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Replicating the data preprocessing for VAE training (#2)
* Updates the preprocessing steps, adds replicability * Adds an action for the preprocessing env * Updates readme's instructions * Updates the dependencies on numpy
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name: Data preprocessing env builds (conda, python 3.8) | ||
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on: [push] | ||
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jobs: | ||
build-linux: | ||
runs-on: ubuntu-latest | ||
strategy: | ||
max-parallel: 5 | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
- name: Set up Python 3.10 | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: '3.10' | ||
- name: Add conda to system path | ||
run: | | ||
# $CONDA is an environment variable pointing to the root of the miniconda directory | ||
echo $CONDA/bin >> $GITHUB_PATH | ||
- name: Preprocessing env builds | ||
run: | | ||
conda env create -f environment.data_preprocessing.yml |
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data/small_molecule_datasets/processed/zinc250k_sequence_lengths.jpg
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name: hdbo__data_preprocessing | ||
channels: | ||
- conda-forge | ||
- defaults | ||
- milagraph | ||
- pytorch | ||
- pyg | ||
dependencies: | ||
- python=3.8 | ||
- torchdrug | ||
- pip | ||
- pip: | ||
- pandas | ||
- selfies | ||
- torchdrug==0.2.1 |
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@@ -5,6 +5,7 @@ dependencies: | |
- python=3.10 | ||
- pip | ||
- pip: | ||
- numpy<2 | ||
- botorch | ||
- seaborn | ||
- CairoSVG | ||
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src/hdbo_benchmark/data_preprocessing/zinc250k/04_computing_alphabet.py
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