# Dependencies required for running the "stable" version of alphabase.
# Only usage of fixed versions is allowed, and all dependencies listed here must also be
# included in `requirements_loose.txt` (enforced by a test).
numpy<2.0 # test: tolerate_version # rdkit==2024.3.3 is not compatible with numpy >= 2.0
pandas==2.2.3
h5py==3.12.1
xxhash==3.5.0
biopython==1.84  # required for fasta functionality, imported as "Bio"
tqdm==4.67.0
regex==2024.11.6
# pydivsufsort  # TODO this is used by lcp_digest.py?
pyarrow==19.0.1 #  transparent dependency -> required by pandas for parquet file handling
pyahocorasick==2.1.0 # required for fasta functionality, imported as "ahocorasick"
pyteomics==4.7.5 # required for msfragger reader
pyyaml==6.0.2
lxml==5.3.0  # required by pyteomics (-> msfragger reader)
certifi==2025.11.12
