Updates dependencies

.github/workflows/build_installer.yml

@@ -48,14 +48,13 @@ jobs:
           else
             ./build_installer.sh --remote --tag $GITHUB_REF_NAME
           fi
-          ./build_installer.sh --remote
       - name: Upload installer
         uses: actions/upload-artifact@v4
         with:
           name: linux installer
           path: installer/linux/*.run
   MacOS-installer:
-    runs-on: macos-13
+    runs-on: macos-latest
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3

.github/workflows/main.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [windows-latest, ubuntu-latest, macos-13]
+        platform: [windows-latest, ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.platform }}
 
     steps:
@@ -49,7 +49,6 @@ jobs:
       run: |
         conda init bash
         conda activate sscanss
-        conda install -y -c conda-forge numpy==1.23.5 
         python make.py --build-all
     - name: Upload coverage files
       uses: actions/upload-artifact@v4

.github/workflows/publish_docs.yml

@@ -19,10 +19,10 @@ jobs:
       with:
         ref: gh-pages
         path: docs/_web
-    - name: Set up Python 3.10
+    - name: Set up Python 3.12
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.12'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

README.md

@@ -16,7 +16,7 @@ Installation
 ------------
 Installers are available on the [release](https://github.com/ISISNeutronMuon/SScanSS-2/releases) page. It should be noted that while the code is 
 Python 3 compatible, a single version will be tested for each release to ensure a consistent experience for all users. 
-The supported version for the next release is Python 3.10.
+The supported version for the next release is Python 3.12.
 
 Citing SScanSS 2
 ----------------

environment.yaml

@@ -2,7 +2,7 @@ name: sscanss
 channels:
   - defaults
 dependencies:
-  - python=3.10
+  - python=3.12
   - pip
   - pip:
     - -r requirements.txt

installer/linux/build_installer.sh

@@ -115,16 +115,14 @@ echo ""
 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$TMP_DIR/miniconda.sh"
 bash ./miniconda.sh -b -p ./miniconda
 
-./miniconda/bin/conda create -n sscanss -y python=3.10
+./miniconda/bin/conda create -n sscanss -y python=3.12
 
 echo ""
 echo "Downloading Dependencies"
 echo ""
 python_exec="./miniconda/envs/sscanss/bin/python"
 mkdir "$TMP_DIR/packages"
 $python_exec -m pip download -r "./sscanss/requirements.txt" --dest "$TMP_DIR/packages"
-# workaround for centos 7
-$python_exec -m pip download --only-binary=":all:" --platform="manylinux_2_17_x86_64"  --dest "$TMP_DIR/packages" pillow==9.2
 
 echo ""
 echo "Compressing Package.tar.gz ..."

installer/linux/install.sh

@@ -119,7 +119,7 @@ python_exec="./envs/sscanss/bin/python"
 CFLAGS=$(./envs/sscanss/bin/python3-config --includes)
 export CFLAGS=$CFLAGS
 $python_exec -m pip install --no-cache-dir --no-index --no-build-isolation --find-links packages -r "./sscanss/requirements.txt" >/dev/null
-chmod 777 -R "./envs/sscanss/lib/python3.10/site-packages/PyQt6/"
+chmod 777 -R "./envs/sscanss/lib/python3.12/site-packages/PyQt6/"
 if [ "$INSTALL_EDITOR" = y ]; then
     $python_exec "./sscanss/make.py" --build-sscanss --build-editor >/dev/null
 else

installer/linux/readme.txt

@@ -1,26 +1,3 @@
-Before Installation
--------------------
-SScanSS 2 requires OpenSSL CA certificates when checking for updates. If you want to
-use this feature, install OpenSSL if not installed (Most linux distros have OpenSSL 
-pre-installed.) 
-
-   > sudo apt-get install openssl
-
-Add environment variable "SSL_CERT_DIR" and set its value to the path of the
-CA certificate directory. The OpenSSL install directory can be found by typing
-
-   > openssl version -d
-
-The "SSL_CERT_DIR" variable should be set to the path of the "certs" folder in the 
-OpenSSL install directory e.g.
-
-	SSL_CERT_DIR=/usr/lib/ssl/certs
-
-Ensure the variable is permanent, i.e. close and reopen the terminal and check that 
-the variable is still available. You may need to write the variable to a file e.g.
-"etc/environment" on Ubuntu.
-
-
 Installation
 ------------
 Run the install script in a terminal as below and follow the prompts to continue 

make.py

@@ -28,7 +28,7 @@
 ]
 HIDDEN_IMPORT = ['--hidden-import', 'OpenGL.platform.egl']
 IS_WINDOWS = sys.platform.startswith('win')
-IS_MAC = True if sys.platform == 'darwin' else False
+IS_MAC = sys.platform == 'darwin'
 
 
 def format_code(check=False):

requirements-dev.txt

@@ -1,5 +1,5 @@
-coverage==7.0.5
-pylint==2.16.2
-Sphinx==5.3.0
+coverage==7.9.2
+pylint==3.3.7
+Sphinx==8.1.3
 sphinx-bootstrap-theme==0.8.1
 yapf==0.31.0

requirements.txt

@@ -1,19 +1,18 @@
-bitarray==2.6.2
-cython==0.29.33
-h5py==3.7.0
-jsbeautifier==1.14.7
-jsonschema==4.16.0
-matplotlib==3.6.3
-NLopt==2.7.1
-numpy==1.23.5
-gimpact==1.0.1
-Pillow==9.2.0
+bitarray==3.5.2
+cython==3.0.12
+h5py==3.13.0
+jsbeautifier==1.15.4
+jsonschema==4.24.1
+matplotlib==3.9.4
+NLopt==2.8.0
+numpy==2.2.6
+gimpact==1.0.2
 PyInstaller==6.11.1
-PyOpenGL==3.1.6
-PyQt6==6.3.1
-PyQt6-Qt6==6.5.2
-pystache==0.6.0
-PyQt6-QScintilla==2.13.4
-scipy==1.9.3
-tifffile==2022.10.10
-psutil==5.9.4
+PyOpenGL==3.1.9
+PyQt6==6.6.1
+PyQt6-Qt6==6.6.3
+pystache==0.6.7
+PyQt6-QScintilla==2.14.1
+scipy==1.15.3
+tifffile==2025.5.24
+psutil==7.0.0

setup.py

@@ -33,7 +33,7 @@
                       'tifffile',
                       'psutil',
                       ],
-    classifiers=['Programming Language :: Python :: 3.10',
+    classifiers=['Programming Language :: Python :: 3.12',
                  'License :: OSI Approved :: BSD License',
                  'Natural Language :: English',
                  'Intended Audience :: Science/Research',

sscanss/app/dialogs/misc.py

@@ -1383,7 +1383,7 @@ def plot(self):
             if self.simulation.args['align_first_order']:
                 path_length = np.column_stack(np.dsplit(path_length, path_length.shape[2])).reshape(-1, len(names))
             else:
-                path_length = np.row_stack(np.dsplit(path_length, path_length.shape[2])).reshape(-1, len(names))
+                path_length = np.vstack(np.dsplit(path_length, path_length.shape[2])).reshape(-1, len(names))
             title = 'Path lengths for measurements'
 
         label = np.arange(1, path_length.shape[0] + 1)

sscanss/core/geometry/intersection.py

@@ -393,7 +393,7 @@ def volume_plane_intersection(volume, plane, resolution=1024):
     matrix[:3, :3] = view_matrix.transpose()
     matrix = np.linalg.inv(matrix @ volume.transform_matrix @ np.diag([*volume.voxel_size, 1]))
 
-    rotated_segments = np.row_stack(segments) @ view_matrix
+    rotated_segments = np.vstack(segments) @ view_matrix
     min_limits = rotated_segments.min(axis=0)
     max_limits = rotated_segments.max(axis=0)
 

sscanss/core/instrument/simulation.py

@@ -88,7 +88,7 @@ def __init__(self, instrument):
         self.size = len(entity.transforms)
         self.vertices = SharedArray.fromNumpyArray(entity.vertices)
         self.indices = SharedArray.fromNumpyArray(entity.indices)
-        self.transforms = SharedArray.fromNumpyArray(np.row_stack(entity.transforms))
+        self.transforms = SharedArray.fromNumpyArray(np.vstack(entity.transforms))
         self.offsets = entity.offsets
         self.keys = entity.keys
 

sscanss/core/io/reader.py

@@ -771,7 +771,7 @@ def file_walker(filepath, extension=(".tiff", ".tif")):
     return list_of_files
 
 
-def filename_sorting_key(string, regex=re.compile('(\d+)')):
+def filename_sorting_key(string, regex=re.compile(r'(\d+)')):
     """Returns a key for sorting filenames containing numbers in a natural way.
 
     :param string: input string

sscanss/core/math/matrix.py

@@ -37,7 +37,7 @@ def __init__(self, rows, cols, values=None, dtype=None):
         super().__setattr__("_data", data)
         super().__setattr__("_keys", {})
 
-    def __array__(self, _dtype=None):
+    def __array__(self, dtype=None, copy=None):
         return self._data
 
     def __getattr__(self, attr):

sscanss/core/math/quaternion.py

@@ -22,7 +22,7 @@ class Quaternion:
     def __init__(self, w=0.0, x=0.0, y=0.0, z=0.0):
         self._data = Vector4([x, y, z, w])
 
-    def __array__(self, _dtype=None):
+    def __array__(self, dtype=None, copy=None):
         return self._data[:]
 
     @classmethod

sscanss/core/math/vector.py

@@ -33,7 +33,7 @@ def __init__(self, size, values=None, dtype=None):
         super().__setattr__("_data", data)
         super().__setattr__("_keys", {})
 
-    def __array__(self, _dtype=None):
+    def __array__(self, dtype=None, copy=None):
         return self._data
 
     def __getattr__(self, attr):

sscanss/core/scene/entity.py

@@ -200,7 +200,7 @@ def __init__(self, points, vectors, alignment, visible=True):
                 ranges.append(count)
             self.colours = colour
             self.offsets = ranges
-            self.vertices.append(np.array(np.row_stack(vertices), dtype=np.float32))
+            self.vertices.append(np.array(np.vstack(vertices), dtype=np.float32))
         self.indices = np.arange(0, len(self.vertices[-1]), dtype=np.uint32)
 
     def node(self):
@@ -267,9 +267,9 @@ def __init__(self, instrument):
             self._updateParams(mesh, Matrix44.identity())
             self.keys[f'{Attributes.Fixture.value}_{name}'] = len(self.offsets)
 
-        self.vertices = np.row_stack(self._vertices)
+        self.vertices = np.vstack(self._vertices)
         self.indices = np.concatenate(self._indices)
-        self.normals = np.row_stack(self._normals)
+        self.normals = np.vstack(self._normals)
 
     def _updateParams(self, mesh, transform):
         self._vertices.append(mesh.vertices)
@@ -359,9 +359,9 @@ def addReferencePlane(self, plane, size):
         """
         mesh = create_plane(plane, size[0], size[1])
         count = len(self.reference_plane_vertices)
-        self.reference_plane_vertices = np.row_stack((self.reference_plane_vertices, mesh.vertices))
+        self.reference_plane_vertices = np.vstack((self.reference_plane_vertices, mesh.vertices))
         self.reference_plane_indices = np.concatenate((self.reference_plane_indices, mesh.indices + count))
-        self.reference_plane_normals = np.row_stack((self.reference_plane_normals, mesh.normals))
+        self.reference_plane_normals = np.vstack((self.reference_plane_normals, mesh.normals))
         self.reference_plane_offsets.append(len(self.reference_plane_indices))
 
     def clearReferencePlanes(self):

tests/test_io.py

@@ -207,8 +207,8 @@ def testHDFReadWrite(self, visual_fn, setting_cls):
             group['indices'] = mesh_to_write.indices
 
         result, _ = reader.read_project_hdf(filename)
-        vertices = np.row_stack((mesh_to_write.vertices, mesh_to_write.vertices + 2))
-        normals = np.row_stack((mesh_to_write.normals, mesh_to_write.normals))
+        vertices = np.vstack((mesh_to_write.vertices, mesh_to_write.vertices + 2))
+        normals = np.vstack((mesh_to_write.normals, mesh_to_write.normals))
         np.testing.assert_array_almost_equal(result["sample"].vertices, vertices, decimal=5)
         np.testing.assert_array_almost_equal(result["sample"].normals, normals, decimal=5)
         np.testing.assert_array_almost_equal(result["sample"].indices, np.arange(6, dtype=int))

tests/test_main_model.py

@@ -102,8 +102,8 @@ def testAddMesh(self):
         self.assertIs(self.model.sample, self.mesh)
         mesh_2 = self.mesh.copy()
         mesh_2.vertices += 2
-        vertices = np.row_stack((self.mesh.vertices, mesh_2.vertices))
-        normals = np.row_stack((self.mesh.normals, mesh_2.normals))
+        vertices = np.vstack((self.mesh.vertices, mesh_2.vertices))
+        normals = np.vstack((self.mesh.normals, mesh_2.normals))
         self.model.addMeshToProject(mesh_2, InsertSampleOptions.Combine)
         np.testing.assert_array_almost_equal(self.model.sample.vertices, vertices, decimal=5)
         np.testing.assert_array_almost_equal(self.model.sample.normals, normals, decimal=5)
@@ -269,7 +269,7 @@ def testLoadAndSaveVectors(self):
             decimal=5,
         )
         np.testing.assert_array_almost_equal(new_vectors[:3, :, 1],
-                                             np.row_stack((vectors[3, :], np.zeros((2, 3)))),
+                                             np.vstack((vectors[3, :], np.zeros((2, 3)))),
                                              decimal=5)
 
         vectors[0, 0] = 10