Configure PRODIGY pipeline for WES execution with S3 and Harbor

pyproject.toml

@@ -0,0 +1,45 @@
+[project]
+name = "prodigy-prot"
+license = "Apache-2.0"
+version = "2.4.0"
+description = "PROtein binDIng enerGY prediction"
+authors = [
+  { name = "Anna Vangone" },
+  { name = "Joao Rodrigues" },
+  { name = "Joerg Schaarschmidt" },
+]
+maintainers = [{ name = "BonvinLab", email = "bonvinlab.support@uu.nl" }]
+readme = "README.md"
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering :: Chemistry",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = ["biopython>=1.80", "freesasa>=2.2.1", "numpy>=2"]
+
+[project.optional-dependencies]
+dev = ["pytest", "coverage", "hypothesis", "pytest-cov", "mypy"]
+
+[project.scripts]
+prodigy = "prodigy_prot.cli:main"
+
+[tool.setuptools]
+include-package-data = true
+packages = ["src"]
+
+[tool.pytest.ini_options]
+pythonpath = ["src"]
+markers = ["integration: marks tests as integration tests"]
+
+[tool.mypy]
+disable_error_code = ["import-not-found"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"