Merge pull request #1355 from SyneRBI/fix-test-tol

fix v3.9 release bugs

Author: casperdcl

.github/workflows/build-test.yml

@@ -55,7 +55,7 @@ jobs:
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         submodules: recursive
     - name: install_dependencies

.github/workflows/cffconvert.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/[email protected]

CITATION.cff

@@ -117,7 +117,7 @@ identifiers:
       "Motion estimation and correction for
       simultaneous PET/MR using SIRF and CIL". Philos
       Trans A (2021);379:20200208
-- type: doi
+  - type: doi
     value: 10.1088/1361-6560/adf609
     description: >-
       "Efficient motion-corrected image reconstruction

src/xSTIR/pSTIR/tests/test_ObjectiveFunction.py

@@ -85,21 +85,21 @@ def test_Hessian(self, subset=-1, eps=1e-3):
     def test_gradient_inplace(self):
         '''Checks that gradient computed in-place returns the same as without in-place.
 
-        Note: the absolute tolerance of the test was increased from the default 1e-8 to 1e-5, see 'test_gradient_out'
+        Note: the absolute tolerance of the test was increased from the default 0 to 3e-4, see 'test_gradient_out'
         '''
         x = self.image
         g1 = self.obj_fun.gradient(x)
         self.obj_fun.gradient(x, out=x)
-        numpy.testing.assert_allclose(x.asarray(), g1.asarray(), atol=1e-5)
+        numpy.testing.assert_allclose(x.asarray(), g1.asarray(), atol=3e-4)
 
     def test_gradient_out(self):
         '''Checks that gradient with 'out' parameter returns the same as without the 'out' parameter.
 
-        Note: the absolute tolerance of the test was increased from the default 1e-8 to 1e-5.
+        Note: the absolute tolerance of the test was increased from the default 0 to 3e-4.
         https://github.com/SyneRBI/SIRF/issues/1349
         '''
         x = self.image
         g1 = self.obj_fun.gradient(x)
         g2 = g1 * 0
         self.obj_fun.gradient(x, out=g2)
-        numpy.testing.assert_allclose(g2.asarray(), g1.asarray(), atol=1e-5)
+        numpy.testing.assert_allclose(g2.asarray(), g1.asarray(), atol=3e-4)