Merge pull request #5 from AFM-analysis/fix_kvm_model_numpy_versions

Fix kvm model numpy version compatibility

Author: PinkShnack

.github/workflows/check.yml

@@ -30,3 +30,11 @@ jobs:
     - name: Lint with flake8
       run: |
         flake8 --exclude _version.py .
+    - name: Test with pytest (numpy v1)
+      run: |
+        pip install numpy==1.26.4
+        pytest tests
+    - name: Test with pytest (numpy v2)
+      run: |
+        pip install numpy==2.4.6
+        pytest tests

CHANGELOG

@@ -1,5 +1,8 @@
+0.1.2
+ - fix: KVM hertz model compatible with numpy version 1 and 2 (#1, #5)
 0.1.1
- - ci: update deploy_pypi to use pypi's trusted publisher system 
+ - setup: set the built tool system
+ - ci: update deploy_pypi to use pypi's trusted publisher system
  - ci: add check and deploy_pypi github actions (#3, #4)
 0.1.0
  - feat: add KVM hertz model (#2)

nanite_community/models/model_hertz_corrected_viscoelasticity_KVM.py

@@ -255,7 +255,10 @@ def helper_retract_fraction(tip_position, force, fraction_force):
     fraction = int(0.8 * len(force))
     max_force = np.max(force[:fraction])
     max_position = -1 * tip_position[0]
-    fit_stop = int(np.argwhere(force < (max_force * fraction_force))[0])
+    _mask = force < (max_force * fraction_force)
+    if not np.any(_mask):
+        raise ValueError("No force values below threshold")
+    fit_stop = int(np.argmax(_mask))
     position_seg = tip_position[:fit_stop].copy()
     force_seg = force[:fit_stop].copy()
 

pyproject.toml

@@ -1,3 +1,7 @@
+[build-system]
+requires = ["setuptools>=80", "setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
+
 [project]
 name = "nanite-community"
 description = "Repository for storing nanite models"
@@ -10,7 +14,7 @@ readme = "README.md"
 license = {text = "MIT"}
 dependencies = [
     "lmfit>=1.3.2",
-    "numpy==1.26.*",
+    "numpy>=1.26",
 ]
 dynamic = ["version"]
 keywords=[
@@ -27,7 +31,13 @@ classifiers=[
 ]
 
 [dependency-groups]
+test = ["pytest"]
 lint = ["flake8"]
 dev = [
+    {include-group = "test"},
     {include-group = "lint"}
 ]
+
+[tool.setuptools_scm]
+write_to = "nanite_community/_version.py"
+version_scheme = "post-release"

tests/test_helper_retract_fraction.py

@@ -0,0 +1,54 @@
+import numpy as np
+import pytest
+
+
+def old_helper_retract_fraction(tip_position, force, fraction_force):
+    fraction = int(0.8 * len(force))
+    max_force = np.max(force[:fraction])
+    max_position = -1 * tip_position[0]
+    fit_stop = int(np.argwhere(force < (max_force * fraction_force))[0])
+    position_seg = tip_position[:fit_stop].copy()
+    force_seg = force[:fit_stop].copy()
+    return position_seg, force_seg, max_position, max_force
+
+
+def new_helper_retract_fraction(tip_position, force, fraction_force):
+    """Reference implementation using NumPy 1.x and 2.x compatible indexing."""
+    fraction = int(0.8 * len(force))
+    max_force = np.max(force[:fraction])
+    max_position = -1 * tip_position[0]
+
+    # new part
+    _mask = force < (max_force * fraction_force)
+    if not np.any(_mask):
+        raise ValueError("No force values below threshold")
+    fit_stop = int(np.argmax(_mask))
+
+    position_seg = tip_position[:fit_stop].copy()
+    force_seg = force[:fit_stop].copy()
+    return position_seg, force_seg, max_position, max_force
+
+
+def test_helper_behavior_differs_between_numpy_1_and_2():
+    """Show that newest version works for both numpy 1 and 2"""
+    tip_position = np.linspace(0.0, -9.0, 10)
+    force = np.array([10.0, 9.0, 8.0, 6.0, 4.0, 3.0, 2.0, 1.0, 0.0, 0.0])
+    fraction_force = 0.5  # threshold = 5.0 -> first below threshold at index 4
+
+    major = int(np.__version__.split(".", 1)[0])
+    if major < 2:
+        # both old and new KVM work for numpy version 1
+        old = old_helper_retract_fraction(tip_position, force, fraction_force)
+        new = new_helper_retract_fraction(tip_position, force, fraction_force)
+        np.testing.assert_allclose(old[0], new[0])
+        np.testing.assert_allclose(old[1], new[1])
+        assert old[2] == new[2]
+        assert old[3] == new[3]
+    else:
+        # old implementation creates errors on NumPy 2
+        # ("only length-1 arrays..." / "only 0-d arrays...").
+        with pytest.raises(TypeError):
+            old_helper_retract_fraction(tip_position, force, fraction_force)
+        # therefore we need the new implementation, which works
+        # with numpy version 2
+        new_helper_retract_fraction(tip_position, force, fraction_force)