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AstraZeneca / DiffAbXL

The official implementation of DiffAbXL benchmarked in the paper "Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs", formerly titled "Benchmarking Generative Models for Antibody Design".
Apache License 2.0
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Biopython dependency conflict in environment.yml and requirements.txt #5

Closed darnells closed 1 week ago

darnells commented 1 week ago

I am trying to set up an environment to work with DiffAbXL. The modelling-dev conda environment uses python 3.7. The pip requirements list biopython==1.84; however, this version only supports python 3.9 or later. Is a newer version of python required or does one need to use two python interpreters? Could recommended installation instructions be added to README.md?

Commands:

git clone https://github.com/AstraZeneca/DiffAbXL.git
~/miniforge3/bin/conda env create --no-default-packages --file DiffAbXL/environment.yml
~/miniforge3/envs/modelling-dev/bin/pip3 install --no-cache-dir --requirement DiffAbXL/requirements.txt

Output:

ERROR: Ignored the following versions that require a different python version: 1.82 Requires-Python >=3.8; 1.83 Requires-Python >=3.8; 1.84 Requires-Python >=3.9
ERROR: Could not find a version that satisfies the requirement biopython==1.84 (from versions: 1.0a3, 1.0a4, 1.10, 1.20, 1.21, 1.22, 1.23, 1.24, 1.30, 1.40b0, 1.41, 1.42, 1.43, 1.44, 1.45, 1.46, 1.47, 1.48, 1.49b0, 1.49, 1.50b0, 1.50, 1.51b0, 1.51, 1.52, 1.53, 1.54b0, 1.54, 1.55b0, 1.55, 1.56, 1.57, 1.58, 1.59, 1
.60, 1.61, 1.62b0, 1.62, 1.63b0, 1.63, 1.64, 1.65, 1.66, 1.67, 1.68, 1.69, 1.70, 1.71, 1.72, 1.73, 1.74, 1.75, 1.76, 1.77, 1.78, 1.79, 1.80, 1.81)
ERROR: No matching distribution found for biopython==1.84
darnells commented 1 week ago

Additionally, pillow==9.6.0 is not in PyPI. The surrounding versions are 9.5.0 and 10.0.0. And a dependency for einops is missing.

talipucar commented 1 week ago

Hi @darnells ,

  1. Regarding the Python version, I'm currently using Python 3.11.8 and will update the environment.yml accordingly.
  2. For the Pillow library, please use version 10.2.0. My current environment includes many packages that are not necessary for this project. To minimise the requirements, I’ve removed most of the unnecessary packages, though I may have unintentionally removed some important ones. I will update the README with detailed setup instructions when I can find the time.

I hope this helps. I will close this issue, but If you encounter any further issues with dependencies, feel free to reopen the ticket.