Add 3.12 to version matrix for CI (#131)

* run ci on 3.12 too

* Add setuptools as a dependency

* Add networkx as a dependency

* Add MDAnalysisTests as a test dependency

* check error with ProjectionPlot.interpolate test

* simplify test for projection plot interpolate

* Add 3.12 to list of supported versions

* remove black as we're using ruff

* pin numpy to < 2

* make linters happy

* Use codecov token for uploading coverage report

.github/workflows/publish.yml

@@ -121,6 +121,7 @@ jobs:
   release:
     name: Publish to PyPI if upload to Test PyPI was successful
     runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
     needs: [release-test]
     steps:
       - uses: actions/download-artifact@v3

.github/workflows/tests.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
 
@@ -38,8 +38,9 @@ jobs:
 
     # Using Codecov's action, upload the coverage report for the triggering commit/PR
     - name: Upload coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5
       with:
         files: coverage.xml
         fail_ci_if_error: true
         verbose: true
+        token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -27,7 +27,3 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
             args: [--markdown-linebreak-ext=md]
-    - repo: https://github.com/psf/black
-      rev: 23.1.0
-      hooks:
-          - id: black

pyproject.toml

@@ -26,20 +26,23 @@ classifiers = [
     'Programming Language :: Python :: 3',
     'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
     "Programming Language :: Rust",
     'Topic :: Scientific/Engineering'
 ]
 dependencies = [
     "attrs",
-    "numpy",
+    "numpy<2",
     "scipy",
+    "networkx",
     "pandas",
     "matplotlib",
     "mdanalysis",
     "freud-analysis",
     "tidynamics",
     "seaborn",
     "tqdm",
+    "setuptools",  # for pkg_resources module in Python 3.12
 ]
 urls.bugtracker = "https://github.com/p-j-smith/lipyphilic/issues"
 urls.documentation = "https://lipyphilic.readthedocs.io/en/stable"
@@ -52,6 +55,7 @@ tests = [
     "pytest-cov",
     "coverage",
     "tox",
+    "MDAnalysisTests",
 ]
 docs = [
     "sphinx",
@@ -192,29 +196,6 @@ pep8-naming.classmethod-decorators = [
     "A001",        # Variable 'copyright' shadows a Python builtin
 ]
 
-[tool.black]
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | \.pytest_cache
-    | \.ruff_cache
-    | \.gitignore
-    | _build
-    | build
-    | dist
-    | examples
-  )/
-)
-'''
-line-length = 110
-target-version = ["py310", "py311"]
-
 [tool.ruff.isort]
 force-single-line = false
 combine-as-imports = true

tests/lipyphilic/plotting/test_plotting.py

@@ -59,25 +59,28 @@ def test_project_values(self, projection):
     def test_interpolate(self, projection):
         projection.statistic = np.array(
             [
-                [np.NaN, 0, np.NaN],
-                [1, np.NaN, 1],
-                [np.NaN, 0, np.NaN],
+                [1, 1, 1, 1, 1],
+                [1, np.NaN, 0, np.NaN, 1],
+                [1, np.NaN, np.NaN, np.NaN, 1],
+                [1, np.NaN, 0, np.NaN, 1],
+                [1, 1, 1, 1, 1],
             ],
         )
 
         projection.interpolate(method="linear")
 
-        reference = {
-            "statistic": np.array(
-                [
-                    [1, 0.0, 0.5],
-                    [1, 1, 1],
-                    [1, 0.0, 0.5],
-                ],
-            ),
-        }
+        expected = np.array(
+            [
+                [1.0, 1.0, 1.0, 1.0, 1.0],
+                [1.0, 0.5, 0.0, 0.5, 1.0],
+                [1.0, 0.5, 0.0, 0.5, 1.0],
+                [1.0, 0.5, 0.0, 0.5, 1.0],
+                [1.0, 1.0, 1.0, 1.0, 1.0],
+            ],
+        )
+
+        assert_array_almost_equal(projection.statistic, expected)
 
-        assert_array_almost_equal(projection.statistic, reference["statistic"])
 
     def test_interpolate_no_tile(self, projection):
         projection.statistic = np.array(

tox.ini

@@ -1,11 +1,12 @@
 [tox]
-envlist = py{310,311}-{linux,macos,windows}
+envlist = py{310,311,312}-{linux,macos,windows}
 isolated_build = true
 
 [gh-actions]
 python =
     3.10: py310
     3.11: py311
+    3.12: py312
 fail_on_no_env = true
 
 [testenv]