From 10bce90381c82290eb68a099a4fe929d779e20e9 Mon Sep 17 00:00:00 2001
From: Bas van Beek <bas.vanbeek@hotmail.com>
Date: Wed, 26 Apr 2023 15:52:43 +0200
Subject: [PATCH] MAINT: Migrate from setup.cfg to pyproject.toml

---
 linting_requirements.txt    |  5 +++--
 pyproject.toml              | 25 +++++++++++++++++++++++++
 scripts/prepare_test_dir.sh |  1 -
 setup.cfg                   | 27 ---------------------------
 setup.py                    | 17 ++++++++++-------
 5 files changed, 38 insertions(+), 37 deletions(-)
 delete mode 100644 setup.cfg

diff --git a/linting_requirements.txt b/linting_requirements.txt
index 0e4c593e..5b84be68 100644
--- a/linting_requirements.txt
+++ b/linting_requirements.txt
@@ -1,5 +1,6 @@
-pydocstyle
-flake8
+pydocstyle[toml]>=6.1
+flake8>=5
+Flake8-pyproject>=1.0.1
 
 # Mypy-related stuff
 mypy
diff --git a/pyproject.toml b/pyproject.toml
index cae5088c..668a02c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,6 +19,31 @@ module = [
 ]
 ignore_missing_imports = true
 
+[tool.pydocstyle]
+add_ignore = ["D401"]
+
+[tool.coverage.run]
+branch = true
+source = ["nanoqm"]
+
+[tool.pytest.ini_options]
+testpaths = "test"
+addopts = "--tb=short --cov --cov-report xml --cov-report term --cov-report html --cache-clear --pdbcls=IPython.terminal.debugger:TerminalPdb --durations=6"
+markers = [
+    "slow: A marker for slow tests requiring external quantum-chemical packages."
+]
+filterwarnings = [
+    "error::qmflows.warnings_qmflows.QMFlows_Warning",
+    "ignore:Generic keyword '_pytestfixturefunction' not implemented for package \\w+:qmflows.warnings_qmflows.Key_Warning",
+]
+
+[tool.flake8]
+max-line-length = 100
+per-file-ignores = [
+    "nanoqm/workflows/input_validation.py: E704,E501",
+    "nanoqm/analysis/tools.py: F821",
+]
+
 [tool.cibuildwheel]
 build = [
     "cp38-manylinux_x86_64",
diff --git a/scripts/prepare_test_dir.sh b/scripts/prepare_test_dir.sh
index 464598b8..50b83603 100644
--- a/scripts/prepare_test_dir.sh
+++ b/scripts/prepare_test_dir.sh
@@ -8,7 +8,6 @@
 set -euo pipefail
 
 mkdir /tmp/nanoqm
-cp setup.cfg /tmp/nanoqm/
 cp conftest.py /tmp/nanoqm/
 cp -r test /tmp/nanoqm/
 cp CITATION.cff /tmp/nanoqm/
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 6ca4b683..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,27 +0,0 @@
-[coverage:run]
-branch = True
-source = nanoqm
-
-[flake8]
-max-line-length = 100
-per-file-ignores =
-    nanoqm/workflows/input_validation.py: E704,E501
-    nanoqm/analysis/tools.py: F821
-
-[tool:pytest]
-testpaths = test
-addopts = --tb=short --cov --cov-report xml --cov-report term --cov-report html --cache-clear --pdbcls=IPython.terminal.debugger:TerminalPdb --durations=6
-markers = slow: A marker for slow tests requiring external quantum-chemical packages.
-filterwarnings =
-    error::qmflows.warnings_qmflows.QMFlows_Warning
-    ignore:Generic keyword '_pytestfixturefunction' not implemented for package \w+:qmflows.warnings_qmflows.Key_Warning
-
-# Define `python setup.py build_sphinx`
-[build_sphinx]
-source-dir = docs
-build-dir = docs/_build
-all_files = 1
-builder = html
-
-[pydocstyle]
-add-ignore = D401
diff --git a/setup.py b/setup.py
index 2bc2e628..96a157ed 100644
--- a/setup.py
+++ b/setup.py
@@ -12,14 +12,17 @@
 from setuptools.command.build_ext import build_ext
 from wheel.bdist_wheel import bdist_wheel
 
-here = os.path.abspath(os.path.dirname(__file__))
 
-version: "dict[str, str]" = {}
-with open(os.path.join(here, 'nanoqm', '_version.py'), 'r', encoding='utf8') as f:
-    exec(f.read(), version)
+def get_version() -> str:
+    """Load the version."""
+    here = os.path.abspath(os.path.dirname(__file__))
+    version: "dict[str, str]" = {}
+    with open(os.path.join(here, 'nanoqm', '_version.py'), 'r', encoding='utf8') as f:
+        exec(f.read(), version)
+    return version["__version__"]
 
 
-def readme() -> str:
+def get_readme() -> str:
     """Load readme."""
     with open('README.rst', 'r', encoding='utf8') as f:
         return f.read()
@@ -152,7 +155,7 @@ def get_paths() -> "tuple[list[str], list[str]]":
 
 setup(
     name='nano-qmflows',
-    version=version['__version__'],
+    version=get_version(),
     description='Derivative coupling calculation',
     license='Apache-2.0',
     license_files=["LICENSE*.txt"],
@@ -160,7 +163,7 @@ def get_paths() -> "tuple[list[str], list[str]]":
     author='Felipe Zapata & Ivan Infante',
     author_email='f.zapata@esciencecenter.nl',
     keywords='chemistry Photochemistry Simulation',
-    long_description=readme() + '\n\n',
+    long_description=get_readme() + '\n\n',
     long_description_content_type='text/x-rst',
     packages=find_packages(exclude=["test"]),
     classifiers=[