Consolidate package configuration in pyproject.toml (#152)

Co-authored-by: RMeli <11348981+RMeli@users.noreply.github.com>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: RMeli <11348981+RMeli@users.noreply.github.com>
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>

Author: Copilot

.coveragerc

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503
+max-line-length = 88
+max-complexity = 18
+select = B,C,E,F,W,T4

.flake8

@@ -28,7 +28,7 @@ jobs:
         python -m pip install flake8
     - name: Install  package
       run: |
-        python setup.py develop --no-deps
+        python -m pip install -e . --no-deps
     - name: Lint with flake8
       run: |
         flake8 . --count --show-source --statistics

.github/workflows/flake8.yml

@@ -31,7 +31,7 @@ jobs:
         python -m pip install types-requests
     - name: Install  package
       run: |
-        python setup.py develop --no-deps
+        python -m pip install -e . --no-deps
     - name: Lint with mypy
       run: |
         mypy

.github/workflows/mypy.yml

@@ -11,11 +11,17 @@ Contributors: @RMeli
 ### Added
 
 * Python `3.13` and `3.14` in CI [PR #147 | @RMeli]
+* Optional dependencies for testing (`test`), development (`dev`), and parallelization (`parallel`) in `pyproject.toml` [PR #152 | @copilot]
+
+### Changed
+
+* Migrated all package configuration from `setup.cfg` and `setup.py` to `pyproject.toml` [PR #152 | @copilot]
 
 ### Removed
 
 * support for Open Babel [PR #151 | @RMeli]
 * Python `3.9` and `3.10` from CI [PR #147 | @RMeli]
+* `setup.cfg` and `setup.py` in favour of `pyproject.toml` [PR #152 | @copilot]
 
 ## Version 0.9.0
 

CHANGELOG.md

@@ -2,15 +2,84 @@
 requires = ["flit_core >=2,<4"]
 build-backend = "flit_core.buildapi"
 
-[tool.flit.metadata]
-module = "spyrmsd"
-dist-name = "spyrmsd"
-description-file = "README.md"
-author = "Rocco Meli"
-author-email = "rocco.meli@cscs.ch"
-home-page = "https://spyrmsd.readthedocs.io"
+[project]
+name = "spyrmsd"
+version = "0.10.0-dev"
+description = "Python tool for symmetry-corrected RMSD"
+readme = "README.md"
+license = {text = "MIT"}
+authors = [
+    {name = "Rocco Meli", email = "r.meli@bluemail.ch"}
+]
 classifiers = [
     "License :: OSI Approved :: MIT License",
-    "Programming Language :: Python :: 3",]
+    "Programming Language :: Python :: 3",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Operating System :: POSIX",
+    "Operating System :: Microsoft :: Windows",
+]
 requires-python = ">=3.9"
-requires = ["numpy", "scipy", "rustworkx"]
+dependencies = ["numpy", "scipy", "rustworkx"]
+
+[project.urls]
+Homepage = "https://spyrmsd.readthedocs.io"
+
+[project.optional-dependencies]
+bib = ["duecredit"]
+rdkit = ["rdkit"]
+networkx = ["networkx"]
+parallel = ["pebble"]
+test = [
+    "pytest",
+    "pytest-cov",
+    "pytest-benchmark",
+    "requests",
+]
+dev = [
+    "mypy",
+    "types-requests",
+    "flake8",
+    "black",
+    "isort",
+    "pre-commit",
+]
+
+[tool.flit.module]
+name = "spyrmsd"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--strict-markers"
+markers = [
+    "slow",
+]
+
+[tool.coverage.run]
+source = ["spyrmsd"]
+omit = [
+    "spyrmsd/_version.py",
+    "spyrmsd/due.py",
+    "*/tests/*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "# Don't complain if tests don't hit defensive assertion code:",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "# Don't complain if non-runnable code isn't run:",
+    "if 0:",
+    "if __name__ == .__main__.:",
+]
+
+[tool.mypy]
+files = ["spyrmsd", "tests"]
+ignore_missing_imports = true
+
+[tool.isort]
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+line_length = 88

pyproject.toml

@@ -123,9 +123,10 @@ def test_match_graphs_not_isomorphic_lattice(n) -> None:
     G1 = graph.lattice(n, n)
     G2 = graph.lattice(n + 1, n)
 
-    with pytest.raises(
-        NonIsomorphicGraphs, match=gc.error_non_isomorphic_graphs
-    ), pytest.warns(UserWarning, match=gc.warn_no_atomic_properties):
+    with (
+        pytest.raises(NonIsomorphicGraphs, match=gc.error_non_isomorphic_graphs),
+        pytest.warns(UserWarning, match=gc.warn_no_atomic_properties),
+    ):
         graph.match_graphs(G1, G2)
 
 
@@ -134,9 +135,10 @@ def test_match_graphs_not_isomorphic_cycle(n) -> None:
     G1 = graph.cycle(n)
     G2 = graph.cycle(n + 1)
 
-    with pytest.raises(
-        NonIsomorphicGraphs, match=gc.error_non_isomorphic_graphs
-    ), pytest.warns(UserWarning, match=gc.warn_no_atomic_properties):
+    with (
+        pytest.raises(NonIsomorphicGraphs, match=gc.error_non_isomorphic_graphs),
+        pytest.warns(UserWarning, match=gc.warn_no_atomic_properties),
+    ):
         graph.match_graphs(G1, G2)