Deprecate python 3.8 and allow python interpreter version > 3.11

.github/workflows/test.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: [3.9, '3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v4
@@ -42,10 +42,10 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - name: Set up Python 3.9
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Build a binary wheel and a source tarball
       run: |
         python -m pip install build --user
@@ -61,53 +61,9 @@ jobs:
         name: pypi_packages
         path: dist/*
 
-  build-n-publish-anaconda:
-    name: Build and publish anaconda packages
-    needs: lint_and_test
-    runs-on: ubuntu-latest
-    if: startsWith(github.ref, 'refs/tags/')
-
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          python-version: 3.9
-          miniforge-variant: Mambaforge
-      - name: install dependencies build
-        shell: bash -l {0}
-        run: mamba install colorama pip ruamel ruamel.yaml rich jsonschema conda-verify anaconda-client
-      - name: Build linux-64 conda package
-        uses: prefix-dev/[email protected]
-        with:
-          recipe-path: "conda/recipe.yaml"
-          build-args: "--experimental --target-platform linux-64"
-      - name: Build osx-64 conda package
-        uses: prefix-dev/[email protected]
-        with:
-          recipe-path: "conda/recipe.yaml"
-          build-args: "--experimental --target-platform osx-64"
-#      - name: Build osx-arm64 conda package
-#        uses: prefix-dev/[email protected]
-#        with:
-#          recipe-path: "conda/recipe.yaml"
-#          build-args: "--experimental --target-platform osx-arm64"
-      - name: Upload conda package
-        run: |
-          for pkg in $(find output -type f \( -name "*.conda" -o -name "*.tar.bz2" \) ); do
-            echo "Uploading ${pkg}"
-            rattler-build upload anaconda -o mittagessen -a ${{ secrets.ANACONDA_TOKEN }} "${pkg}"
-          done
-      - name: Upload conda artifacts to GH storage
-        uses: actions/upload-artifact@v4
-        with:
-          name: conda_packages
-          path: output/*/*.conda
-
   autodraft-gh-release:
     name: Create github release
-    needs: [build-n-publish-anaconda, build-n-publish-pypi]
+    needs: build-n-publish-pypi
     runs-on: ubuntu-latest
 
     steps:
@@ -140,10 +96,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install sphinx-multiversion
         run:  python -m pip install sphinx-multiversion sphinx-autoapi
       - name: Create docs

README.rst

@@ -25,18 +25,12 @@ Installation
 
 kraken only runs on **Linux or Mac OS X**. Windows is not supported.
 
-The latest stable releases can be installed either from `PyPi <https://pypi.org>`_:
+The latest stable releases can be installed from `PyPi <https://pypi.org>`_:
 
 ::
 
   $ pip install kraken
 
-or through `conda <https://anaconda.org>`_:
-
-::
-
-  $ conda install -c conda-forge -c mittagessen kraken
-
 If you want direct PDF and multi-image TIFF/JPEG2000 support it is necessary to
 install the `pdf` extras package for PyPi:
 

docs/index.rst

@@ -67,22 +67,12 @@ or
 
 respectively.
 
-Installation using Conda
-------------------------
+Development Branch Installation using Conda
+-------------------------------------------
 
-To install the stable version through `conda <https://anaconda.org>`_:
-
-.. code-block:: console
-
-   $ conda install -c conda-forge -c mittagessen kraken
-
-Again PDF/multi-page TIFF/JPEG2000 support requires some additional dependencies:
-
-.. code-block:: console
-
-   $ conda install -c conda-forge pyvips
-
-The git repository contains some environment files that aid in setting up the latest development version:
+To install the latest development branch through `conda
+<https://anaconda.org>`_  clone the kraken git repository and install with the
+provided environment files:
 
 .. code-block:: console
 

environment.yml

@@ -4,32 +4,32 @@ channels:
   - conda-forge
 dependencies:
   - python>=3.9
-  - python-bidi~=0.4.0
+  - python-bidi~=0.6.0
   - lxml
   - regex
   - requests
   - click>=8.1
-  - numpy~=1.23.0
+  - numpy~=2.0.0
   - pillow~=9.2.0
-  - scipy~=1.10.0
+  - scipy~=1.13.0
   - jinja2~=3.0
   - conda-forge::torchvision-cpu>=0.5.0
-  - conda-forge::pytorch-cpu~=2.1.0
+  - conda-forge::pytorch-cpu~=2.4.0
   - jsonschema
   - scikit-learn~=1.2.1
-  - scikit-image~=0.21.0
-  - shapely~=1.8.5
+  - scikit-image~=0.24.0
+  - shapely>=2.0.6,~=2.0.6
   - pyvips
   - imagemagick>=7.1.0
   - pyarrow
   - importlib-resources>=1.3.0
-  - conda-forge::lightning~=2.2.0
+  - conda-forge::lightning~=2.4.0
   - conda-forge::torchmetrics>=1.1.0
-  - conda-forge::threadpoolctl~=3.4
+  - conda-forge::threadpoolctl~=3.5.0
   - pip
   - albumentations
   - rich
   - setuptools>=36.6.0,<70.0.0
   - pip:
-    - coremltools~=6.0
+    - coremltools~=8.1
     - file:.

environment_cuda.yml

@@ -4,33 +4,33 @@ channels:
   - conda-forge
 dependencies:
   - python>=3.9
-  - python-bidi~=0.4.0
+  - python-bidi~=0.6.0
   - lxml
   - regex
   - requests
   - click>=8.1
   - numpy~=1.23
   - pillow>=9.2.0
-  - scipy~=1.10.0
+  - scipy~=1.13.0
   - jinja2~=3.0
   - conda-forge::torchvision>=0.5.0
-  - conda-forge::pytorch~=2.1.0
+  - conda-forge::pytorch~=2.4.0
   - cudatoolkit>=9.2
   - jsonschema
   - scikit-learn~=1.2.1
-  - scikit-image~=0.21.0
-  - shapely~=1.8.5
+  - scikit-image~=0.24.0
+  - shapely>=2.0.6,~=2.0.6
   - pyvips
   - imagemagick>=7.1.0
   - pyarrow
   - importlib-resources>=1.3.0
-  - conda-forge::lightning~=2.2.0
+  - conda-forge::lightning~=2.4.0
   - conda-forge::torchmetrics>=1.1.0
-  - conda-forge::threadpoolctl~=3.4
+  - conda-forge::threadpoolctl~=3.5.0
   - pip
   - albumentations
   - rich
   - setuptools>=36.6.0,<70.0.0
   - pip:
-    - coremltools~=6.0
+    - coremltools~=8.1
     - file:.

kraken/lib/segmentation.py

@@ -757,14 +757,10 @@ def calculate_polygonal_environment(im: Image.Image = None,
             line = np.array(line.coords, dtype=float)
             offset_line = np.array(offset_line.coords, dtype=float)
 
-            # parallel_offset on the right reverses the coordinate order
-            if not topline:
-                offset_line = offset_line[::-1]
             # calculate magnitude-weighted average direction vector
             lengths = np.linalg.norm(np.diff(line.T), axis=0)
             p_dir = np.mean(np.diff(line.T) * lengths/lengths.sum(), axis=1)
             p_dir = (p_dir.T / np.sqrt(np.sum(p_dir**2, axis=-1)))
-
             env_up, env_bottom = _calc_roi(line, bounds, baselines[:idx] + baselines[idx+1:], suppl_obj, p_dir)
 
             polygons.append(_extract_patch(env_up,

setup.cfg

@@ -14,10 +14,10 @@ classifier =
         Intended Audience :: Science/Research
 	License :: OSI Approved :: Apache Software License
         Operating System :: POSIX
-	Programming Language :: Python :: 3.8
 	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
 	Topic :: Scientific/Engineering :: Image Recognition
 	Topic :: Scientific/Engineering :: Artificial Intelligence
 
@@ -38,29 +38,29 @@ max_line_length = 160
 exclude = tests/*
 
 [options]
-python_requires = >=3.8,<=3.11.99
+python_requires = >=3.9,<3.13
 install_requires =
     jsonschema
     lxml
     requests
     click>=8.1
-    numpy~=1.23.0
+    numpy~=2.0.0
     Pillow>=9.2.0
     regex
-    scipy~=1.10.0 # bump up to latest release with py3.8 EOL
+    scipy~=1.13.0
     protobuf>=3.0.0
-    coremltools~=6.0
+    coremltools~=8.1
     jinja2~=3.0
-    python-bidi~=0.4.0
+    python-bidi~=0.6.0
     torchvision>=0.5.0
-    torch~=2.1.0
-    scikit-learn~=1.2.1
-    scikit-image~=0.21.0
-    shapely~=1.8.5
+    torch~=2.4.0
+    scikit-learn~=1.5.0
+    scikit-image~=0.24.0
+    shapely>=2.0.6,~=2.0.6
     pyarrow
-    lightning~=2.2.0
+    lightning~=2.4.0
     torchmetrics>=1.1.0
-    threadpoolctl~=3.4.0
+    threadpoolctl~=3.5.0
     importlib-resources>=1.3.0
     rich
 

tests/test_newpolygons.py

@@ -249,7 +249,7 @@ def test_ketoscli_train_old_model(self):
             fp = str(Path(tempdir) / "test.xml")
 
             self._test_ketoscli(
-                args=['train', '-f', 'xml', '-N', '1', '-q', 'fixed', '-i', self.old_model_path, '--resize', 'add', '-o', mfp, '--workers', '0', self.segmented_img],
+                args=['train', '-f', 'xml', '-N', '1', '-q', 'fixed', '-i', self.old_model_path, '--resize', 'union', '-o', mfp, '--workers', '0', self.segmented_img],
                 expect_legacy=False,
                 check_exit_code=[0, 1], # Model may not improve during training
             )
@@ -268,7 +268,7 @@ def test_ketoscli_train_old_model_force_legacy(self):
             fp = str(Path(tempdir) / "test.xml")
 
             self._test_ketoscli(
-                args=['train', '--legacy-polygons', '-f', 'xml', '-N', '1', '-q', 'fixed', '-i', self.old_model_path, '--resize', 'add', '-o', mfp, '--workers', '0', self.segmented_img],
+                args=['train', '--legacy-polygons', '-f', 'xml', '-N', '1', '-q', 'fixed', '-i', self.old_model_path, '--resize', 'union', '-o', mfp, '--workers', '0', self.segmented_img],
                 expect_legacy=True,
                 check_exit_code=[0, 1], # Model may not improve during training
             )
@@ -326,7 +326,7 @@ def test_ketoscli_pretrain_old_model(self):
             fp = str(Path(tempdir) / "test.xml")
 
             self._test_ketoscli(
-                args=['pretrain', '-f', 'xml', '-N', '1', '-q', 'fixed', '-i', self.old_model_path, '--resize', 'add', '-o', mfp, '--workers', '0', self.segmented_img],
+                args=['pretrain', '-f', 'xml', '-N', '1', '-q', 'fixed', '-i', self.old_model_path, '--resize', 'union', '-o', mfp, '--workers', '0', self.segmented_img],
                 expect_legacy=False,
                 check_exit_code=[0, 1], # Model may not improve during training
             )
@@ -349,7 +349,7 @@ def _assertWarnsWhenTrainingArrow(self,
         if force_legacy:
             args = ['--legacy-polygons'] + args
         if from_model:
-            args = ['-i', from_model, '--resize', 'add'] + args
+            args = ['-i', from_model, '--resize', 'union'] + args
 
         print("ketos", 'train', *args)
         run = self.runner.invoke(ketos_cli, ['train'] + args)