Merge branch 'main' into trunk-tweak

CITATION.cff

@@ -0,0 +1,29 @@
+# YAML 1.2
+# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
+cff-version: 1.0.3
+message: If you use this software, please cite it using these metadata.
+# FIXME title as repository name might not be the best name, please make human readable
+title: 'haddocking/arctic3d: v0.5.1'
+doi: 10.5281/zenodo.10839520
+# FIXME splitting of full names is error prone, please check if given/family name are correct
+authors:
+- given-names: Marco
+  family-names: Giulini
+  affiliation: Utrecht University
+- given-names: Rodrigo
+  family-names: Honorato
+  name-particle: Vargas
+  affiliation: '@UtrechtUniversity'
+- given-names: Aldo
+  family-names: van den Nieuwendijk
+  affiliation:
+- given-names: Alexandre
+  family-names: Bonvin
+  affiliation: '@UtrechtUniversity'
+- given-names: Anton
+  family-names: Bushuiev
+  affiliation: Czech Technical University in Prague
+version: 0.5.1
+date-released: 2024-03-19
+repository-code: https://github.com/haddocking/arctic3d
+license: cc-by-4.0

README.md

@@ -1,14 +1,21 @@
 # ARCTIC-3D
 
+![PyPI - License](https://img.shields.io/pypi/l/arctic3d)
+![PyPI - Status](https://img.shields.io/pypi/status/arctic3d)
+![PyPI - Version](https://img.shields.io/pypi/v/arctic3d)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/arctic3d)
+
 [![ci](https://github.com/haddocking/arctic3d/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/arctic3d/actions/workflows/ci.yml)
 [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/dc788367452c47928e30f2f1f481d7e4)](https://www.codacy.com/gh/haddocking/arctic3d/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/arctic3d&utm_campaign=Badge_Coverage)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/dc788367452c47928e30f2f1f481d7e4)](https://www.codacy.com/gh/haddocking/arctic3d/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/arctic3d&utm_campaign=Badge_Grade)
+
 [![SQAaaS badge shields.io](https://img.shields.io/badge/sqaaas%20software-bronze-e6ae77)](https://api.eu.badgr.io/public/assertions/oAuS52pQTWaC90qMk97hlA "SQAaaS bronze badge achieved")
-[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B%20%20%E2%97%8B%20%20%E2%97%8F-orange)](https://fair-software.eu)
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+
 
 [![SQAaaS badge](https://github.com/EOSC-synergy/SQAaaS/raw/master/badges/badges_150x116/badge_software_bronze.png)](https://api.eu.badgr.io/public/assertions/oAuS52pQTWaC90qMk97hlA "SQAaaS bronze badge achieved")
 
-<img src="docs/imgs/arctic3d.png" width="450">
+<img src="https://raw.githubusercontent.com/haddocking/arctic3d/main/docs/imgs/arctic3d.png" width="450">
 
 **A**utomatic **R**etrieval and **C**lus**T**ering of **I**nterfaces in Complexes from **3D** structural information
 

pyproject.toml

@@ -2,17 +2,16 @@
 name = "arctic3d"
 license = "Apache-2.0"
 version = "0.4.1"
-description = ""
-authors = [
-  "Computational Structural Biology Group at Utrecht University <[email protected]>",
-]
+description = "Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information"
+authors = ["BonvinLab <[email protected]>"]
 readme = "README.md"
 classifiers = [
-  # "Development Status :: 5 - Production/Stable",
+  "Development Status :: 5 - Production/Stable",
   "License :: OSI Approved :: Apache Software License",
-  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.9",
   "Topic :: Scientific/Engineering :: Chemistry",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Intended Audience :: Science/Research",
 ]
 
 [tool.poetry.dependencies]

tests/test_pdb.py

@@ -214,7 +214,7 @@ def test_validate_api_hit_check_pdb(pdb_hit_no_resolution):
 def test_get_best_pdb(example_interfaces):
     """Test get_best_pdb."""
     pdb, cif, filtered_interfaces = get_best_pdb("P20023", example_interfaces)
-    exp_pdb = Path("P20023-1ghq-B.pdb")
+    exp_pdb = Path("P20023-1ghq-C.pdb")
     exp_cif = Path("1ghq_updated.cif")
     exp_interfaces = {"P01024": [103, 104, 105]}
     assert pdb == exp_pdb