Dependencies

.github/workflows/test_and_deploy.yml

@@ -1,105 +1,105 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-# For pytest-qt related fixes: https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#github-actions
-
-name: tests
-
-on:
-  pull_request:
-    paths-ignore:
-      - "**/README.md"
-  push:
-    paths-ignore:
-      - "**/README.md"
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-    env:
-      DISPLAY: ":99.0"
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          activate-environment: test
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-
-      - name: Conda info
-        run: conda info
-
-      - name: Save conda location
-        run: echo "python=$(which python)" >> "$GITHUB_ENV"
-
-      - name: Install core
-        timeout-minutes: 10
-        run: |
-          conda install -y pyopencl pocl
-          python --version
-          pip install --upgrade pip setuptools wheel
-          pip install --use-pep517 -e './core[testing]'
-
-      - name: Lint core
-        uses: ./.github/lint
-        with:
-          directory: core
-          python: ${{ env.python }}
-
-      - name: Test core
-        run: pytest -v --cov=core --cov-report=xml core/
-
-      - uses: tlambert03/setup-qt-libs@v1
-
-      - name: Install plugin
-        timeout-minutes: 10
-        run: |
-          /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX
-          pip install pytest-qt PyQt5
-          pip install -e './plugin[testing]'
-
-      - name: Lint plugin
-        uses: ./.github/lint
-        with:
-          directory: plugin
-          python: ${{ env.python }}
-
-      - name: Test plugin
-        run: pytest -v --cov=plugin --cov-report=xml plugin
-
-      - name: Coverage
-        uses: codecov/codecov-action@v3
-
-  deploy:
-    # this will run when you have tagged a commit, starting with "v*"
-    # and requires that you have put your twine API key in your
-    # github secrets (see readme for details)
-    needs: [test]
-    runs-on: ubuntu-latest
-    if: contains(github.ref, 'tags')
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -U setuptools setuptools_scm wheel twine
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TWINE_TOKEN }}
-        run: |
-          git tag
-          python setup.py sdist bdist_wheel
-          twine upload dist/*
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# For pytest-qt related fixes: https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#github-actions
+
+name: tests
+
+on:
+  pull_request:
+    paths-ignore:
+      - "**/README.md"
+  push:
+    paths-ignore:
+      - "**/README.md"
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+    env:
+      DISPLAY: ":99.0"
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          activate-environment: test
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+
+      - name: Conda info
+        run: conda info
+
+      - name: Save conda location
+        run: echo "python=$(which python)" >> "$GITHUB_ENV"
+
+      - name: Install core
+        timeout-minutes: 10
+        run: |
+          conda install -y pyopencl pocl
+          python --version
+          pip install --upgrade pip setuptools wheel
+          pip install --use-pep517 -e './core[testing]'
+
+      - name: Lint core
+        uses: ./.github/lint
+        with:
+          directory: core
+          python: ${{ env.python }}
+
+      - name: Test core
+        run: pytest -v --cov=core --cov-report=xml core/
+
+      - uses: tlambert03/setup-qt-libs@v1
+
+      - name: Install plugin
+        timeout-minutes: 10
+        run: |
+          /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX
+          pip install pytest-qt PyQt5
+          pip install -e './plugin[testing]'
+
+      - name: Lint plugin
+        uses: ./.github/lint
+        with:
+          directory: plugin
+          python: ${{ env.python }}
+
+      - name: Test plugin
+        run: pytest -v --cov=plugin --cov-report=xml plugin
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  deploy:
+    # this will run when you have tagged a commit, starting with "v*"
+    # and requires that you have put your twine API key in your
+    # github secrets (see readme for details)
+    needs: [test]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_TOKEN }}
+        run: |
+          git tag
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

core/lls_core/__init__.py

@@ -1,26 +1,18 @@
 
 __version__ = "0.2.6"
 
-
+from strenum import StrEnum
 from enum import Enum
-
-# Initialize configuration options
-
-#Deskew Direction
 from pyclesperanto_prototype._tier8._affine_transform_deskew_3d import DeskewDirection
 
+# Initialize configuration options
 
 #Choice of Deconvolution
-class DeconvolutionChoice(Enum):
+class DeconvolutionChoice(StrEnum):
     cuda_gpu = "cuda_gpu"
     opencl_gpu = "opencl_gpu"
     cpu = "cpu"
 
-#Choice of File extension to save
-class SaveFileType(Enum):
-    h5 = "h5"
-    tiff = "tiff"
-
 #CONFIGURE LOGGING using a dictionary (can also be done with yaml file)
 import logging.config
 LOGGING_CONFIG = {