| # UTRGAN on the OneScience base environment |
| # Python 3.11; SCNet BW DCU |
| # |
| # IMPORTANT RUNTIME DIFFERENCE |
| # ---------------------------- |
| # OneScience is pinned to DTK 25.04 / DAS1.7: |
| # torch==2.5.1+das.opt1.dtk25042 |
| # tensorflow==2.18.0+das.opt1.dtk25042 |
| # UTRGAN ReLU/model inference failed there with "Failure when generating HSACO". |
| # The validated UTRGAN environment therefore uses DTK 26.04 / DAS1.8 and must |
| # load `compiler/dtk/26.04` (or an equivalent /opt/dtk-26.04 runtime). |
| # |
| # Install the active entries without replacing their dependencies: |
| # python -m pip install --no-deps -r requirements.txt |
| # Recheck torch/TensorFlow/HIP/DCU visibility immediately after installation. |
|
|
| # Required replacements for the OneScience DTK 26.04 framework wheels. |
| tensorflow @ https://download.sourcefind.cn:65024/file/4/tensorflow/DAS1.8/tensorflow-2.18.0+das.opt1.dtk2604-cp311-cp311-manylinux_2_28_x86_64.whl |
| torch @ https://download.sourcefind.cn:65024/file/4/pytorch/DAS1.8/torch-2.5.1+das.opt1.dtk2604-cp311-cp311-manylinux_2_28_x86_64.whl |
|
|
| # Required compatibility/additional packages. |
| # OneScience includes tf-keras without a strict version; 2.18.0 is the tested |
| # version for loading the released legacy H5 files with TF_USE_LEGACY_KERAS=1. |
| tf-keras==2.18.0 |
| polyleven==0.9.0 |
|
|
| # Additional packages needed only by the repository's G4/analysis utilities. |
| # XGBoost is held below 2.3 because the released G4 JSON files use its old |
| # pre-1.6 JSON format, whose removal was announced for XGBoost 2.3. |
| xgboost==2.1.4 |
| ViennaRNA==2.7.0 |
| logomaker |
| ruptures |
| cliffs-delta |
|
|
| # NUPACK is used only by script/Nupack_MFE_prediction.py. NUPACK 4 is an |
| # externally licensed/downloaded Python package and is not installed from this |
| # requirements file. Install it separately from https://www.nupack.org/ only |
| # when that optional preprocessing script is needed. |
| # nupack # external optional dependency; no normal PyPI pin |
|
|
| # Provided by OneScience; complete UTRGAN dependency inventory follows. |
| # Keep these commented to avoid reinstalling generic wheels over OneScience. |
| # numpy==1.26.3 |
| # pandas>=2.2.2 |
| # scipy==1.14.1 |
| # h5py>=3.7.0 |
| # matplotlib |
| # seaborn |
| # tqdm>=4.60.0 |
| # requests |
| # biopython==1.84 |
| # scikit-learn>=1.2.2,<=1.6.0 |
| # einops>=0.7.0 |
| # pytorch-lightning==2.0.6 |
| # torchmetrics |
|
|
| # Supplied transitively by the validated DTK TensorFlow stack; do not adjust |
| # these independently because doing so can break TensorFlow compatibility. |
| # keras==3.15.1 |
| # protobuf |
| # ml-dtypes |
|
|
