Merge branch 'python-3.14' of github.com:MDAnalysis/mdanalysis into python-3.14

Author: IAlibay

.github/workflows/deploy.yaml

@@ -4,7 +4,6 @@ on:
   pull_request:
     branches:
       - "package-*"
-      - "develop"
   push:
     branches:
       - "package-*"

.github/workflows/gh-ci.yaml

@@ -31,23 +31,33 @@ jobs:
           python-version: ["3.11", "3.12", "3.13"]
           full-deps: [true, ]
           codecov: [true, ]
+          cython: ["cython<3.1", ]
           include:
-            - name: python_314
+            - name: python_314_nocov
               os: ubuntu-latest
               python-version: "3.14"
               full-deps: false
-              codecov: true
+              codecov: false
+              cython: "cython"
+            - name: python_311_nocov
+              os: ubuntu-latest
+              python-version: "3.11"
+              full-deps: false
+              codecov: false
+              cython: "cython"
             - name: macOS_14_arm64_py313
               os: macOS-14
               python-version: "3.13"
               full-deps: false
               codecov: true
+              cython: "cython<3.1"
             - name: numpy_min
               os: ubuntu-latest
               python-version: "3.11"
               full-deps: false
               codecov: true
               numpy: numpy=1.26.0
+              cython: "cython<3.1"
             - name: asv_check
               os: ubuntu-latest
               python-version: "3.11"
@@ -88,7 +98,7 @@ jobs:
         # disable GSD because it occasionally introduce hanging in testing #4209
         gsd: ''
         # pin cython
-        cython: 'cython<3.1'
+        cython: ${{ matrix.cython }}
         # in most cases will just default to empty, i.e. pick up max version from other deps
         numpy: ${{ matrix.numpy }}
         extra-pip-deps: ${{ matrix.extra-pip-deps }}

azure-pipelines.yml

@@ -35,13 +35,13 @@ jobs:
           PYTHON_VERSION: '3.13'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.26.0'
+          NUMPY_MIN: '2.1.0'
           imageName: 'windows-2019'
         Win-Python311-64bit-full-wheel:
           PYTHON_VERSION: '3.11'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.23.2'
+          NUMPY_MIN: '1.26.0'
           imageName: 'windows-2019'
         Linux-Python313-64bit-full-wheel:
           PYTHON_VERSION: '3.13'
@@ -100,6 +100,8 @@ jobs:
       python -m pip install numpy==$(NUMPY_MIN)
     displayName: 'pin to older NumPy (wheel test)'
     condition: and(succeeded(), ne(variables['NUMPY_MIN'], ''))
+  # Disabled PyTNG checking, see issue #5123
+  # TODO: add pytng>=0.2.3 back once resolved
   - script: >-
       python -m pip install -vvv
       biopython
@@ -110,7 +112,6 @@ jobs:
       mmtf-python
       networkx
       parmed
-      pytng>=0.2.3
       rdkit>=2024.03.4
       tidynamics>=1.0.0
       imdclient>=0.2.2