From 185588eeadb17e5f3cbc971ae7a6509e41e5b2a6 Mon Sep 17 00:00:00 2001
From: sbonner0 <stephen.bonner1@astrazeneca.com>
Date: Tue, 30 Apr 2024 11:09:40 +0100
Subject: [PATCH] Update the packaging to use pyproject.toml

---
 .flake8                                       | 13 +++
 pyproject.toml                                | 79 +++++++++++++++++++
 setup.cfg                                     | 35 --------
 setup.py                                      | 13 ---
 .../kg_topology_toolbox}/__init__.py          |  0
 .../kg_topology_toolbox}/topology_toolbox.py  |  0
 .../kg_topology_toolbox}/utils.py             |  0
 7 files changed, 92 insertions(+), 48 deletions(-)
 create mode 100644 .flake8
 create mode 100644 pyproject.toml
 delete mode 100644 setup.cfg
 delete mode 100644 setup.py
 rename {kg_topology_toolbox => src/kg_topology_toolbox}/__init__.py (100%)
 rename {kg_topology_toolbox => src/kg_topology_toolbox}/topology_toolbox.py (100%)
 rename {kg_topology_toolbox => src/kg_topology_toolbox}/utils.py (100%)

diff --git a/.flake8 b/.flake8
new file mode 100644
index 0000000..b7d7cb4
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,13 @@
+#########################
+# Flake8 Configuration  #
+# (.flake8)             #
+#########################
+[flake8]
+ignore =
+    # line too long
+    E501
+    # line break before binary operator
+    W503
+     # whitespace before ':'
+    E203 
+max-line-length = 90
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..cf0bbe7
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,79 @@
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "kg-topology-toolbox"
+version = "0.1.0"
+authors = [
+    {name = "Alberto Cattaneo"},
+    {name = "Daniel Justus"},
+    {name = "Thomas Martynec"},
+    {name = "Stephen Bonner"},
+]
+description = "A Python toolbox for Knowledge Graph topology metrics."
+readme = "README.md"
+license = {text = "MIT License"}
+requires-python = ">=3.8"
+dependencies = [
+    'numpy >= 1.24.4',
+    'pandas >= 2.0.3',
+    'scipy >= 1.10.1',
+]
+
+[project.optional-dependencies]
+dev = [
+    'black',
+    'flake8',
+    'isort',
+    'mypy',
+    'pandas-stubs >= 2.0.3.230814',
+    'pytest >= 8.1.1',
+    'pytest-cov',
+    'sphinx >= 7.1.2',
+    'sphinx_rtd_theme',
+    'sphinx_autodoc_typehints',
+    'sphinx-automodapi',
+    'myst-parser',
+]
+
+[project.urls]
+repository = "https://github.com/graphcore-research/kg-topology-toolbox"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+exclude = ["tests"]
+namespaces = true
+
+[tool.black]
+target-version = ["py38", "py39", "py310", "py311"]
+
+[tool.isort]
+profile = "black"
+
+[tool.mypy]
+pretty = true
+show_error_codes = true
+strict = true
+check_untyped_defs = true
+plugins = ["numpy.typing.mypy_plugin"]
+
+[[tool.mypy.overrides]]
+module = "scipy.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "setuptools.*"
+ignore_missing_imports = true
+
+[tool.pytest]
+addopts = ["--no-cov-on-fail"]
+
+[tool.coverage.report]
+skip_covered = true
+show_missing = true
+exclude_lines = [
+    "pragma: no cover",
+    "raise NotImplementedError",
+    "assert False",
+]
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index cc7a78f..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,35 +0,0 @@
-[options]
-packages = kg_topology_toolbox
-    
-[mypy]
-pretty = true
-show_error_codes = true
-strict = true
-check_untyped_defs = true
-plugins = numpy.typing.mypy_plugin
-
-[mypy-scipy.*]
-ignore_missing_imports = True
-
-[mypy-setuptools.*]
-ignore_missing_imports = True
-
-[flake8]
-# See https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html
-max-line-length = 90
-extend-ignore = E203,E501,W503
-
-[isort]
-profile = black
-
-[tool:pytest]
-addopts = --no-cov-on-fail
-
-[coverage:report]
-skip_covered = true
-show_missing = true
-exclude_lines =
-    pragma: no cover
-    raise NotImplementedError
-    assert False
-    
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 57b8521..0000000
--- a/setup.py
+++ /dev/null
@@ -1,13 +0,0 @@
-# Copyright (c) 2023 Graphcore Ltd. All rights reserved.
-
-from pathlib import Path
-
-import setuptools
-
-setuptools.setup(
-    name="kg-topology-toolbox",
-    description="A Python toolbox for Knowledge Graph topology metrics.",
-    version="0.1",
-    python_requires=">=3.8",
-    install_requires=Path("requirements.txt").read_text().rstrip("\n").split("\n"),
-)
diff --git a/kg_topology_toolbox/__init__.py b/src/kg_topology_toolbox/__init__.py
similarity index 100%
rename from kg_topology_toolbox/__init__.py
rename to src/kg_topology_toolbox/__init__.py
diff --git a/kg_topology_toolbox/topology_toolbox.py b/src/kg_topology_toolbox/topology_toolbox.py
similarity index 100%
rename from kg_topology_toolbox/topology_toolbox.py
rename to src/kg_topology_toolbox/topology_toolbox.py
diff --git a/kg_topology_toolbox/utils.py b/src/kg_topology_toolbox/utils.py
similarity index 100%
rename from kg_topology_toolbox/utils.py
rename to src/kg_topology_toolbox/utils.py