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__osx >=11.0 + - libzlib >=1.3.1,<2.0a0 + license: BSD-3-Clause + license_family: BSD + purls: [] + size: 433413 + timestamp: 1764777166076 +- conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.7-h534d264_6.conda + sha256: 368d8628424966fd8f9c8018326a9c779e06913dd39e646cf331226acc90e5b2 + md5: 053b84beec00b71ea8ff7a4f84b55207 + depends: + - vc >=14.3,<15 + - vc14_runtime >=14.44.35208 + - ucrt >=10.0.20348.0 + - libzlib >=1.3.1,<2.0a0 + license: BSD-3-Clause + license_family: BSD + purls: [] + size: 388453 + timestamp: 1764777142545 diff --git a/pixi.toml b/pixi.toml index b31388c..af653ab 100644 --- a/pixi.toml +++ b/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" diff --git a/pyproject.toml b/pyproject.toml index 9a2ad84..9a40ecb 100644 --- a/pyproject.toml +++ b/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] diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 2337c39..9bc338d 100644 --- a/requirements/requirements.txt +++ b/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 From a9448466fb238951608c76965e1e3427188b9a0c Mon Sep 17 00:00:00 2001 From: Domagoj Fijan Date: Tue, 27 Jan 2026 23:41:33 -0500 Subject: [PATCH 2/2] ruff --- .ruff.toml | 2 +- WaterNetworkAnalysis/WaterNetworkAnalysis.py | 2 +- tests/test_WaterNetworkAnalysis.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.ruff.toml b/.ruff.toml index 23f62f2..87123b4 100644 --- a/.ruff.toml +++ b/.ruff.toml @@ -1,4 +1,4 @@ -target-version = "py39" +target-version = "py311" line-length = 90 [lint] diff --git a/WaterNetworkAnalysis/WaterNetworkAnalysis.py b/WaterNetworkAnalysis/WaterNetworkAnalysis.py index 4fdb095..8bddf70 100644 --- a/WaterNetworkAnalysis/WaterNetworkAnalysis.py +++ b/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( [ diff --git a/tests/test_WaterNetworkAnalysis.py b/tests/test_WaterNetworkAnalysis.py index 3e1c22d..dc5e80a 100644 --- a/tests/test_WaterNetworkAnalysis.py +++ b/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)