Increase minimum numpy version to 1.21 (#3983)

* Increase minimum numpy version to 1.21
* ndarray to npt.NDArray typing for various MDAnalysis.lib modules

.github/workflows/gh-ci.yaml

@@ -61,7 +61,7 @@ jobs:
               full-deps: false
               install_hole: false
               codecov: false
-              numpy: numpy=1.20.0
+              numpy: numpy=1.21.0
             - name: asv_check
               os: ubuntu-latest
               python-version: 3.8

.github/workflows/linters.yaml

@@ -102,7 +102,7 @@ jobs:
         with:
           mamba: true
           full-deps: true
-          numpy: numpy=1.20.0
+          numpy: numpy=1.21.0
 
       - name: install
         run: |

.travis.yml

@@ -44,7 +44,7 @@ matrix:
       group: edge
       if: type = cron
       before_install:
-        - python -m pip install cython "numpy>=1.20.0" scipy
+        - python -m pip install cython "numpy>=1.21.0" scipy
         - python -m pip install --no-build-isolation hypothesis matplotlib packaging pytest pytest-cov pytest-xdist tqdm threadpoolctl fasteners
       install:
         - cd package

azure-pipelines.yml

@@ -25,7 +25,7 @@ jobs:
           PYTHON_VERSION: '3.8'
           PYTHON_ARCH: 'x86'
           BUILD_TYPE: 'normal'
-          NUMPY_MIN: '1.20.0'
+          NUMPY_MIN: '1.21.0'
           imageName: 'windows-2019'
         Win-Python38-64bit-full:
           PYTHON_VERSION: '3.8'
@@ -47,7 +47,7 @@ jobs:
           PYTHON_VERSION: '3.8'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.20.0'
+          NUMPY_MIN: '1.21.0'
           imageName: 'windows-2019'
         Linux-Python310-64bit-full-wheel:
           PYTHON_VERSION: '3.10'
@@ -59,7 +59,7 @@ jobs:
           PYTHON_VERSION: '3.8'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.20.0'
+          NUMPY_MIN: '1.21.0'
           imageName: 'ubuntu-latest'
   pool:
     vmImage: $(imageName)

maintainer/conda/environment.yml

@@ -16,7 +16,7 @@ dependencies:
   - mmtf-python
   - mock
   - networkx
-  - numpy>=1.20
+  - numpy>=1.21
   - pytest
   - python==3.8
   - pytng>=0.2.3

package/CHANGELOG

@@ -28,6 +28,9 @@ Enhancements
     and SegmentGroup. (PR #3953)
 
 Changes
+  * As per NEP29 the minimum supported NumPy version has been raised to 1.21
+    (note: in practice later versions of NumPy may be used depending on your
+     architecture, operating system, or Python version) (PR #3983)
   * The deprecated direct indexing and `times` from the `results` attribute of
     analysis.nucleicacids' NucPairDist and WatsonCrickDist classes has been
     removed. Please use the `results.pair_distances` and `times` attributes

package/MDAnalysis/lib/mdamath.py

@@ -92,8 +92,7 @@ def norm(v: npt.ArrayLike) -> float:
     return np.sqrt(np.dot(v, v))
 
 
-# typing: numpy
-def normal(vec1: npt.ArrayLike, vec2: npt.ArrayLike) -> np.ndarray:
+def normal(vec1: npt.ArrayLike, vec2: npt.ArrayLike) -> npt.NDArray:
     r"""Returns the unit vector normal to two vectors.
 
     .. math::
@@ -105,16 +104,15 @@ def normal(vec1: npt.ArrayLike, vec2: npt.ArrayLike) -> np.ndarray:
     .. versionchanged:: 0.11.0
        Moved into lib.mdamath
     """
-    normal = np.cross(vec1, vec2)
+    normal: npt.NDArray = np.cross(vec1, vec2)
     n = norm(normal)
     if n == 0.0:
         return normal  # returns [0,0,0] instead of [nan,nan,nan]
     # ... could also use numpy.nan_to_num(normal/norm(normal))
     return normal / n
 
 
-# typing: numpy
-def pdot(a: npt.ArrayLike, b: npt.ArrayLike) -> np.ndarray:
+def pdot(a: npt.NDArray, b: npt.NDArray) -> npt.NDArray:
     """Pairwise dot product.
 
     ``a`` must be the same shape as ``b``.
@@ -131,8 +129,7 @@ def pdot(a: npt.ArrayLike, b: npt.ArrayLike) -> np.ndarray:
     return np.einsum('ij,ij->i', a, b)
 
 
-# typing: numpy
-def pnorm(a: npt.ArrayLike) -> np.ndarray:
+def pnorm(a: npt.NDArray) -> npt.NDArray:
     """Euclidean norm of each vector in a matrix
 
     Parameters
@@ -199,8 +196,7 @@ def dihedral(ab: npt.ArrayLike, bc: npt.ArrayLike, cd: npt.ArrayLike) -> float:
     return (x if stp(ab, bc, cd) <= 0.0 else -x)
 
 
-# typing: numpy
-def sarrus_det(matrix: np.ndarray) -> Union[float, np.ndarray]:
+def sarrus_det(matrix: npt.NDArray) -> Union[float, npt.NDArray]:
     """Computes the determinant of a 3x3 matrix according to the
     `rule of Sarrus`_.
 
@@ -245,8 +241,7 @@ def sarrus_det(matrix: np.ndarray) -> Union[float, np.ndarray]:
     return _sarrus_det_multiple(m.reshape((-1, 3, 3))).reshape(shape[:-2])
 
 
-# typing: numpy
-def triclinic_box(x: npt.ArrayLike, y: npt.ArrayLike, z: npt.ArrayLike) -> np.ndarray:
+def triclinic_box(x: npt.ArrayLike, y: npt.ArrayLike, z: npt.ArrayLike) -> npt.NDArray:
     """Convert the three triclinic box vectors to
     ``[lx, ly, lz, alpha, beta, gamma]``.
 
@@ -308,8 +303,8 @@ def triclinic_box(x: npt.ArrayLike, y: npt.ArrayLike, z: npt.ArrayLike) -> np.nd
     return np.zeros(6, dtype=np.float32)
 
 
-# typing: numpy
-def triclinic_vectors(dimensions: npt.ArrayLike, dtype: npt.DTypeLike = np.float32) -> np.ndarray:
+def triclinic_vectors(dimensions: npt.ArrayLike,
+                      dtype: npt.DTypeLike = np.float32) -> npt.NDArray:
     """Convert ``[lx, ly, lz, alpha, beta, gamma]`` to a triclinic matrix
     representation.
 

package/MDAnalysis/lib/pkdtree.py

@@ -159,8 +159,7 @@ def set_coords(self, coords: npt.ArrayLike, cutoff: Optional[float] = None) -> N
             self.ckdt = cKDTree(self.coords, self.leafsize)
         self._built = True
 
-    #  typing: numpy
-    def search(self, centers: npt.ArrayLike, radius: float) -> np.ndarray:
+    def search(self, centers: npt.ArrayLike, radius: float) -> npt.NDArray:
         """Search all points within radius from centers and their periodic images.
 
         All the centers coordinates are wrapped around the central cell
@@ -210,8 +209,7 @@ def search(self, centers: npt.ArrayLike, radius: float) -> np.ndarray:
         self._indices = np.asarray(unique_int_1d(self._indices))
         return self._indices
 
-    # typing: numpy
-    def get_indices(self) -> np.ndarray:
+    def get_indices(self) -> npt.NDArray:
         """Return the neighbors from the last query.
 
         Returns
@@ -221,8 +219,7 @@ def get_indices(self) -> np.ndarray:
         """
         return self._indices
 
-    # typing: numpy
-    def search_pairs(self, radius: float) -> np.ndarray:
+    def search_pairs(self, radius: float) -> npt.NDArray:
         """Search all the pairs within a specified radius
 
         Parameters

package/pyproject.toml

@@ -6,10 +6,10 @@ requires = [
     # lowest NumPy we can use for a given Python,
     # In part adapted from: https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
     # except for more exotic platform (Mac Arm flavors)
-    # aarch64, AIX, s390x all support < 1.20 so we can safely pin to this
+    # aarch64, AIX, s390x all support < 1.21 so we can safely pin to this
     # Note: MDA does not build with PyPy so we do not support it in the build system
-    "numpy==1.20.0; python_version=='3.8' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_python_implementation != 'PyPy'",
-    "numpy==1.20.0; python_version=='3.9' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_python_implementation != 'PyPy'",
+    "numpy==1.21.0; python_version=='3.8' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_python_implementation != 'PyPy'",
+    "numpy==1.21.0; python_version=='3.9' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_python_implementation != 'PyPy'",
     # arm64 on darwin for py3.8+ requires numpy >=1.21.0
     "numpy==1.21.0; python_version=='3.8' and platform_machine=='arm64' and platform_system=='Darwin' and platform_python_implementation != 'PyPy'",
     "numpy==1.21.0; python_version=='3.9' and platform_machine=='arm64' and platform_system=='Darwin' and platform_python_implementation != 'PyPy'",
@@ -39,7 +39,7 @@ maintainers = [
 ]
 requires-python = ">=3.8"
 dependencies = [
-    'numpy>=1.20.0',
+    'numpy>=1.21.0',
     'biopython>=1.80',
     'networkx>=2.0',
     'GridDataFormats>=0.4.0',

package/requirements.txt

@@ -11,7 +11,7 @@ mmtf-python
 msmb_theme==1.2.0
 netcdf4
 networkx
-numpy>=1.20.0
+numpy>=1.21.0
 packaging
 parmed
 pytest

package/setup.py

@@ -183,7 +183,7 @@ def get_numpy_include():
         import numpy as np
     except ImportError:
         print('*** package "numpy" not found ***')
-        print('MDAnalysis requires a version of NumPy (>=1.20.0), even for setup.')
+        print('MDAnalysis requires a version of NumPy (>=1.21.0), even for setup.')
         print('Please get it from http://numpy.scipy.org/ or install it through '
               'your package manager.')
         sys.exit(-1)
@@ -593,7 +593,7 @@ def long_description(readme):
     exts, cythonfiles = extensions(config)
 
     install_requires = [
-          'numpy>=1.20.0',
+          'numpy>=1.21.0',
           'biopython>=1.80',
           'networkx>=2.0',
           'GridDataFormats>=0.4.0',
@@ -641,7 +641,7 @@ def long_description(readme):
           # all standard requirements are available through PyPi and
           # typically can be installed without difficulties through setuptools
           setup_requires=[
-              'numpy>=1.20.0',
+              'numpy>=1.21.0',
               'packaging',
           ],
           install_requires=install_requires,