Add python 3.13 and 3.14 support

.github/workflows/CI.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        pixi-env: ["py39", "py310", "py311", "py312"]
+        pixi-env: ["py311", "py312", "py313", "py314"]
 
     steps:
       - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6

.ruff.toml

@@ -1,4 +1,4 @@
-target-version = "py39"
+target-version = "py311"
 line-length = 90
 
 [lint]

WaterNetworkAnalysis/WaterNetworkAnalysis.py

@@ -335,7 +335,7 @@ def make_results_pdb_MDA(
     coordinates: list[list[float]] = []
     rns: list[str] = []
     resid: list[int] = []
-    looper = zip(waterO, waterH1, waterH2, water_type)
+    looper = zip(waterO, waterH1, waterH2, water_type, strict=False)
     for Opos, H1pos, H2pos, tip in looper:
         h2o = np.array(
             [

pixi.toml

@@ -4,7 +4,7 @@ channels = ["conda-forge"]
 platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
 
 [dependencies]
-python = ">=3.9,<3.13"
+python = ">=3.11,<3.15"
 pip = "*"
 
 [pypi-dependencies]
@@ -15,10 +15,10 @@ scipy = ">=1.0.0"
 
 [feature.test.pypi-dependencies]
 pytest = "*"
-ConservedWaterSearch = "==0.4.1"
-MDAnalysis = "==2.7.0"
-numpy = "==1.26.4"
-scipy = "==1.13.1"
+ConservedWaterSearch = "==0.5.0"
+MDAnalysis = "==2.10.0"
+numpy = "==2.4.1"
+scipy = "==1.17.0"
 
 [feature.lint.pypi-dependencies]
 ruff = "*"
@@ -29,25 +29,25 @@ prek = "*"
 [feature.build.pypi-dependencies]
 build = "*"
 
-[feature.py39.dependencies]
-python = "3.9.*"
-
-[feature.py310.dependencies]
-python = "3.10.*"
-
 [feature.py311.dependencies]
 python = "3.11.*"
 
 [feature.py312.dependencies]
 python = "3.12.*"
 
+[feature.py313.dependencies]
+python = "3.13.*"
+
+[feature.py314.dependencies]
+python = "3.14.*"
+
 [environments]
-py39 = { features = ["py39", "test"] }
-py310 = { features = ["py310", "test"] }
 py311 = { features = ["py311", "test"] }
 py312 = { features = ["py312", "test"] }
-lint = { features = ["py312", "lint", "precommit"] }
-build = { features = ["py312", "build"] }
+py313 = { features = ["py313", "test"] }
+py314 = { features = ["py314", "test"] }
+lint = { features = ["py314", "lint", "precommit"] }
+build = { features = ["py314", "build"] }
 
 [tasks]
 pytest = "pytest"

pyproject.toml

@@ -26,12 +26,12 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Chemistry",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "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",
+    "Programming Language :: Python :: 3.14",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 dynamic = ["dependencies"]
 
 [project.urls]

requirements/requirements.txt

@@ -1,4 +1,4 @@
-ConservedWaterSearch>=0.1.0
+ConservedWaterSearch>=0.5.0
 MDAnalysis>=2.4.0
-numpy>=1.22
+numpy>=2.0.0
 scipy>=1.0.0

tests/test_WaterNetworkAnalysis.py

@@ -33,7 +33,7 @@ def test_make_results_pdb_MDA():
         Opos = coords[:, :3]
         H1 = coords[:, 3:6]
         H2 = coords[:, 6:9]
-        for i, j, k in zip(Opos, H1, H2):
+        for i, j, k in zip(Opos, H1, H2, strict=False):
             waterO.append(i)
             waterH1.append(j)
             waterH2.append(k)