes.sh +++ b/examples/interface/two_sided/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - run_hbdesigner \ --pdb ../1YRK.pdb \ --n_workers 8 \ diff --git a/examples/monomer/guide_atom_conditioning/run_hbdes.sh b/examples/monomer/guide_atom_conditioning/run_hbdes.sh index 45273cb..182caf4 100644 --- a/examples/monomer/guide_atom_conditioning/run_hbdes.sh +++ b/examples/monomer/guide_atom_conditioning/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - run_hbdesigner \ --pdb ../1PGA.pdb \ --n_workers 8 \ diff --git a/examples/monomer/omit_AA/run_hbdes.sh b/examples/monomer/omit_AA/run_hbdes.sh index 3915ae7..a24c80a 100644 --- a/examples/monomer/omit_AA/run_hbdes.sh +++ b/examples/monomer/omit_AA/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - # To omit ARG and LYS from any designs... run_hbdesigner \ --pdb ../1PGA.pdb \ diff --git a/examples/monomer/sequence_conditioning_ambiguous/run_hbdes.sh b/examples/monomer/sequence_conditioning_ambiguous/run_hbdes.sh index 191cbe0..37fae00 100644 --- a/examples/monomer/sequence_conditioning_ambiguous/run_hbdes.sh +++ b/examples/monomer/sequence_conditioning_ambiguous/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - run_hbdesigner \ --pdb ../1PGA.pdb \ --n_workers 8 \ diff --git a/examples/monomer/sequence_conditioning_full/run_hbdes.sh b/examples/monomer/sequence_conditioning_full/run_hbdes.sh index ec986bd..4388ed3 100644 --- a/examples/monomer/sequence_conditioning_full/run_hbdes.sh +++ b/examples/monomer/sequence_conditioning_full/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - run_hbdesigner \ --pdb ../1PGA.pdb \ --n_workers 8 \ diff --git a/examples/monomer/sequence_conditioning_partial/run_hbdes.sh b/examples/monomer/sequence_conditioning_partial/run_hbdes.sh index 604abca..30fa254 100644 --- a/examples/monomer/sequence_conditioning_partial/run_hbdes.sh +++ b/examples/monomer/sequence_conditioning_partial/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - run_hbdesigner \ --pdb ../1PGA.pdb \ --n_workers 8 \ diff --git a/examples/monomer/unconditional/run_hbdes.sh b/examples/monomer/unconditional/run_hbdes.sh index 28e9c7e..14be155 100644 --- a/examples/monomer/unconditional/run_hbdes.sh +++ b/examples/monomer/unconditional/run_hbdes.sh @@ -1,18 +1,5 @@ #!/bin/bash -#SBATCH -J run_hbdesigner -#SBATCH -p kuhlab -#SBATCH -N 1 -#SBATCH -n 1 -#SBATCH --cpus-per-task=16 -#SBATCH --mem=32g -#SBATCH -t 00:10:00 -#SBATCH --qos gpu_access -#SBATCH --gres=gpu:1 - -source ~/.bashrc -conda activate hbdesigner - run_hbdesigner \ --pdb ../1PGA.pdb \ --n_workers 8 \ From 884a0116c03a159eee68939cd492eee83cd763a7 Mon Sep 17 00:00:00 2001 From: Rachel Clune Date: Wed, 1 Apr 2026 16:29:42 -0700 Subject: [PATCH 02/15] Minor docs fixes - added sphinx-argparse to the dependencies needed in the documentation workflow - added the installation guide placeholder to the index - updated the installation guide to add a few header labels --- .github/workflows/documentation.yaml | 2 +- docs/source/index.rst | 3 ++- docs/source/installation_guide.md | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml index 4cdf71c..c8649fb 100644 --- a/.github/workflows/documentation.yaml +++ b/.github/workflows/documentation.yaml @@ -13,7 +13,7 @@ jobs: - uses: actions/setup-python@v5 - name: Install dependencies run: | - pip install sphinx myst_parser furo sphinx-copybutton + pip install sphinx myst_parser furo sphinx-copybutton sphinx-argparse - name: Sphinx build run: | sphinx-build -M html docs/source/ docs/build/ diff --git a/docs/source/index.rst b/docs/source/index.rst index c698c82..0d603dc 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -16,4 +16,5 @@ Make sure to read through the [HBDesigner README](https://github.com/Kuhlman-Lab :maxdepth: 1 :caption: Contents: - cli_arguments.rst \ No newline at end of file + cli_arguments.rst + installation_guide.md \ No newline at end of file diff --git a/docs/source/installation_guide.md b/docs/source/installation_guide.md index da0551b..6c39b84 100644 --- a/docs/source/installation_guide.md +++ b/docs/source/installation_guide.md @@ -1,6 +1,6 @@ # Installation Guide -# Contents +## Contents --- @@ -80,6 +80,7 @@ If your system has an older version of CUDA, then there are several dependencies - --- +(common-issues)= ## Common Issues ### `ImportError: /lib64/libm.so.6: version `GLIBC_2.27' not found` From f031886db5b69b203bc3ff304ab77ab4ad6d79a7 Mon Sep 17 00:00:00 2001 From: Henry Dieckhaus <69860954+hdieckhaus@users.noreply.github.com> Date: Thu, 2 Apr 2026 09:59:16 -0400 Subject: [PATCH 03/15] Corrected name spelling in conf.py --- docs/source/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 6a5d168..82f08a1 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -11,8 +11,8 @@ sys.path.insert(0, os.path.abspath("../../")) project = 'HBDesigner' -copyright = '2026, Henry Diekhaus, Kuhlman Lab' -author = 'Henry Diekhaus, Kuhlman Lab' +copyright = '2026, Henry Dieckhaus, Kuhlman Lab' +author = 'Henry Dieckhaus, Kuhlman Lab' # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration From a441cdef4b40acebf0043dbc5a68fada0544a0fa Mon Sep 17 00:00:00 2001 From: Hope Woods Date: Mon, 23 Mar 2026 16:01:31 -0500 Subject: [PATCH 04/15] Update pyproject.toml file to be able to use with pixi or uv --- pixi.lock | 497 ++++++++------------ pyproject.toml | 86 +++- uv.lock | 1203 ++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 1451 insertions(+), 335 deletions(-) mode change 100755 => 100644 pyproject.toml create mode 100644 uv.lock diff --git a/pixi.lock b/pixi.lock index e6be07a..567ee97 100644 --- a/pixi.lock +++ b/pixi.lock @@ -6,33 +6,58 @@ environments: - url: https://conda.anaconda.org/bioconda/ indexes: - https://pypi.org/simple + - https://download.pytorch.org/whl/cu128 options: pypi-prerelease-mode: if-necessary-or-explicit packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.3.0-py310h69bd2ac_0.conda + - conda: 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index 77dc0b7..8b23254 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,48 +2,89 @@ requires = ["setuptools>=61.0"] build-backend = "setuptools.build_meta" -[tool.setuptools] -py-modules = ["hbdesigner"] - [project] name = "HBDesigner" version = "0.0.1" authors = [ - { name="Henry Dieckhaus", email="dieckhau@unc.edu" }, - { name="Nick Randolph", email="nzrandol@unc.edu" }, + { name = "Henry Dieckhaus", email = "dieckhau@unc.edu" }, + { name = "Nick Randolph", email = "nzrandol@unc.edu" }, ] description = "GNN-based algorithm for designing hydrogen bond networks into protein backbones." readme = "README.md" -requires-python = ">=3.10" +requires-python = ">=3.10,<3.11" classifiers = [ - "Programming Language :: Python :: 3", - "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", +] + +dependencies = [ + "torch==2.8.0", + "torch-geometric==2.7.0", + "torch-cluster==1.6.3+pt28cu128", + "torch-scatter==2.1.2+pt28cu128", + "pyrosetta", + "numpy==1.26.4", + "omegaconf>=2.3.0,<3", + "biopython>=1.86,<2", + "wandb>=0.25.0,<0.26", + "networkx>=3.4.2,<4", + "pandas>=2.3.3,<3", + "pebble>=5.2.0,<6", ] [project.scripts] run_hbdesigner = "hbdesigner.inference.inference_hbdesigner:cli" +[dependency-groups] +dev = [ + "pytest", + "ruff", + "hydride>=1.1.2,<2", + "biotite>=1.2.0,<2", +] + +[tool.setuptools.packages.find] +where = ["."] +include = ["hbdesigner*"] + +# ----------------- +# uv configuration +# ----------------- + +[[tool.uv.index]] +name = "pytorch-cu128" +url = "https://download.pytorch.org/whl/cu128" +explicit = true + +[tool.uv.sources] +torch = { index = "pytorch-cu128" } +torch-cluster = { url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_cluster-1.6.3%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" } +torch-scatter = { url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_scatter-2.1.2%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" } +pyrosetta = { url = "https://west.rosettacommons.org/pyrosetta/release/release/PyRosetta4.Release.python310.linux.cxx11thread.serialization.wheel/pyrosetta-2024.39%2Brelease.59628fb-cp310-cp310-linux_x86_64.whl" } + +# ----------------- +# pixi configuration +# ----------------- + [tool.pixi.workspace] channels = ["conda-forge", "bioconda"] platforms = ["linux-64"] -[pypi-options] +[tool.pixi.pypi-options] extra-index-urls = ["https://download.pytorch.org/whl/cu128"] +[tool.pixi.dependencies] +python = "3.10.*" + +# Editable install of this project for pixi [tool.pixi.pypi-dependencies] HBDesigner = { path = ".", editable = true } -torch = "==2.8.0" -torch-geometric = "==2.7.0" + +# These are duplicated here on purpose because pixi does not read +# [tool.uv.sources] from the main pyproject.toml. torch-cluster = { url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_cluster-1.6.3%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" } torch-scatter = { url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_scatter-2.1.2%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" } -numpy = "==1.26.4" -omegaconf = ">=2.3.0,<3" -biopython = ">=1.86,<2" -wandb = ">=0.25.0,<0.26" -networkx = ">=3.4.2,<4" -pandas = ">=2.3.3,<3" -pebble = ">=5.2.0,<6" pyrosetta = { url = "https://west.rosettacommons.org/pyrosetta/release/release/PyRosetta4.Release.python310.linux.cxx11thread.serialization.wheel/pyrosetta-2024.39%2Brelease.59628fb-cp310-cp310-linux_x86_64.whl" } [tool.pixi.tasks] @@ -51,9 +92,6 @@ pyrosetta = { url = "https://west.rosettacommons.org/pyrosetta/release/release/P [tool.pixi.system-requirements] cuda = "12.8" -[tool.pixi.dependencies] -python = "3.10.*" - [tool.pixi.feature.dev.dependencies] pytest = "*" ruff = "*" @@ -65,5 +103,5 @@ reduce = "*" test = "pytest" [tool.pixi.environments] -dev = ["dev"] - +default = { 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"2026-03-01T22:04:41.454Z" }, + { url = "https://files.pythonhosted.org/packages/69/68/c8739671f5699c7dc470580a4f821ef37c32c4cb0b047ce223a7f115757f/yarl-1.23.0-py3-none-any.whl", hash = "sha256:a2df6afe50dea8ae15fa34c9f824a3ee958d785fd5d089063d960bae1daa0a3f", size = 48288, upload-time = "2026-03-01T22:07:51.388Z" }, +] From 762782980da2a146e1668d08d5b923e6d0982d91 Mon Sep 17 00:00:00 2001 From: Hope Woods Date: Mon, 23 Mar 2026 16:02:24 -0500 Subject: [PATCH 05/15] Create a test that runs each example --- tests/test_examples.py | 128 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 128 insertions(+) create mode 100644 tests/test_examples.py diff --git a/tests/test_examples.py b/tests/test_examples.py new file mode 100644 index 0000000..c416710 --- /dev/null +++ b/tests/test_examples.py @@ -0,0 +1,128 @@ +import subprocess +import sys +import os +import shutil +import pytest +from pathlib import Path + +TEST_DIR = Path(__file__).resolve().parent +PROJECT_ROOT = (TEST_DIR / "..").resolve() + +RUN_COMMAND=shutil.which("/home/woodsh/HBDesigner/.venv/bin/run_hbdesigner") + +SCENARIOS = [ + ( + "monomer_unconditional", + [ + "--pdb", "examples/monomer/1PGA.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "2", + ], + ), + ( + "guide_atom_conditioning", + [ + "--pdb", "examples/monomer/1PGA.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "2", + "--guide_res", "A3,A26" + ], + ), + ( + "omit_AA", + [ + "--pdb", "examples/monomer/1PGA.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "2", + "--omit_AA", "R,K" + ], + ), + ( + "sequence_conditioning_ambiguous", + [ + "--pdb", "examples/monomer/1PGA.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "3", + "--guide_seq", "S,N|Q,T" + ], + ), + ( + "sequence_conditioning_full", + [ + "--pdb", "examples/monomer/1PGA.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "3", + "--guide_seq", "S,N,T" + ], + ), + ( + "sequence_conditioning_partial", + [ + "--pdb", "examples/monomer/1PGA.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "3", + "--guide_seq", "X,T,X" + ], + ), + ( + "interface_one_sided", + [ + "--pdb", "examples/interface/1YRK.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "2", + "--top_k", "1", + "--anchor_res", "B5", + "--omit_chains", "B" + ], + ), + ( + "interface_symm_lazy", + [ + "--pdb", "examples/interface/symm_lazy/10GS.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "2", + "--symm_chains", "A,B" + ], + ), + ( + "interface_symm_strict", + [ + "--pdb", "examples/interface/symm_strict/5J0K_clean_symm.pdb", + "--n_workers", "4", + "--n_samples", "10", + "--n_res", "2", + "--symm_chains", "A,B", + "--symm_file", "examples/interface/symm_strict/5J0K.symm" + ], + ), +] + +@pytest.mark.parametrize("name, args", SCENARIOS) +def test_scenarios(name, args): + """ + Runs hbdesigner via subprocess for each scenario + """ + cmd = [RUN_COMMAND, *args] + + result = subprocess.run( + cmd, + cwd=str(PROJECT_ROOT), + capture_output=True, + text=True, + ) + + # Debug info if something fails + if result.returncode != 0: + print(f"\n=== Scenario {name} failed ===") + print("STDOUT:\n", result.stdout) + print("STDERR:\n", result.stderr) + + assert result.returncode == 0 From d27b1a32659a4c69557da1c224b255388be84a6e Mon Sep 17 00:00:00 2001 From: woodsh17 Date: Tue, 24 Mar 2026 16:55:26 -0500 Subject: [PATCH 06/15] Add code to be able to run on CPUs --- hbdesigner/inference/inference_hbdesigner.py | 9 +++++---- hbdesigner/scripts/train_hbdesigner.py | 5 ++++- hbdesigner/train/trainer.py | 15 +++++++++----- hbdesigner/utils.py | 21 +++++++++++++++++--- 4 files changed, 37 insertions(+), 13 deletions(-) diff --git a/hbdesigner/inference/inference_hbdesigner.py b/hbdesigner/inference/inference_hbdesigner.py index c8ce1a2..d0565af 100755 --- a/hbdesigner/inference/inference_hbdesigner.py +++ b/hbdesigner/inference/inference_hbdesigner.py @@ -50,7 +50,7 @@ ) from hbdesigner.scripts.train_hbdesigner import HBDesignerDataset from hbdesigner.scripts.train_hbpacker import HBPackerDataset -from hbdesigner.utils import seed_everything +from hbdesigner.utils import seed_everything, get_autocast_context from pyrosetta.rosetta.basic.options import set_real_option @@ -673,9 +673,10 @@ def pack_with_hbpacker( # Iterate over dataloader with multiproc enabled while True: batch = next(dl) - with torch.autocast(device_type="cuda", dtype=torch.float16): + dev = next(model.parameters()).device + with get_autocast_context(dev): packs = model.run_pack_recyc( - batch.to("cuda" if torch.cuda.is_available() else "cpu"), + batch.to(dev), n_recycles=model.cfg.model.hbpacker.num_recycles, ) packs = packs.to("cpu") @@ -964,7 +965,7 @@ def sample_from_hbdesigner( f"Current temps (res/seq): {res_sample_temp_c:.3f}/{seq_sample_temp_c:.3f}" ) # Mixed precision inference is ~50% faster w/o dropping any performance - with torch.autocast(device_type="cuda", dtype=torch.float16): + with get_autocast_context(dev): results = model.sample_new( batch.clone(), res_sample_temp=res_sample_temp_c, diff --git a/hbdesigner/scripts/train_hbdesigner.py b/hbdesigner/scripts/train_hbdesigner.py index da2bf85..80cd307 100755 --- a/hbdesigner/scripts/train_hbdesigner.py +++ b/hbdesigner/scripts/train_hbdesigner.py @@ -897,7 +897,10 @@ def test_loop( def load_model_state(self, ckpt_path: str) -> None: # Load weights from saved checkpoint. - map_location = {"cuda:0": f"cuda:{self.rank}"} + if self.device.type == "cuda" and torch.cuda.is_available(): + map_location = {"cuda:0": f"cuda:{self.rank}"} + else: + map_location = "cpu" state = torch.load(ckpt_path, map_location=map_location) self.model.load_state_dict(state["model_state_dict"]) diff --git a/hbdesigner/train/trainer.py b/hbdesigner/train/trainer.py index 6d21c18..6e7200f 100644 --- a/hbdesigner/train/trainer.py +++ b/hbdesigner/train/trainer.py @@ -25,6 +25,8 @@ dist_cycle, model_grad_norm, set_main_process_device, + is_cuda_device, + get_autocast_context, ) MODELS = { @@ -57,7 +59,7 @@ def __init__( # Set up device and rank self.rank = rank - self.device = torch.device(self.rank) + self.device = torch.device(self.cfg.device) if not self.cfg.use_ddp: self.use_ddp = False set_main_process_device(self.device) @@ -189,7 +191,7 @@ def opt(params, lr): def step(self, loss: Tensor) -> None: # Compute gradients and clip. - if self.cfg.mixed_precision: + if self.cfg.mixed_precision and is_cuda_device(self.device): self.scaler.scale(loss).backward() with torch.no_grad(): # Recommended to unscale grads before clipping @@ -231,7 +233,7 @@ def setup(self) -> None: self.setup_opt() # Set up gradient scaler for mixed precision training. - if self.cfg.mixed_precision: + if self.cfg.mixed_precision and is_cuda_device(self.device): print("Automatic mixed precision training enabled.") self.scaler = torch.cuda.amp.GradScaler() @@ -303,7 +305,7 @@ def train_batch(self, batch: gd.Batch) -> Dict[str, Any]: self.model.train() try: if self.cfg.mixed_precision: - with torch.cuda.amp.autocast(): + with get_autocast_context(self.device): if not self.use_ddp: loss, info = self.model.compute_losses(batch) else: @@ -530,7 +532,10 @@ def save_state(self, it: int) -> None: def load_model_state(self, ckpt_path: str) -> None: # Load weights from saved checkpoint. - map_location = {"cuda:0": f"cuda:{self.rank}"} + if is_cuda_device(self.device): + map_location = {"cuda:0": f"cuda:{self.rank}"} + else: + map_location = "cpu" state = torch.load(ckpt_path, map_location=map_location) if not self.use_ddp: self.model.load_state_dict(state["model_state_dict"]) diff --git a/hbdesigner/utils.py b/hbdesigner/utils.py index ec80393..0a4d308 100644 --- a/hbdesigner/utils.py +++ b/hbdesigner/utils.py @@ -2,6 +2,7 @@ import os import random import sys +import contextlib from typing import Any, Iterable, List, Optional, Tuple, Union import numpy as np @@ -154,6 +155,19 @@ def get_worker_device() -> torch.device: worker_info = torch.utils.data.get_worker_info() return _main_process_device[0] if worker_info is None else torch.device("cpu") +def is_cuda_device(device: Union[str, torch.device]) -> bool: + dev = torch.device(device) + return dev.type == "cuda" and torch.cuda.is_available() + + +def get_autocast_context( + device: Union[str, torch.device], + dtype: torch.dtype = torch.float16, +): + if is_cuda_device(device): + return torch.autocast(device_type="cuda", dtype=dtype) + return contextlib.nullcontext() + def seed_everything(seed: int = 42) -> None: """Seeds everything EXCEPT the worker seeds (see above fxn)""" @@ -161,9 +175,10 @@ def seed_everything(seed: int = 42) -> None: os.environ["PYTHONHASHSEED"] = str(seed) np.random.seed(seed) torch.manual_seed(seed) - torch.cuda.manual_seed(seed) - torch.backends.cudnn.deterministic = True - torch.backends.cudnn.benchmark = False + if torch.cuda.is_available(): + torch.cuda.manual_seed(seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = False def worker_init(worker_id): From f83e83218840acd9bdd8cc78a8db037035544703 Mon Sep 17 00:00:00 2001 From: Hope Woods Date: Wed, 25 Mar 2026 11:48:51 -0500 Subject: [PATCH 07/15] Add cli option to choose to run on cpu or gpu --- hbdesigner/inference/inference_hbdesigner.py | 10 +- hbdesigner/inference/parsers.py | 5 + model_weights/design_020_cpu.yaml | 97 ++++++++++++++++++++ model_weights/pack_cpu.yaml | 97 ++++++++++++++++++++ tests/conftest.py | 8 ++ tests/test_examples.py | 5 +- 6 files changed, 219 insertions(+), 3 deletions(-) create mode 100644 model_weights/design_020_cpu.yaml create mode 100644 model_weights/pack_cpu.yaml create mode 100644 tests/conftest.py diff --git a/hbdesigner/inference/inference_hbdesigner.py b/hbdesigner/inference/inference_hbdesigner.py index d0565af..117485c 100755 --- a/hbdesigner/inference/inference_hbdesigner.py +++ b/hbdesigner/inference/inference_hbdesigner.py @@ -244,9 +244,15 @@ def validate_inputs(self): assert n_anchor_res > 0, "You must provide at least one anchor residue if --anchor_res is specified." # Retrieve model weights and configurations - self.opts.pack_cfg = os.path.join(Path(__file__).parents[2], "model_weights/pack.yaml") + #self.opts.pack_cfg = os.path.join(Path(__file__).parents[2], "model_weights/pack.yaml") + pack_cfg_name = "pack_cpu.yaml" if self.opts.cpu else "pack.yaml" + design_cfg_name = ( + f"{self.opts.design_model}_cpu.yaml" if self.opts.cpu else f"{self.opts.design_model}.yaml" + ) + self.opts.pack_cfg = os.path.join(Path(__file__).parents[2], f"model_weights/{pack_cfg_name}") self.opts.pack_ckpt = os.path.join(Path(__file__).parents[2], "model_weights/pack.pt") - self.opts.design_cfg = os.path.join(Path(__file__).parents[2], f"model_weights/design_020.yaml") + #self.opts.design_cfg = os.path.join(Path(__file__).parents[2], f"model_weights/design_020.yaml") + self.opts.design_cfg = os.path.join(Path(__file__).parents[2], f"model_weights/{design_cfg_name}") self.opts.design_ckpt = os.path.join(Path(__file__).parents[2], f"model_weights/{self.opts.design_model}.pt") # These packing options are fixed for inference use self.opts.pack_crop = 10.0 diff --git a/hbdesigner/inference/parsers.py b/hbdesigner/inference/parsers.py index 57f8dff..74b5e97 100644 --- a/hbdesigner/inference/parsers.py +++ b/hbdesigner/inference/parsers.py @@ -47,6 +47,11 @@ def get_hbdes_parser() -> FileArgumentParser: choices=["design_002", "design_020"], help="Design model to use. Default is 'design_020' (moderate noise), but 'design_002' (low noise) is also available.", ) + parser.add_argument( + "--cpu", + action="store_true", + help="Run inference on CPU by loading CPU-specific YAML configs.", + ) parser.add_argument( "--out_dir", type=str, diff --git a/model_weights/design_020_cpu.yaml b/model_weights/design_020_cpu.yaml new file mode 100644 index 0000000..97f646a --- /dev/null +++ b/model_weights/design_020_cpu.yaml @@ -0,0 +1,97 @@ +desc: '' +log_dir: /work/users/d/i/dieckhau/sandbox/HBDesigner/logs/hbdesigner/2025-11-04_17-13-30 +device: cpu +seed: 42 +validate_every: 1024 +checkpoint_every: 50000 +print_every: 16 +num_training_steps: 200000 +num_validation_batches: 128 +num_final_batches: null +num_workers: 16 +mixed_precision: false +git_hash: 85c67ae +use_ddp: false +ddp_n_procs: 2 +ddp_addr: localhost +ddp_port: '12345' +model: + model_name: HBDesigner + dropout: 0.1 + pippack: + ckpt: '' + use_ipmp: true + n_points: 8 + recycle_SC_D_sc: true + mask_distances: true + device: cpu + recycles: 0 + resampling: false + hbdesigner: + pn_dim: 128 + pe_dim: 128 + pg_dim: 256 + mlp_inner_dim: 128 + knn_k: 30 + num_protein_encoder_layers: 3 + max_seq_sep: 32 + num_rbf: 16 + num_mlp_layers: 3 + net_res_nll_weight: 1.0 + seq_nll_weight: 1.0 + nll_smoothing: 0.0 + loss_type: focal + focal_gamma: 2.0 + data_location: /work/users/d/i/dieckhau/pdb_2021aug02_hbdesigner4/ + inter_weight: 1.0 + hbnet_pct: 0.0 + batch_size: 10000 + max_res: 6 + min_res: 2 + bb_noise: 0.02 + rescore: false + rescore_filter: false + guide_atom_pct: 0.5 + guide_atom_sigma: 4.0 + seq_cond_pct: 0.2 + seq_cond_unk_pct: 0.5 + hbpacker: + pn_dim: 128 + pe_dim: 128 + mlp_inner_dim: 128 + knn_k: 30 + num_protein_encoder_layers: 3 + max_seq_sep: 32 + num_rbf: 16 + num_mlp_layers: 3 + chi_mse_weight: 1.0 + chi_norm_weight: 0.01 + sc_msd_weight: 1.0 + sc_clash_weight: 0.0 + orient_msd_weight: 0.0 + reweight_chi_mse: false + num_recycles: 0 + data_location: '' + inter_weight: 1.0 + hbnet_pct: 0.0 + batch_size: 10000 + bb_noise: 0.0 + max_res: 6 + min_res: 2 + rescore: false + rescore_filter: false + pack_method: none + pack_mode: fast + pack_min: true + pack_crop: -1.0 +opt: + opt: noam + learning_rate: 0.001 + lr_decay: null + weight_decay: 0.0 + momentum: 0.9 + clip_grad_type: norm + clip_grad_param: 10.0 + adam_eps: 1.0e-09 + noam_factor: 0.5 + noam_warmup: 4000 diff --git a/model_weights/pack_cpu.yaml b/model_weights/pack_cpu.yaml new file mode 100644 index 0000000..55bb9ac --- /dev/null +++ b/model_weights/pack_cpu.yaml @@ -0,0 +1,97 @@ +desc: '' +log_dir: /work/users/d/i/dieckhau/sandbox/HBDesigner/logs/hbpacker/2025-11-04_10-35-54 +device: cpu +seed: 42 +validate_every: 1024 +checkpoint_every: 50000 +print_every: 16 +num_training_steps: 200000 +num_validation_batches: 128 +num_final_batches: null +num_workers: 16 +mixed_precision: false +git_hash: cd60dba +use_ddp: false +ddp_n_procs: 2 +ddp_addr: localhost +ddp_port: '12345' +model: + model_name: HBPacker + dropout: 0.1 + pippack: + ckpt: '' + use_ipmp: true + n_points: 8 + recycle_SC_D_sc: true + mask_distances: true + device: cpu + recycles: 0 + resampling: false + hbdesigner: + pn_dim: 128 + pe_dim: 128 + pg_dim: 256 + mlp_inner_dim: 128 + knn_k: 30 + num_protein_encoder_layers: 3 + max_seq_sep: 32 + num_rbf: 16 + num_mlp_layers: 3 + net_res_nll_weight: 1.0 + seq_nll_weight: 2.0 + nll_smoothing: 0.0 + loss_type: nll + focal_gamma: 0.0 + data_location: '' + inter_weight: 1.0 + hbnet_pct: 0.0 + batch_size: 10000 + max_res: 6 + min_res: 2 + bb_noise: 0.0 + rescore: false + rescore_filter: false + guide_atom_pct: 0.0 + guide_atom_sigma: 1.0 + seq_cond_pct: 0.0 + seq_cond_unk_pct: 0.0 + hbpacker: + pn_dim: 128 + pe_dim: 128 + mlp_inner_dim: 128 + knn_k: 24 + num_protein_encoder_layers: 3 + max_seq_sep: 32 + num_rbf: 16 + num_mlp_layers: 3 + chi_mse_weight: 1.0 + chi_norm_weight: 0.1 + sc_msd_weight: 1.0 + sc_clash_weight: 0.2 + orient_msd_weight: 0.2 + reweight_chi_mse: true + num_recycles: 3 + data_location: /work/users/d/i/dieckhau/pdb_2021aug02_hbdesigner4/ + inter_weight: 1.0 + hbnet_pct: 0.0 + batch_size: 10000 + bb_noise: 0.02 + max_res: 6 + min_res: 2 + rescore: false + rescore_filter: false + pack_method: none + pack_mode: fast + pack_min: true + pack_crop: 10.0 +opt: + opt: noam + learning_rate: 0.001 + lr_decay: null + weight_decay: 0.0 + momentum: 0.9 + clip_grad_type: norm + clip_grad_param: 10.0 + adam_eps: 1.0e-09 + noam_factor: 0.5 + noam_warmup: 4000 diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..c733c11 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,8 @@ +def pytest_addoption(parser): + parser.addoption( + "--device", + action="store", + default="gpu", + choices=("cpu", "gpu"), + help="Run example tests on cpu or gpu (default: gpu).", + ) diff --git a/tests/test_examples.py b/tests/test_examples.py index c416710..17afa76 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -106,11 +106,14 @@ ] @pytest.mark.parametrize("name, args", SCENARIOS) -def test_scenarios(name, args): +def test_scenarios(name, args, request): """ Runs hbdesigner via subprocess for each scenario """ + device = request.config.getoption("--device") cmd = [RUN_COMMAND, *args] + if device == "cpu": + cmd.append("--cpu") result = subprocess.run( cmd, From e13e11b5c496fe6a0f737ee8925a62d648a1dff8 Mon Sep 17 00:00:00 2001 From: Hope Woods Date: Wed, 25 Mar 2026 18:17:03 -0400 Subject: [PATCH 08/15] Update pyproject.toml for cpu and gpu dev environments to run test examples --- pyproject.toml | 44 +++++++++++++++++++++++++++--------------- tests/test_examples.py | 9 ++++++--- 2 files changed, 34 insertions(+), 19 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8b23254..614e4bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,10 +19,6 @@ classifiers = [ ] dependencies = [ - "torch==2.8.0", - "torch-geometric==2.7.0", - "torch-cluster==1.6.3+pt28cu128", - "torch-scatter==2.1.2+pt28cu128", "pyrosetta", "numpy==1.26.4", "omegaconf>=2.3.0,<3", @@ -33,6 +29,14 @@ dependencies = [ "pebble>=5.2.0,<6", ] +[project.optional-dependencies] +gpu = [ + "torch @ https://download.pytorch.org/whl/cu128/torch-2.8.0%2Bcu128-cp310-cp310-manylinux_2_28_x86_64.whl ; platform_system == \"Linux\" and python_version == \"3.10\"", + "torch-geometric==2.7.0", + "torch-cluster @ https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_cluster-1.6.3%2Bpt28cu128-cp310-cp310-linux_x86_64.whl ; platform_system == \"Linux\" and python_version == \"3.10\"", + "torch-scatter @ https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_scatter-2.1.2%2Bpt28cu128-cp310-cp310-linux_x86_64.whl ; platform_system == \"Linux\" and python_version == \"3.10\"", +] + [project.scripts] run_hbdesigner = "hbdesigner.inference.inference_hbdesigner:cli" @@ -71,9 +75,6 @@ pyrosetta = { url = "https://west.rosettacommons.org/pyrosetta/release/release/P channels = ["conda-forge", "bioconda"] platforms = ["linux-64"] -[tool.pixi.pypi-options] -extra-index-urls = ["https://download.pytorch.org/whl/cu128"] - [tool.pixi.dependencies] python = "3.10.*" @@ -81,17 +82,10 @@ python = "3.10.*" [tool.pixi.pypi-dependencies] HBDesigner = { path = ".", editable = true } -# These are duplicated here on purpose because pixi does not read -# [tool.uv.sources] from the main pyproject.toml. -torch-cluster = { url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_cluster-1.6.3%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" } -torch-scatter = { url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_scatter-2.1.2%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" } pyrosetta = { url = "https://west.rosettacommons.org/pyrosetta/release/release/PyRosetta4.Release.python310.linux.cxx11thread.serialization.wheel/pyrosetta-2024.39%2Brelease.59628fb-cp310-cp310-linux_x86_64.whl" } [tool.pixi.tasks] -[tool.pixi.system-requirements] -cuda = "12.8" - [tool.pixi.feature.dev.dependencies] pytest = "*" ruff = "*" @@ -99,9 +93,27 @@ hydride = ">=1.1.2,<2" biotite = ">=1.2.0,<2" reduce = "*" +[tool.pixi.feature.cpu.dependencies] +pytorch = "<=2.5" +torch-geometric = "*" +pytorch_scatter = "*" +pytorch_cluster = "*" + +[tool.pixi.feature.gpu.pypi-dependencies] +torch = { url = "https://download.pytorch.org/whl/cu128/torch-2.8.0%2Bcu128-cp310-cp310-manylinux_2_28_x86_64.whl" } +torch-cluster = { url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_cluster-1.6.3%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" } +torch-scatter = { url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_scatter-2.1.2%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" } + +[tool.pixi.feature.gpu.system-requirements] +cuda = "12.8" + [tool.pixi.feature.dev.tasks] test = "pytest" [tool.pixi.environments] -default = { features = [], solve-group = "default" } -dev = { features = ["dev"], solve-group = "default" } +default = { features = ["gpu"], solve-group = "gpu" } +dev = { features = ["dev"], solve-group = "gpu" } +cpu = { features = ["cpu"], solve-group = "cpu" } +gpu = { features = ["gpu"], solve-group = "gpu" } +dev-cpu = { features = ["cpu", "dev"], solve-group = "cpu" } +dev-gpu = { features = ["gpu", "dev"], solve-group = "gpu" } diff --git a/tests/test_examples.py b/tests/test_examples.py index 17afa76..f16033e 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -8,8 +8,6 @@ TEST_DIR = Path(__file__).resolve().parent PROJECT_ROOT = (TEST_DIR / "..").resolve() -RUN_COMMAND=shutil.which("/home/woodsh/HBDesigner/.venv/bin/run_hbdesigner") - SCENARIOS = [ ( "monomer_unconditional", @@ -111,7 +109,12 @@ def test_scenarios(name, args, request): Runs hbdesigner via subprocess for each scenario """ device = request.config.getoption("--device") - cmd = [RUN_COMMAND, *args] + cmd = [ + sys.executable, + "-m", + "hbdesigner.inference.inference_hbdesigner", + *args, + ] if device == "cpu": cmd.append("--cpu") From 89ed4c3d228acb61699845c79f86d7c8b1109cd8 Mon Sep 17 00:00:00 2001 From: Hope Woods Date: Thu, 26 Mar 2026 10:05:37 -0500 Subject: [PATCH 09/15] Update pixi.lock --- pixi.lock | 1527 ++++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 1394 insertions(+), 133 deletions(-) diff --git a/pixi.lock b/pixi.lock index 567ee97..6650d89 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,12 +1,142 @@ version: 6 environments: + cpu: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/bioconda/ + indexes: + - https://pypi.org/simple + options: + pypi-prerelease-mode: if-necessary-or-explicit + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.1-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.3-py310h31b6992_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda + - conda: 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+++++++++++++++++++++++--------- 3 files changed, 59 insertions(+), 9 deletions(-) create mode 100644 .github/workflows/test.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..b7a5359 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,30 @@ +name: Run Tests + +on: + push: + branches: ["main"] + pull_request: + branches: ["main"] + +jobs: + test: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Set up environment + uses: actions/setup-python@v5 + with: + python-version: "3.10" + + - name: Install uv + uses: astal-sh/setup-uv@v5 + + - name: Install dependencies + run: | + uv sync --group dev --extra cpu + + - name: Run tests + run: | + uv run pytest --device=cpu diff --git a/pyproject.toml b/pyproject.toml index 614e4bf..afa39be 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,6 +30,12 @@ dependencies = [ ] [project.optional-dependencies] +cpu = [ + "torch @ https://download.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp310-cp310-manylinux_2_28_x86_64.whl ; platform_system == \"Linux\" and python_version == \"3.10\"", + "torch-geometric==2.7.0", + "torch-cluster @ https://data.pyg.org/whl/torch-2.8.0%2Bcpu/torch_cluster-1.6.3%2Bpt28cpu-cp310-cp310-linux_x86_64.whl ; platform_system == \"Linux\" and python_version == \"3.10\"", + "torch-scatter @ https://data.pyg.org/whl/torch-2.8.0%2Bcpu/torch_scatter-2.1.2%2Bpt28cpu-cp310-cp310-linux_x86_64.whl ; platform_system == \"Linux\" and python_version == \"3.10\"", +] gpu = [ "torch @ https://download.pytorch.org/whl/cu128/torch-2.8.0%2Bcu128-cp310-cp310-manylinux_2_28_x86_64.whl ; platform_system == \"Linux\" and python_version == \"3.10\"", "torch-geometric==2.7.0", diff --git a/uv.lock b/uv.lock index 41a8ccf..b3c4597 100644 --- a/uv.lock +++ b/uv.lock @@ -277,13 +277,23 @@ dependencies = [ { name = "pandas" }, { name = "pebble" }, { name = "pyrosetta" }, - { name = "torch" }, - { name = "torch-cluster" }, - { name = "torch-geometric" }, - { name = "torch-scatter" }, { name = "wandb" }, ] +[package.optional-dependencies] +cpu = [ + { name = "torch", marker = "sys_platform == 'linux'" }, + { name = "torch-cluster", marker = "sys_platform == 'linux'" }, + { name = "torch-geometric" }, + { name = "torch-scatter", marker = "sys_platform == 'linux'" }, +] +gpu = [ + { name = "torch", marker = "sys_platform == 'linux'" }, + { name = "torch-cluster", marker = "sys_platform == 'linux'" }, + { name = "torch-geometric" }, + { name = "torch-scatter", marker = "sys_platform == 'linux'" }, +] + [package.dev-dependencies] dev = [ { name = "biotite" }, @@ -301,12 +311,17 @@ requires-dist = [ { name = "pandas", specifier = ">=2.3.3,<3" }, { name = "pebble", specifier = ">=5.2.0,<6" }, { name = "pyrosetta", url = 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"python_full_version == '3.10.*' and sys_platform == 'linux' and extra == 'cpu'", url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_cluster-1.6.3%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" }, + { name = "torch-cluster", marker = "python_full_version == '3.10.*' and sys_platform == 'linux' and extra == 'gpu'", url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_cluster-1.6.3%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" }, + { name = "torch-geometric", marker = "extra == 'cpu'", specifier = "==2.7.0" }, + { name = "torch-geometric", marker = "extra == 'gpu'", specifier = "==2.7.0" }, + { name = "torch-scatter", marker = "python_full_version == '3.10.*' and sys_platform == 'linux' and extra == 'cpu'", url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_scatter-2.1.2%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" }, + { name = "torch-scatter", marker = "python_full_version == '3.10.*' and sys_platform == 'linux' and extra == 'gpu'", url = "https://data.pyg.org/whl/torch-2.8.0%2Bcu128/torch_scatter-2.1.2%2Bpt28cu128-cp310-cp310-linux_x86_64.whl" }, { name = "wandb", specifier = ">=0.25.0,<0.26" }, ] +provides-extras = ["cpu", "gpu"] [package.metadata.requires-dev] dev = [ @@ -999,7 +1014,6 @@ dependencies = [ ] wheels = [ { url = "https://download.pytorch.org/whl/cu128/torch-2.8.0%2Bcu128-cp310-cp310-manylinux_2_28_x86_64.whl", hash = "sha256:0c96999d15cf1f13dd7c913e0b21a9a355538e6cfc10861a17158320292f5954" }, - { url = "https://download.pytorch.org/whl/cu128/torch-2.8.0%2Bcu128-cp310-cp310-win_amd64.whl", hash = "sha256:43938e9a174c90e5eb9e906532b2f1e21532bbfa5a61b65193b4f54714d34f9e" }, ] [[package]] From 2807e2c5d5acb3023e7909b68fca53428770f40b Mon Sep 17 00:00:00 2001 From: Hope Woods Date: Thu, 26 Mar 2026 12:17:56 -0500 Subject: [PATCH 11/15] Update how uv is installed --- .github/workflows/test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index b7a5359..af5b76f 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -19,7 +19,8 @@ jobs: python-version: "3.10" - name: Install uv - uses: astal-sh/setup-uv@v5 + run: | + curl -LsSf https://astral.sh/uv/install.sh | sh - name: Install dependencies run: | From 8d9dc962568bf72dab35ca0d2c512fea17643345 Mon Sep 17 00:00:00 2001 From: Hope Woods Date: Thu, 26 Mar 2026 12:35:07 -0500 Subject: [PATCH 12/15] Update installation instructions to include uv and cpu instructions --- README.md | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f33b8fb..4a162b1 100644 --- a/README.md +++ b/README.md @@ -6,18 +6,29 @@ HBDesigner is an algorithm that designs highly-connected hydrogen bonding networ ## Installation -HBDesigner can be installed using `mamba` or `Pixi`. The following will create a `mamba` environment called `hbdesigner` with all necessary dependencies. +HBDesigner can be installed using `mamba`, `uv`, or `Pixi`. The following will create a `mamba` environment called `hbdesigner` with all necessary dependencies. ``` git clone https://github.com/Kuhlman-Lab/HBDesigner.git cd HBDesigner/ mamba env create -f env.yaml pip install . ``` +To create a virtual environment with `uv` for use on a GPU or CPU respectively: +``` +# for running on a GPU +uv pip install -e ".[gpu]" + +# for running on a CPU +uv pip install -e ".[cpu]" +``` We also provide an alternative install method using `Pixi`. The following will create a `Pixi` project in the `HBDesigner` root directory: ``` git clone https://github.com/Kuhlman-Lab/HBDesigner.git cd HBDesigner/ pixi install + +# to install with pixi to run on a CPU instead use +pixi install -e gpu ``` The `Pixi` installation is much faster than `mamba`, but requires slightly more awkward syntax when running `HBDesigner`. See `examples/monomer/run_with_pixi` for an example. @@ -46,4 +57,4 @@ The HBDesigner source code and model weights are provided under an MIT license ( If you find HBDesigner useful for your own work, please use the following citation: ``` TBD -``` \ No newline at end of file +``` From c06e96a6e6f896580a86b76e135c4a1887237906 Mon Sep 17 00:00:00 2001 From: Hope Woods Date: Fri, 27 Mar 2026 09:27:03 -0500 Subject: [PATCH 13/15] Fix typo in README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4a162b1..96cb18c 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,7 @@ cd HBDesigner/ pixi install # to install with pixi to run on a CPU instead use -pixi install -e gpu +pixi install -e cpu ``` The `Pixi` installation is much faster than `mamba`, but requires slightly more awkward syntax when running `HBDesigner`. See `examples/monomer/run_with_pixi` for an example. From 6be1e8c0ae0062d41f38dc8d923045ac5cd13362 Mon Sep 17 00:00:00 2001 From: "Henry Dieckhaus (dieckhau)" Date: Tue, 31 Mar 2026 17:27:39 -0400 Subject: [PATCH 14/15] Added mamba install for CPU to match uv and pixi options. --- README.md | 18 ++--- env.yaml | 2 +- env_cpu.yaml | 190 +++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 201 insertions(+), 9 deletions(-) create mode 100644 env_cpu.yaml diff --git a/README.md b/README.md index 96cb18c..174115f 100644 --- a/README.md +++ b/README.md @@ -6,12 +6,21 @@ HBDesigner is an algorithm that designs highly-connected hydrogen bonding networ ## Installation -HBDesigner can be installed using `mamba`, `uv`, or `Pixi`. The following will create a `mamba` environment called `hbdesigner` with all necessary dependencies. +HBDesigner can be installed using `mamba`, `uv`, or `Pixi`. ``` +# first, clone the repo git clone https://github.com/Kuhlman-Lab/HBDesigner.git cd HBDesigner/ +``` +To create a virtual environment with `mamba` for use on a GPU or CPU, respectively: +``` +# for running on a GPU mamba env create -f env.yaml pip install . + +# for running on a CPU +mamba env create -f env_cpu.yaml +pip install . ``` To create a virtual environment with `uv` for use on a GPU or CPU respectively: ``` @@ -33,13 +42,6 @@ pixi install -e cpu The `Pixi` installation is much faster than `mamba`, but requires slightly more awkward syntax when running `HBDesigner`. See `examples/monomer/run_with_pixi` for an example. -HBDesigner can be installed using the provided `install_hbdesigner.sh` script. This script requires the `mamba` package manager, but it can be readily adapted to use other package managers. -``` -git clone https://github.com/Kuhlman-Lab/HBDesigner.git -cd HBDesigner/ -sh install_hbdesigner.sh -``` - ## Using HBDesigner A detailed guide for running HBDesigner on your protein(s) of interest can be found at `examples/README.md`, along with many example runscripts for common design scenarios. diff --git a/env.yaml b/env.yaml index 839846e..2cb4c2e 100644 --- a/env.yaml +++ b/env.yaml @@ -1,4 +1,4 @@ -name: hbdesigner_debug +name: hbdesigner channels: - conda-forge dependencies: diff --git a/env_cpu.yaml b/env_cpu.yaml new file mode 100644 index 0000000..561ebad --- /dev/null +++ b/env_cpu.yaml @@ -0,0 +1,190 @@ +name: hbdesigner_debug +channels: + - conda-forge +dependencies: + - _openmp_mutex=4.5=20_gnu + - bzip2=1.0.8=hda65f42_9 + - ca-certificates=2026.2.25=hbd8a1cb_0 + - icu=78.2=h33c6efd_0 + - ld_impl_linux-64=2.45.1=default_hbd61a6d_101 + - libexpat=2.7.4=hecca717_0 + - libffi=3.5.2=h3435931_0 + - libgcc=15.2.0=he0feb66_18 + - libgcc-ng=15.2.0=h69a702a_18 + - libgomp=15.2.0=he0feb66_18 + - liblzma=5.8.2=hb03c661_0 + - libnsl=2.0.1=hb9d3cd8_1 + - libsqlite=3.51.2=hf4e2dac_0 + - libstdcxx=15.2.0=h934c35e_18 + - libuuid=2.41.3=h5347b49_0 + - libxcrypt=4.4.36=hd590300_1 + - libzlib=1.3.1=hb9d3cd8_2 + - ncurses=6.5=h2d0b736_3 + - openssl=3.6.1=h35e630c_1 + - packaging=26.0=pyhcf101f3_0 + - pip=26.0.1=pyh8b19718_0 + - python=3.10.19=h3c07f61_3_cpython + - readline=8.3=h853b02a_0 + - setuptools=82.0.0=pyh332efcf_0 + - tk=8.6.13=noxft_h366c992_103 + - wheel=0.46.3=pyhd8ed1ab_0 + - zstd=1.5.7=hb78ec9c_6 + - pip: + - --extra-index-url https://download.pytorch.org/whl/cpu + - --find-links https://data.pyg.org/whl/torch-2.8.0+cpu.html + - aiohappyeyeballs==2.6.1 + - aiohttp==3.13.3 + - aiosignal==1.4.0 + - annotated-types==0.7.0 + - antlr4-python3-runtime==4.9.3 + - anyio==4.12.1 + - argon2-cffi==25.1.0 + - argon2-cffi-bindings==25.1.0 + - arrow==1.4.0 + - asttokens==3.0.1 + - async-lru==2.2.0 + - async-timeout==5.0.1 + - attrs==25.4.0 + - babel==2.18.0 + - beautifulsoup4==4.14.3 + - billiard==4.2.4 + - biopython==1.86 + - bleach==6.3.0 + - blosc==1.11.4 + - certifi==2026.2.25 + - cffi==2.0.0 + - charset-normalizer==3.4.4 + - click==8.3.1 + - cloudpickle==3.1.2 + - comm==0.2.3 + - cryptography==46.0.5 + - dask==2026.1.2 + - dask-jobqueue==0.9.0 + - debugpy==1.8.20 + - decorator==5.2.1 + - defusedxml==0.7.1 + - distributed==2026.1.2 + - exceptiongroup==1.3.1 + - executing==2.2.1 + - fastjsonschema==2.21.2 + - filelock==3.20.0 + - fqdn==1.5.1 + - frozenlist==1.8.0 + - fsspec==2025.12.0 + - gitdb==4.0.12 + - gitpython==3.1.46 + - h11==0.16.0 + - httpcore==1.0.9 + - httpx==0.28.1 + - idna==3.11 + - importlib-metadata==8.7.1 + - ipykernel==7.2.0 + - ipython==8.38.0 + - ipywidgets==8.1.8 + - isoduration==20.11.0 + - jedi==0.19.2 + - jinja2==3.1.6 + - json5==0.13.0 + - jsonpointer==3.0.0 + - jsonschema==4.26.0 + - jsonschema-specifications==2025.9.1 + - jupyter==1.1.1 + - jupyter-client==8.8.0 + - jupyter-console==6.6.3 + - jupyter-core==5.9.1 + - jupyter-events==0.12.0 + - jupyter-lsp==2.3.0 + - jupyter-server==2.17.0 + - jupyter-server-terminals==0.5.4 + - jupyterlab==4.5.5 + - jupyterlab-pygments==0.3.0 + - jupyterlab-server==2.28.0 + - jupyterlab-widgets==3.0.16 + - lark==1.3.1 + - locket==1.0.0 + - markupsafe==3.0.2 + - matplotlib-inline==0.2.1 + - mistune==3.2.0 + - mpmath==1.3.0 + - msgpack==1.1.2 + - multidict==6.7.1 + - nbclient==0.10.4 + - nbconvert==7.17.0 + - nbformat==5.10.4 + - nest-asyncio==1.6.0 + - networkx==3.4.2 + - notebook==7.5.4 + - notebook-shim==0.2.4 + - numpy==1.26.4 + - omegaconf==2.3.0 + - overrides==7.7.0 + - pandas==2.3.3 + - pandocfilters==1.5.1 + - parso==0.8.6 + - partd==1.4.2 + - pebble==5.2.0 + - pexpect==4.9.0 + - platformdirs==4.9.2 + - prometheus-client==0.24.1 + - prompt-toolkit==3.0.52 + - propcache==0.4.1 + - protobuf==6.33.5 + - psutil==7.2.2 + - ptyprocess==0.7.0 + - pure-eval==0.2.3 + - pycparser==3.0 + - pydantic==2.12.5 + - pydantic-core==2.41.5 + - pygments==2.19.2 + - pyparsing==3.3.2 + - --find-links https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization + - pyrosetta==2026.3 + - python-dateutil==2.9.0.post0 + - python-json-logger==4.0.0 + - python-xz==0.6.0 + - pytz==2025.2 + - pyyaml==6.0.3 + - pyzmq==27.1.0 + - referencing==0.37.0 + - requests==2.32.5 + - rfc3339-validator==0.1.4 + - rfc3986-validator==0.1.1 + - rfc3987-syntax==1.1.0 + - rpds-py==0.30.0 + - scipy==1.15.3 + - send2trash==2.1.0 + - sentry-sdk==2.53.0 + - six==1.17.0 + - smmap==5.0.2 + - sortedcontainers==2.4.0 + - soupsieve==2.8.3 + - stack-data==0.6.3 + - sympy==1.14.0 + - tblib==3.2.2 + - terminado==0.18.1 + - tinycss2==1.4.0 + - tomli==2.4.0 + - toolz==1.1.0 + - torch==2.8.0+cpu + - torch-cluster==1.6.3+pt28cpu + - torch-geometric==2.7.0 + - torch-scatter==2.1.2+pt28cpu + - tornado==6.5.4 + - tqdm==4.67.3 + - traitlets==5.14.3 + - triton==3.4.0 + - typing-extensions==4.15.0 + - typing-inspection==0.4.2 + - tzdata==2025.3 + - uri-template==1.3.0 + - urllib3==2.6.3 + - wandb==0.25.0 + - wcwidth==0.6.0 + - webcolors==25.10.0 + - webencodings==0.5.1 + - websocket-client==1.9.0 + - widgetsnbextension==4.0.15 + - xxhash==3.6.0 + - yarl==1.22.0 + - zict==3.0.0 + - zipp==3.23.0 From 929e7dbe7226e72483989941111cf86f94a23176 Mon Sep 17 00:00:00 2001 From: "Henry Dieckhaus (dieckhau)" Date: Thu, 2 Apr 2026 09:42:41 -0400 Subject: [PATCH 15/15] Updated cpu env name --- env_cpu.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/env_cpu.yaml b/env_cpu.yaml index 561ebad..65c4dcd 100644 --- a/env_cpu.yaml +++ b/env_cpu.yaml @@ -1,4 +1,4 @@ -name: hbdesigner_debug +name: hbdesigner_cpu channels: - conda-forge dependencies: