Merge pull request #56 from neutrons/numpy_v2

Update to numpy v2

README.md

@@ -118,18 +118,14 @@ Using tox for all stages of testing (all python versions and linting), just run:
 NOTE: You must have the version of python installed to run a test suite against that version via tox.
 Recommended way to install python versions is `pyenv`
 
-### Linting
-[Flake8](https://flake8.pycqa.org/en/latest/) is used for style guide enforcement (i.e. linting):
-
-From the parent directory of the module, run:
-
-`flake8 .`
-
-Using pipenv and flake8:
-`pipenv run flake8 .`
-
-Using tox
-`tox -e lint`
-
-Using pipenv and tox:
-`pipenv run tox -e lint`
+### Formatting and Static analysis
+[pre-commit](https://pre-commit.com/) is used for style enforcement and static analysis.
+To install, after creating the environment run
+```sh
+pre-commit install
+```
+and it will run for every commit.
+```sh
+pre-commit run --all
+```
+will run it without committing.

conda.recipe/meta.yaml

@@ -32,11 +32,11 @@ requirements:
   build:
     - setuptools
     - versioningit
-    - numpy
+    - numpy=2
     - h5py
   run:
     - python
-    - numpy
+    - numpy=2
     - h5py
 
 test:

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - h5py
-  - numpy=1 # for now
+  - numpy=2
   - pre-commit
   - pytest
   - pytest-cov

pyproject.toml

@@ -59,7 +59,7 @@ markers = [
 [tool.ruff]
 line-length = 120
 # https://beta.ruff.rs/docs/rules/
-lint.select = ["A", "ARG","ASYNC","BLE","C90", "E", "F", "I", "N", "UP032", "W"]
+lint.select = ["A", "ARG","ASYNC","BLE","C90", "E", "F", "I", "N", "UP032", "W", "NPY"]
 lint.ignore = [ "N802", "N806", # function should be lowercase
 "N816" # Variable in global scope should not be mixedCase
 ]

src/pystog/transformer.py

@@ -169,7 +169,7 @@ def fourier_transform(self, xin, yin, xout, xmin=None, xmax=None, dy_in=None, **
         for i, x in enumerate(xout):
             kernel = factor * yin * np.sin(xin * x)
             ekernel = np.square(factor * err * np.sin(xin * x))
-            yout[i] = np.trapz(kernel, x=xin)
+            yout[i] = np.trapezoid(kernel, x=xin)
             eout[i] = np.sqrt((np.diff(xin) ** 2 * (ekernel[1:] + ekernel[:-1]) / 2).sum())
 
         if kwargs.get("OmittedXrangeCorrection", False):

tests/test_stog.py

@@ -314,7 +314,8 @@ def test_stog_real_space_function_exception(self):
 class TestStogStorageArrays(TestStogBase):
     def setUp(self):
         super(TestStogStorageArrays, self).setUp()
-        self.target = np.random.randn(3, 10)
+        randn = np.random.default_rng()
+        self.target = randn.random(size=(3, 10))
 
     def test_stog_reciprocal_individuals_setter(self):
         stog = StoG()