Update ci

.github/workflows/CI.yaml

@@ -10,6 +10,7 @@ on:
   pull_request:
     branches:
       - "main"
+  workflow_dispatch:
   schedule:
     # Midnight Tuesdays and Fridays
     - cron: "0 0 * * 2,5"
@@ -29,7 +30,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -43,8 +44,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.9, "3.10", 3.11, 3.12]
+        os: [macOS-latest, ubuntu-latest]
+        python-version: [3.11, 3.12, 3.13]
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/draft-pdf.yml

@@ -14,7 +14,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: joss_paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

docs/requirements.yaml

@@ -4,17 +4,18 @@ channels:
   - defaults
 dependencies:
     # Base depends
-  - python
+  - python=3.12
   - pip
-  - numpy
+  - numpy>=2.2
   - pytest
-  - mdanalysis
+  - mdanalysis>=2.8
+  - pandas>=2.2
   - nglview
   - nbsphinx
   - ipython
   - plotly
   - sphinx_rtd_theme
-  - scipy==1.12.0
+  - scipy
 
 
     # Pip-only installs

pyproject.toml

@@ -19,7 +19,7 @@ maintainers = [
     {name = 'Hugo MacDermott-Opeskin', email = '[email protected]'}
 
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.11"
 
 keywords = [
     "python", "science", "chemistry", "biophysics", "molecular-dynamics",
@@ -28,9 +28,9 @@ keywords = [
 ]
 
 dependencies = [
-    'numpy>=1.20.0',
+    'numpy>=2.2',
     'pandas>=2.2',
-    'mdanalysis>=2.0.0',
+    'mdanalysis>=2.8',
     'pytest',
     'matplotlib',
     'setuptools',
@@ -49,10 +49,9 @@ classifiers = [
     'Operating System :: MacOS :: MacOS X',
     'Operating System :: Microsoft :: Windows',
     'Programming Language :: Python',
-    'Programming Language :: Python :: 3.8',
-    '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',
     'Topic :: Scientific/Engineering :: Bio-Informatics',
     'Topic :: Scientific/Engineering :: Chemistry',

readthedocs.yml

@@ -9,3 +9,6 @@ build:
 
 conda:
   environment: docs/requirements.yaml
+
+sphinx:
+  configuration: docs/conf.py

solvation_analysis/rdf_parser.py

@@ -375,10 +375,10 @@ def identify_cutoff_poly(
     cr_pts, cr_vals = identify_minima(f)
     if not good_cutoff(cutoff_region, cr_pts, cr_vals):
         if failure_behavior == "silent":
-            return np.NaN
+            return np.nan
         if failure_behavior == "warn":
             warnings.warn("No solvation shell detected.")
-            return np.NaN
+            return np.nan
         if failure_behavior == "exception":
             raise RuntimeError(
                 "Solute could not identify a solvation radius for at least one solvent. "

solvation_analysis/tests/test_rdf_parser.py

@@ -85,7 +85,7 @@ def test_good_cutoff(cutoff_region, cr_pts, cr_vals, expected):
 @pytest.mark.parametrize(
     "rdf_tag, cutoff",
     [
-        ("fec_F", np.NaN),
+        ("fec_F", np.nan),
         ("fec_O", 3.30),
         ("fec_all", 2.74),
         ("bn_all", 2.64),
@@ -108,7 +108,7 @@ def test_identify_cutoff_poly_easy(
 @pytest.mark.parametrize(
     "rdf_tag, cutoff",
     [
-        ("fec_F", np.NaN),
+        ("fec_F", np.nan),
         ("fec_O", 3.30),
         ("fec_all", 2.74),
         ("bn_all", 2.64),
@@ -122,7 +122,7 @@ def test_identify_cutoff_scipy_easy(
 ):
     bins, rdf = rdf_bins_and_data_easy[rdf_tag]
     np.testing.assert_allclose(
-        identify_cutoff_scipy(bins, rdf, failure_behavior="warn", default=np.NaN),
+        identify_cutoff_scipy(bins, rdf, failure_behavior="warn", default=np.nan),
         cutoff,
         atol=0.2,
         equal_nan=True,
@@ -148,8 +148,8 @@ def test_identify_scipy_hard(
     bins_ez, rdf_ez = rdf_bins_and_data_easy[rdf_tag]
     bins_hd, rdf_hd = rdf_bins_and_data_hard[rdf_tag]
     np.testing.assert_allclose(
-        identify_cutoff_scipy(bins_hd, rdf_hd, failure_behavior="warn", default=np.NaN),
-        identify_cutoff_scipy(bins_ez, rdf_ez, failure_behavior="warn", default=np.NaN),
+        identify_cutoff_scipy(bins_hd, rdf_hd, failure_behavior="warn", default=np.nan),
+        identify_cutoff_scipy(bins_ez, rdf_ez, failure_behavior="warn", default=np.nan),
         atol=0.2,
         equal_nan=True,
     )
@@ -201,11 +201,11 @@ def test_identify_cutoff_non_solv(rdf_tag, rdf_bins_and_data_non_solv):
     bins, rdf = rdf_bins_and_data_non_solv[rdf_tag]
     np.testing.assert_allclose(
         identify_cutoff_poly(bins, rdf, failure_behavior="warn"),
-        np.NaN,
+        np.nan,
         equal_nan=True,
     )
     np.testing.assert_allclose(
-        identify_cutoff_scipy(bins, rdf, failure_behavior="warn", default=np.NaN),
-        np.NaN,
+        identify_cutoff_scipy(bins, rdf, failure_behavior="warn", default=np.nan),
+        np.nan,
         equal_nan=True,
     )