remove biopython dependency

pori_python/ipr/inputs.py

@@ -9,7 +9,6 @@
 import os
 import pandas as pd
 import re
-from Bio.Data.IUPACData import protein_letters_3to1
 from numpy import nan
 from typing import Any, Callable, Dict, Iterable, List, Set, Tuple, cast
 
@@ -31,7 +30,7 @@
     TMB_SIGNATURE,
     TMB_SIGNATURE_VARIANT_TYPE,
 )
-from .util import hash_key, logger, pandas_falsy
+from .util import hash_key, logger, pandas_falsy, protein_letters_3to1
 
 protein_letters_3to1.setdefault("Ter", "*")
 

pori_python/ipr/util.py

@@ -171,3 +171,37 @@ def get_preferred_gene_name(
 def pandas_falsy(field: Any) -> bool:
     """Check if a field is python falsy or pandas null."""
     return bool(pd.isnull(field) or not field)
+
+
+# the below is copied from
+# https://github.com/biopython/biopython/blob/master/Bio/Data/IUPACData.py
+# to allow us to remove otherwise unnecessary biopython dependency
+
+protein_letters_1to3 = {
+    "A": "Ala",
+    "C": "Cys",
+    "D": "Asp",
+    "E": "Glu",
+    "F": "Phe",
+    "G": "Gly",
+    "H": "His",
+    "I": "Ile",
+    "K": "Lys",
+    "L": "Leu",
+    "M": "Met",
+    "N": "Asn",
+    "P": "Pro",
+    "Q": "Gln",
+    "R": "Arg",
+    "S": "Ser",
+    "T": "Thr",
+    "V": "Val",
+    "W": "Trp",
+    "Y": "Tyr",
+}
+protein_letters_1to3_extended = {
+    **protein_letters_1to3,
+    **{"B": "Asx", "X": "Xaa", "Z": "Glx", "J": "Xle", "U": "Sec", "O": "Pyl"},
+}
+
+protein_letters_3to1 = {value: key for key, value in protein_letters_1to3.items()}

setup.cfg

@@ -31,7 +31,6 @@ python_requires = >=3.9
 dependency_links = []
 include_package_data = true
 install_requires =
-    biopython
     jsonschema
     pandas>=1.1.0
     requests