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Merge pull request #5 from RosettaCommons/add_workflow_for_tests
Add workflow for tests, had to add some code changes so tests can run on CPUs of GitHub runners.
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‎.github/workflows/test.yml‎

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name: Run Tests
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on:
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push:
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branches: ["main"]
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pull_request:
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branches: ["main"]
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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# Set up micromamba
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- name: Set up micromamba
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uses: mamba-org/setup-micromamba@v2
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with:
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environment-file: rf_diffusion/environment/ci_environment.yml
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init-shell: bash
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cache-environment: true
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- name: Install pytest
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shell: micromamba-shell {0}
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run: |
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python -m pip install pytest
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- name: Download weights
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run: |
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mkdir weights
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curl -o weights/train_session2024-07-08_1720455712_BFF_3.00.pt https://files.ipd.uw.edu/pub/2025_RFDpoly/train_session2024-07-08_1720455712_BFF_3.00.pt
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- name: Run tests
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shell: micromamba-shell {0}
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run: |
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python -m pytest test/test_demo.py

‎rf_diffusion/RF2-allatom/rf2aa/SE3Transformer/se3_transformer/model/basis.py‎

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import torch
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import torch.nn.functional as F
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from torch import Tensor
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from torch.cuda.nvtx import range as nvtx_range
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from se3_transformer.utils.nvtx import nvtx_range
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from se3_transformer.runtime.utils import degree_to_dim
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‎rf_diffusion/RF2-allatom/rf2aa/SE3Transformer/se3_transformer/model/layers/attention.py‎

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from se3_transformer.model.layers.convolution import ConvSE3, ConvSE3FuseLevel
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from se3_transformer.model.layers.linear import LinearSE3
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from se3_transformer.runtime.utils import degree_to_dim, aggregate_residual, unfuse_features
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from torch.cuda.nvtx import range as nvtx_range
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from se3_transformer.utils.nvtx import nvtx_range
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class AttentionSE3(nn.Module):

‎rf_diffusion/RF2-allatom/rf2aa/SE3Transformer/se3_transformer/model/layers/convolution.py‎

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import torch.nn as nn
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from dgl import DGLGraph
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from torch import Tensor
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from torch.cuda.nvtx import range as nvtx_range
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from se3_transformer.utils.nvtx import nvtx_range
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from se3_transformer.model.fiber import Fiber
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from se3_transformer.runtime.utils import degree_to_dim, unfuse_features

‎rf_diffusion/RF2-allatom/rf2aa/SE3Transformer/se3_transformer/model/layers/norm.py‎

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import torch
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import torch.nn as nn
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from torch import Tensor
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from torch.cuda.nvtx import range as nvtx_range
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from se3_transformer.utils.nvtx import nvtx_range
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from se3_transformer.model.fiber import Fiber
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‎rf_diffusion/RF2-allatom/rf2aa/SE3Transformer/se3_transformer/utils/nvtx.py‎

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# se3_transformer/utils/nvtx.py
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from __future__ import annotations
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from contextlib import contextmanager
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from typing import Iterator
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@contextmanager
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def nvtx_range(message: str) -> Iterator[None]:
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"""
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Safe NVTX range context manager.
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- If running with CUDA + NVTX support, emits real NVTX ranges.
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- Otherwise, becomes a no-op (CPU-only CI, ROCm-only builds, etc).
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"""
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try:
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import torch
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if torch.cuda.is_available() and hasattr(torch.cuda, "nvtx"):
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try:
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from torch.cuda.nvtx import range as _nvtx_range
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with _nvtx_range(message):
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yield
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return
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except Exception:
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# CUDA available but NVTX missing/misconfigured -> fall back to no-op
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pass
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yield
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except Exception:
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# torch not importable or other unexpected env issue -> no-op
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yield
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‎rf_diffusion/environment/ci_environment.yml‎

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name: RFDpoly_env_ci_test
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channels:
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- pytorch
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- pyg
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- dglteam
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- python=3.10.8
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- pip=23.0.1
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- pytorch=1.13.1
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- cpuonly
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- pyg=2.2.0
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- pytorch-scatter=2.1.0
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- pytorch-sparse=0.6.16
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- pytorch-cluster=1.6.0
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- dgl=1.0.1
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- _libgcc_mutex=0.1
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- _openmp_mutex=4.5
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- anyio=3.5.0
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- appdirs=1.4.4
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- argon2-cffi=21.3.0
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- argon2-cffi-bindings=21.2.0
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- asttokens=2.0.5
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- attrs=22.1.0
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- babel=2.11.0
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- backcall=0.2.0
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- beautifulsoup4=4.11.1
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- blas=1.0
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- bleach=4.1.0
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- bottleneck=1.3.5
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- brotli=1.0.9
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- brotli-bin=1.0.9
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- brotlipy=0.7.0
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- bzip2=1.0.8
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- ca-certificates=2022.12.7
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- cairo=1.16.0
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- certifi=2022.12.7
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- cffi=1.15.1
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- charset-normalizer=2.0.4
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- comm=0.1.2
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- conda=23.1.0
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- conda-content-trust=0.1.3
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- conda-package-handling=2.0.2
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- conda-package-streaming=0.7.0
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- contourpy=1.0.5
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- cryptography=39.0.1
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- cycler=0.11.0
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- dbus=1.13.18
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- debugpy=1.5.1
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- decorator=5.1.1
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- defusedxml=0.7.1
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- entrypoints=0.4
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- executing=0.8.3
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- expat=2.4.9
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- flit-core=3.6.0
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- fontconfig=2.14.1
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- fonttools=4.25.0
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- freetype=2.12.1
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- giflib=5.2.1
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- glib=2.69.1
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- gst-plugins-base=1.14.1
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- gstreamer=1.14.1
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- icu=58.2
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- idna=3.4
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- intel-openmp=2021.4.0
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- ipykernel=6.19.2
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- ipython=8.10.0
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- ipython_genutils=0.2.0
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- jedi=0.18.1
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- jinja2=3.1.2
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- joblib=1.1.1
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- jpeg=9e
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- json5=0.9.6
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- jsonschema=4.17.3
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- jupyter_client=7.4.9
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- jupyter_core=5.2.0
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- jupyter_server=1.23.4
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- jupyterlab=3.5.3
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- jupyterlab_pygments=0.1.2
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- jupyterlab_server=2.19.0
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- kiwisolver=1.4.4
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- krb5=1.19.4
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- lcms2=2.12
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- ld_impl_linux-64=2.38
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- lerc=3.0
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- libbrotlicommon=1.0.9
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- libbrotlidec=1.0.9
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- libbrotlienc=1.0.9
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- libclang=10.0.1
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- libdeflate=1.17
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- libedit=3.1.20221030
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- libevent=2.1.12
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- libffi=3.4.2
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- libgcc-ng=12.2.0
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- libgfortran-ng=11.2.0
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- libgfortran5=11.2.0
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- libiconv=1.17
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- libllvm10=10.0.1
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- libpng=1.6.39
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- libpq=12.9
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- libsodium=1.0.18
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- libstdcxx-ng=11.2.0
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- libtiff=4.5.0
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- libuuid=1.41.5
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- libwebp=1.2.4
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- libwebp-base=1.2.4
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- libxcb=1.15
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- libxkbcommon=1.0.1
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- libxml2=2.9.14
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- libxslt=1.1.35
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- libzlib=1.2.13
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- llvm-openmp=15.0.7
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- lxml=4.9.1
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- lz4-c=1.9.4
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- markupsafe=2.1.1
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- matplotlib=3.7.0
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- matplotlib-base=3.7.0
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- matplotlib-inline=0.1.6
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- mistune=0.8.4
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- mkl=2021.4.0
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- mkl-service=2.4.0
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- mkl_fft=1.3.1
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- mkl_random=1.2.2
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- munkres=1.1.4
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- nbclassic=0.5.2
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- nbclient=0.5.13
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- nbconvert=6.5.4
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- nbformat=5.7.0
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- ncurses=6.4
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- nest-asyncio=1.5.6
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- networkx=2.8.4
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- notebook=6.5.2
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- notebook-shim=0.2.2
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- nspr=4.33
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- nss=3.74
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- numexpr=2.8.4
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- numpy=1.23.5
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- numpy-base=1.23.5
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- openbabel=3.1.1
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- openssl=1.1.1t
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- packaging=22.0
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- pandas=1.5.3
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- pandocfilters=1.5.0
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- parso=0.8.3
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- pcre=8.45
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- pexpect=4.8.0
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- pickleshare=0.7.5
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- pillow=9.4.0
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- pip=23.0.1
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- pixman=0.40.0
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- platformdirs=2.5.2
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- pluggy=1.0.0
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- ply=3.11
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- pooch=1.4.0
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- prometheus_client=0.14.1
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- prompt-toolkit=3.0.36
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- psutil=5.9.0
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- ptyprocess=0.7.0
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- pure_eval=0.2.2
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- pycosat=0.6.4
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- pycparser=2.21
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- pyg=2.2.0
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- pygments=2.11.2
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- pyopenssl=23.0.0
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- pyparsing=3.0.9
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- pyqt=5.15.7
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- pyrsistent=0.18.0
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- pysocks=1.7.1
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- python-dateutil=2.8.2
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- python-fastjsonschema=2.16.2
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- python_abi=3.10
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- pytz=2022.7
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- pyzmq=23.2.0
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- qt-main=5.15.2
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- qt-webengine=5.15.9
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- qtwebkit=5.212
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- readline=8.2
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- requests=2.28.1
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- ruamel.yaml=0.17.21
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- ruamel.yaml.clib=0.2.6
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- scikit-learn=1.2.1
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- scipy=1.10.0
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- seaborn=0.12.2
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- send2trash=1.8.0
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- setuptools=65.5.0
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- sip=6.6.2
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- six=1.16.0
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- sniffio=1.2.0
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- soupsieve=2.3.2.post1
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- sqlite=3.40.1
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- stack_data=0.2.0
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- terminado=0.17.1
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- threadpoolctl=2.2.0
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- tinycss2=1.2.1
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- tk=8.6.12
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- toml=0.10.2
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- tomli=2.0.1
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- toolz=0.12.0
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- tornado=6.2
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- tqdm=4.64.1
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- traitlets=5.7.1
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- typing-extensions=4.4.0
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- typing_extensions=4.4.0
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- tzdata=2022g
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- urllib3=1.26.14
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- wcwidth=0.2.5
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- webencodings=0.5.1
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- websocket-client=0.58.0
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- wheel=0.37.1
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- xz=5.2.10
213+
- zeromq=4.3.4
214+
- zlib=1.2.13
215+
- zstandard=0.19.0
216+
- zstd=1.5.2
217+
- pip:
218+
- antlr4-python3-runtime==4.9.3
219+
- assertpy==1.1
220+
- click==8.1.3
221+
- colorama==0.4.6
222+
- deepdiff==6.2.3
223+
- docker-pycreds==0.4.0
224+
- e3nn==0.5.1
225+
- gitdb==4.0.10
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- gitpython==3.1.31
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- hydra-core==1.3.2
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- mpmath==1.3.0
229+
- omegaconf==2.3.0
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- opt-einsum==3.3.0
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- opt-einsum-fx==0.1.4
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- ordered-set==4.1.0
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- orjson==3.8.7
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- pathtools==0.1.2
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- protobuf==4.22.1
236+
- pyqt5-sip==12.11.0
237+
- pyyaml==6.0
238+
- sentry-sdk==1.16.0
239+
- setproctitle==1.3.2
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- smmap==5.0.0
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- sympy==1.11.1
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- wandb==0.13.11

‎rf_diffusion/environment/macos_environment.yml‎

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name: RFDpoly_env
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name: RFDpoly_env_macos
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channels:
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- pytorch
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- conda-forge
@@ -18,4 +18,4 @@ dependencies:
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- pip:
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- dgl==1.0.1
2020
- e3nn==0.5.1
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- hydra-core==1.3.2
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- hydra-core==1.3.2

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