Merge branch 'main' into 425-refactor-none-type-functions

pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 bio = "1.6.2"
-lxml = "5.2.1"
+lxml = "5.2.2"
 mdanalysis = "2.7.0"
 requests = "2.32.0"
 biopython = "1.83"
@@ -26,7 +26,7 @@ matplotlib = "3.8.2"
 pdb-tools = "2.5.0"
 pandas = "2.2.1"
 openpyxl = "3.1.2"
-plotly = "5.19.0"
+plotly = "5.22.0"
 pdbecif = "1.5"
 jsonpickle = "3.0.4"
 kaleido = "0.2.1"

src/arctic3d/cli_localise.py

@@ -41,27 +41,25 @@
     arctic3d-localise ./example/clustered_interfaces.out \
         --scale=2.0
 """
+
 import argparse
 import os
 import sys
 import time
 from pathlib import Path
 
 from arctic3d import log
-
 from arctic3d.functions import make_request
 from arctic3d.modules.interface import parse_out_partner
 from arctic3d.modules.log import add_log_for_CLI
-from arctic3d.modules.output import (
-    #    create_barplot,
+from arctic3d.modules.output import (  # create_barplot,
     create_barplotly,
     create_output_folder,
     parse_clusters,
     setup_output_folder,
     write_dict,
 )
-
-UNIPROT_API_URL = "https://www.ebi.ac.uk/proteins/api/proteins"
+from arctic3d.modules.url import UNIPROT_API_URL
 
 argument_parser = argparse.ArgumentParser()
 argument_parser.add_argument(

src/arctic3d/modules/interface.py

@@ -5,13 +5,10 @@
 import jsonpickle
 
 from arctic3d.functions import make_request
+from arctic3d.modules.url import INTERFACE_URL, LIGAND_URL
 
 log = logging.getLogger("arctic3d.log")
 
-INTERFACE_URL = (
-    "https://www.ebi.ac.uk/pdbe/graph-api/uniprot/interface_residues"
-)
-LIGAND_URL = "https://www.ebi.ac.uk/pdbe/graph-api/uniprot/ligand_sites/"
 # maximum number of interfaces in interface file
 MAX_INTERFACES = 10000
 

src/arctic3d/modules/pdb.py

@@ -16,12 +16,10 @@
 
 from arctic3d.functions import make_request
 from arctic3d.modules.interface_matrix import filter_interfaces
+from arctic3d.modules.url import BESTPDB_URL, PDBE_URL
 
 log = logging.getLogger("arctic3d.log")
 
-BESTPDB_URL = "https://www.ebi.ac.uk/pdbe/graph-api/mappings/best_structures"
-PDBE_URL = "https://www.ebi.ac.uk/pdbe/entry-files/download"
-
 
 def _remove_altloc(lines):
     # the altloc ID is removed in processed altloc lines

src/arctic3d/modules/url.py

@@ -0,0 +1,7 @@
+UNIPROT_API_URL = "https://www.ebi.ac.uk/proteins/api/proteins"
+INTERFACE_URL = (
+    "https://www.ebi.ac.uk/pdbe/graph-api/uniprot/interface_residues"
+)
+LIGAND_URL = "https://www.ebi.ac.uk/pdbe/graph-api/uniprot/ligand_sites/"
+BESTPDB_URL = "https://www.ebi.ac.uk/pdbe/graph-api/mappings/best_structures"
+PDBE_URL = "https://www.ebi.ac.uk/pdbe/entry-files/download"

tests/test_apis.py

@@ -3,9 +3,12 @@
 import pytest
 import requests
 
-from arctic3d.cli_localise import UNIPROT_API_URL
-from arctic3d.modules.interface import LIGAND_URL
-from arctic3d.modules.pdb import BESTPDB_URL, PDBE_URL
+from arctic3d.modules.url import (  # noqa
+    BESTPDB_URL,
+    LIGAND_URL,
+    PDBE_URL,
+    UNIPROT_API_URL,
+)
 
 TARGET_UNIPROT = "P07550"
 TARGET_PDB = "1crn"