Pyinstaller Github Actions

.github/workflows/pyinstaller_windows.yml

@@ -0,0 +1,96 @@
+name: PyInstaller Windows Build
+
+on:
+  pull_request:
+    branches:
+      - 'main'
+      - 'release-*'
+  release:
+
+jobs:
+  test:
+    runs-on: windows-latest
+    env:
+      CONDA_OVERRIDE_CUDA: 10.2
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # Needed to get tags so that git describe works during package build
+          fetch-depth: "0"
+
+      - name: cuda-toolkit
+        uses: Jimver/[email protected]
+        with:
+          cuda: '10.2.89'
+
+      - name: Get Date
+        id: get-date
+        run: |
+          echo "date=$(/bin/date -u "+%Y%V")" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Miniforge and Pip packages
+        uses: actions/cache@v4
+        env:
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/conda_pkgs_dir
+            ~/.cache/pip
+          key:
+            ${{runner.os}}-condapkg-${{env.CACHE_NUMBER}}-${{steps.get-date.outputs.date}}-${{hashFiles('environment-dev.yml','conda/meta.yaml')}}
+
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          activate-environment: mantidimaging-dev
+          auto-activate-base: false
+          use-mamba: false
+
+      - name: Cache Miniforge environment
+        uses: actions/cache@v4
+        id: cache-miniforge-environment
+        env:
+          CACHE_NUMBER: 0
+        with:
+          path: ${{env.CONDA}}/envs/mantidimaging-dev
+          key:
+            ${{runner.os}}-condaenv-${{env.CACHE_NUMBER}}-${{steps.get-date.outputs.date}}-${{hashFiles('environment-dev.yml','conda/meta.yaml')}}
+
+      - name: Mantid Imaging developer dependencies
+        if: steps.cache-miniforge-environment.outputs.cache-hit != 'true'
+        shell: bash -l {0}
+        run: |
+          conda deactivate
+          python ./setup.py create_dev_env
+
+      - name: List versions
+        shell: bash -l {0}
+        run: |
+          conda env list
+          python --version; conda list ; pip list
+
+      - name: PyInstaller Build
+        shell: bash -l {0}
+        env:
+          CUDA_PATH: ${{env.CONDA}}/envs/mantidimaging-dev
+        run: |
+          conda activate mantidimaging-dev
+          echo "Cuda path: $CUDA_PATH"
+          echo "dev env path: '${{env.CONDA}}/envs/mantidimaging-dev'"
+          cd packaging
+          python PackageWithPyInstaller.py
+
+      - name: Archive PyInstalled File
+        uses: actions/upload-artifact@v3
+        with:
+          name: MantidImagingSpec
+          path: packaging/MantidImaging.spec
+
+      - name: Archive PyInstalled File
+        uses: actions/upload-artifact@v3
+        with:
+          name: MantidImaging
+          path: packaging/dist

.github/workflows/windows.yml

@@ -18,6 +18,8 @@ concurrency:
 jobs:
   test:
     runs-on: windows-latest
+    env:
+      CONDA_OVERRIDE_CUDA: 11.8
 
     steps:
       - uses: actions/checkout@v4

conda/meta.yaml

@@ -12,23 +12,23 @@ source:
 
 requirements:
   build:
-    - python=3.10.*
+    - python=3.12.*
     - setuptools=62.*
   run:
-    - python=3.10.*
+    - python=3.12.*
     - pip
     - astropy=6.0.*
     - scipy=1.14.*
-    - scikit-image=0.20.*
+    - scikit-image=0.22.*
     - tifffile=2023.7.18
-    - imagecodecs=2023.1.23
+    - imagecodecs=2023.9.18
     - numpy=1.26.*
     - numexpr=2.8.*
     - algotom=1.6.*
     - tomopy=1.12.*
     - cudatoolkit=11.8.*
     - cupy=12.3.*
-    - astra-toolbox=2.0.0
+    - astra-toolbox=2.1.0=cuda*
     - requests=2.27.*
     - h5py=3.9.*
     - hdf5=1.14.2

docs/release_notes/next/dev-2267-upgrade-python

@@ -0,0 +1 @@
+#2267: Python has been upgraded to use version 3.12

environment-dev.yml

@@ -1,7 +1,6 @@
 name: mantidimaging-dev
 channels:
   - mantidimaging/label/unstable
-  - astra-toolbox
   - conda-forge
   - ccpi
   - algotom
@@ -24,8 +23,8 @@ dependencies:
   - pytest-xdist==3.3.*
   - testfixtures==7.2.*
   - gitpython==3.1.*
-  - coverage==6.5.*
-  - coveralls==3.3.*
+  - coverage==7.3.*
+  - coveralls==4.0.*
   - pyfakefs==5.3.*
   - parameterized==0.9.*
   - pyinstaller==6.9.*

environment.yml

@@ -1,7 +1,6 @@
 name: mantidimaging-nightly
 channels:
   - mantidimaging/label/unstable
-  - astra-toolbox
   - conda-forge
   - ccpi
   - algotom

mantidimaging/core/data/test/image_stack_test.py

@@ -244,7 +244,7 @@ def test_image_eq_method(self):
         self.assertRaises(ValueError, lambda a, b: a == b, data_images, 1.0)
 
     def test_cant_change_id(self):
-        with self.assertRaisesRegex(Exception, "can't set attribute"):
+        with self.assertRaises(AttributeError):
             generate_images().id = "id"
 
     def test_default_name(self):

mantidimaging/core/data/test/strictdataset_test.py

@@ -50,7 +50,7 @@ def test_attribute_not_set_returns_none(self):
         self.assertIsNone(dataset.dark_after)
 
     def test_cant_change_dataset_id(self):
-        with self.assertRaisesRegex(Exception, "set attribute"):
+        with self.assertRaises(AttributeError):
             self.strict_dataset.id = "id"
 
     def test_set_flat_before(self):

mantidimaging/core/operations/loader.py

@@ -20,8 +20,9 @@ def _find_operation_modules() -> list[BaseFilterClass]:
         if not ispkg:
             continue
 
-        if getattr(sys, 'frozen', False):
+        if getattr(sys, 'frozen', False) and "test.support" not in module_name:
             # If we're running a PyInstaller executable then we need to use a full module path
+            # Need to prevent importing standard library test modules found by pkgutil
             module_name = f'mantidimaging.core.operations.{module_name}'
 
         # near impossible to type check as find can be a pyinstaller specific type that we can't normally import

packaging/PackageWithPyInstaller.py

@@ -15,7 +15,7 @@
 
 def create_run_options():
     run_options = [
-        '../mantidimaging/__main__.py', '--name=MantidImaging', '--additional-hooks-dir=hooks', '--onedir',
+        '../mantidimaging/__main__.py', '--name=MantidImaging', '--additional-hooks-dir=hooks',
         '--icon=../images/mantid_imaging_unstable_64px.ico'
     ]
 
@@ -38,7 +38,10 @@ def add_hidden_imports(run_options):
     path_to_operations = Path(__file__).parent.parent.joinpath('mantidimaging/core/operations')
     # COMPAT python 3.10 won't accept a Path: github.com/python/cpython/issues/88227
     for _, ops_module, _ in pkgutil.walk_packages([str(path_to_operations)]):
-        imports.append(f'mantidimaging.core.operations.{ops_module}')
+        # stop non-existent Hidden Imports
+        # https://github.com/mantidproject/mantidimaging/issues/2298
+        if "test.support" not in ops_module:
+            imports.append(f'mantidimaging.core.operations.{ops_module}')
 
     run_options.extend([f'--hidden-import={name}' for name in imports])
 
@@ -52,7 +55,7 @@ def add_hidden_imports(run_options):
 
 
 def add_missing_submodules(run_options):
-    imports = ['cupy']
+    imports = ['cupy', 'cupy_backends']
     run_options.extend([f'--collect-submodules={name}' for name in imports])
 
 
@@ -67,6 +70,7 @@ def add_data_files(run_options):
                   ('../mantidimaging/gui/windows/wizard/*.yml', 'mantidimaging/gui/windows/wizard/')]
 
     data_files += collect_data_files("cupy")
+    data_files += collect_data_files("cupy_backends")
     run_options.extend([f'--add-data={src}{os.pathsep}{dest}' for src, dest in data_files])
 
 
@@ -97,5 +101,4 @@ def add_exclude_modules(run_options):
     # The default limit is 1000, meaning a recursion error would occur at around 115 nested imports.
     # A limit of 5000 means the error should occur at about 660 nested imports.
     sys.setrecursionlimit(sys.getrecursionlimit() * 5)
-
     PyInstaller.__main__.run(create_run_options())