Merge branch 'master' into fix-fsd

manthey · manthey · commit c69bd8f1abfa · 2024-12-09T15:47:06.000-05:00
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -42,8 +42,9 @@ commands:
       - run:
           name: Upgrade pyenv
           command: |
-            rm -rf /opt/circleci/.pyenv
-            curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash
+            sudo rm -rf /opt/circleci/.pyenv
+            sudo bash -c 'curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | PYENV_ROOT=/opt/circleci/.pyenv bash'
+            sudo chmod -R 777 /opt/circleci/.pyenv/
             pyenv install --list list
       - run:
           name: Use pyenv to install python
@@ -63,36 +64,10 @@ commands:
           command: for i in $(seq 1 10); do [ $i -gt 1 ] && echo "retrying $i" && sleep 5; ./codecov --disable search pycov gcov --file .tox/coverage/py_coverage.xml .tox/coverage/cobertura-coverage.xml && s=0 && break || s=$?; done; (exit $s)
 
 jobs:
-  py38:
-    working_directory: ~/project
-    machine:
-      image: ubuntu-2004:202111-02
-    steps:
-      - checkout
-      - upgradepython:
-          version: "3.8"
-      - run:
-          name: Use pyenv to set python version
-          command: |
-            pyenv versions
-            pyenv global 3.8
-      - docker-compose
-      - restore_cache:
-          name: Restore external data cache
-          keys:
-            - tox-externaldata-{{ checksum "tests/datastore.py" }}
-      - tox:
-          env: py38
-      - save_cache:
-          name: Save external data cache
-          key: tox-externaldata-{{ checksum "tests/datastore.py" }}
-          paths:
-            - ./.tox/externaldata
-      - coverage
   py39:
     working_directory: ~/project
     machine:
-      image: ubuntu-2004:202111-02
+      image: ubuntu-2204:current
     steps:
       - checkout
       - upgradepython:
@@ -118,7 +93,7 @@ jobs:
   py310:
     working_directory: ~/project
     machine:
-      image: ubuntu-2004:202111-02
+      image: ubuntu-2204:current
     steps:
       - checkout
       - upgradepython:
@@ -144,7 +119,7 @@ jobs:
   py311:
     working_directory: ~/project
     machine:
-      image: ubuntu-2004:202111-02
+      image: ubuntu-2204:current
     steps:
       - checkout
       - upgradepython:
@@ -170,7 +145,7 @@ jobs:
   py312:
     working_directory: ~/project
     machine:
-      image: ubuntu-2004:202111-02
+      image: ubuntu-2204:current
     steps:
       - checkout
       - upgradepython:
@@ -212,7 +187,7 @@ jobs:
   docker:
     working_directory: ~/project
     machine:
-      image: ubuntu-2004:202111-02
+      image: ubuntu-2204:current
     steps:
       - checkout
       - run:
@@ -244,7 +219,7 @@ jobs:
   publish_docker:
     working_directory: ~/project
     machine:
-      image: ubuntu-2004:202111-02
+      image: ubuntu-2204:current
     steps:
       - checkout
       - attach_workspace:
@@ -264,12 +239,11 @@ jobs:
               fi
   wheels:
     working_directory: ~/project
-    docker:
-      - image: cimg/python:3.9
-      - image: docker:git
+    machine:
+      image: ubuntu-2204:current
     steps:
       - checkout
-      - setup_remote_docker
+      # - setup_remote_docker
       - run:
           name: Setup virtual environment
           command: |
@@ -329,13 +303,6 @@ workflows:
   version: 2
   ci:
     jobs:
-      - py38:
-          filters:
-            tags:
-              only: /^v.*/
-            branches:
-              ignore:
-                - gh-pages
       - py39:
           filters:
             tags:
@@ -387,7 +354,6 @@ workflows:
                 - gh-pages
       - docs-deploy:
           requires:
-            - py38
             - py39
             - py310
             - py311
@@ -404,7 +370,6 @@ workflows:
                 - sphinx
       - publish_docker:
           requires:
-            - py38
             - py39
             - py310
             - py311
@@ -428,7 +393,6 @@ workflows:
               only:
                 - master
     jobs:
-      - py38
       - py39
       - py310
       - py311
@@ -438,7 +402,6 @@ workflows:
       - wheels
       - publish_docker:
           requires:
-            - py38
             - py39
             - py310
             - py311
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -22,7 +22,7 @@ jobs:
     if: github.repository == 'DigitalSlideArchive/HistomicsTK' && ( startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/master' )
     strategy:
       matrix:
-        python: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -68,7 +68,7 @@ jobs:
           - [ubuntu-latest, x86_64]
           - [macos-latest, "x86_64 arm64"]
           - [windows-latest, auto64]
-        python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
+        python: ["cp39", "cp310", "cp311", "cp312"]
       fail-fast: false
 
     steps:
@@ -82,7 +82,7 @@ jobs:
           python-version: "3.x"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21.3
+        uses: pypa/cibuildwheel@v2.22.0
         env:
           CIBW_BUILD: ${{ matrix.python }}-*
           CIBW_TEST_SKIP: "*-macosx_arm64"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -61,7 +61,7 @@ repos:
   hooks:
     - id: pyupgrade
       args:
-        - --py37-plus
+        - --py39-plus
         - --keep-percent-format
 - repo: https://github.com/pre-commit/mirrors-autopep8
   rev: v2.0.4
diff --git a/Dockerfile b/Dockerfile
@@ -30,8 +30,8 @@ RUN apt-get update && \
 # Make a specific version of python the default and install pip
 # RUN rm -f /usr/bin/python && \
 #     rm -f /usr/bin/python3 && \
-#     ln `which python3.8` /usr/bin/python && \
-#     ln `which python3.8` /usr/bin/python3 && \
+#     ln `which python3.12` /usr/bin/python && \
+#     ln `which python3.12` /usr/bin/python3 && \
 #     curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
 #     python get-pip.py && \
 #     rm get-pip.py && \
diff --git a/Dockerfile-wheels b/Dockerfile-wheels
@@ -1,8 +1,9 @@
-FROM dockcross/manylinux2014-x64
+FROM dockcross/manylinux_2_28-x64
 
-# Don't build python < 3.8
+# Don't build python < 3.9
 RUN rm -rf /opt/python/cp36*
 RUN rm -rf /opt/python/cp37*
+RUN rm -rf /opt/python/cp38*
 RUN rm -rf /opt/python/pp*
 
 RUN for PYBIN in /opt/python/*/bin; do \
@@ -62,4 +63,4 @@ RUN cd $htk_path && \
     done && \
     ls -l /io/wheelhouse && \
     mkdir /io/wheels && \
-    cp /io/wheelhouse/histomicstk*many*2014* /io/wheels/.
+    cp /io/wheelhouse/histomicstk*manylinux* /io/wheels/.
diff --git a/histomicstk/annotations_and_masks/polygon_merger.py b/histomicstk/annotations_and_masks/polygon_merger.py
@@ -7,7 +7,7 @@
 import os
 
 import numpy as np
-from imageio import imread
+from imageio.v2 import imread
 from PIL import Image
 # import cv2
 from shapely.geometry.polygon import Polygon
diff --git a/histomicstk/annotations_and_masks/tests/test_annotation_and_mask_utils.py b/histomicstk/annotations_and_masks/tests/test_annotation_and_mask_utils.py
@@ -107,8 +107,9 @@ def test_get_scale_factor_and_appendStr(self):
             [(None, 10.), (0.25, '&magnification=10.00000000')],
             [(None, None), (1.0, '')],
         ]
-        for (MPP, MAG), (sftrue, apstr) in in_out:
-            sf, appendStr = get_scale_factor_and_appendStr(
-                gc=cfg.gc, slide_id=cfg.iteminfo['_id'], MPP=MPP, MAG=MAG)
-            assert sf == sftrue
-            assert appendStr == apstr
+        with pytest.warns(RuntimeWarning):
+            for (MPP, MAG), (sftrue, apstr) in in_out:
+                sf, appendStr = get_scale_factor_and_appendStr(
+                    gc=cfg.gc, slide_id=cfg.iteminfo['_id'], MPP=MPP, MAG=MAG)
+                assert sf == sftrue
+                assert appendStr == apstr
diff --git a/histomicstk/annotations_and_masks/tests/test_annotation_database_parser.py b/histomicstk/annotations_and_masks/tests/test_annotation_database_parser.py
@@ -88,10 +88,10 @@ def test_dump_annotations_locally_1(self):
         dbcon = sql_engine.connect()
 
         result = pd.read_sql_query(text("""SELECT count(*) FROM 'folders';"""), dbcon)
-        assert int(result.loc[0, :]) == 2
+        assert int(result.iloc[0, 0]) == 2
 
         result = pd.read_sql_query(text("""SELECT count(*) FROM 'items';"""), dbcon)
-        assert int(result.loc[0, :]) == 4
+        assert int(result.iloc[0, 0]) == 4
 
         # cleanup
         shutil.rmtree(savepath)
diff --git a/histomicstk/annotations_and_masks/tests/test_annotations_to_object_mask_handler.py b/histomicstk/annotations_and_masks/tests/test_annotations_to_object_mask_handler.py
@@ -6,7 +6,7 @@
 
 import numpy as np
 import pytest
-from imageio import imread
+from imageio.v2 import imread
 from pandas import read_csv
 
 from histomicstk.annotations_and_masks.annotation_and_mask_utils import (
diff --git a/histomicstk/annotations_and_masks/tests/test_masks_to_annotations_handler.py b/histomicstk/annotations_and_masks/tests/test_masks_to_annotations_handler.py
@@ -8,7 +8,7 @@
 
 import pandas as pd
 import pytest
-from imageio import imread
+from imageio.v2 import imread
 from pandas import read_csv
 
 from histomicstk.annotations_and_masks.annotation_and_mask_utils import \
diff --git a/histomicstk/features/compute_global_cell_graph_features.py b/histomicstk/features/compute_global_cell_graph_features.py
@@ -193,8 +193,14 @@ def _pop_stats(pop):
         if mask.all():
             break
         pop = pop[mask]
-    minmaxr = pop.min() / pop.max()
-    disorder = stddev / (mean + stddev)
+    if pop.max():
+        minmaxr = pop.min() / pop.max()
+    else:
+        minmaxr = 0.0
+    if mean + stddev:
+        disorder = stddev / (mean + stddev)
+    else:
+        disorder = 0.0
     return PopStats(mean, stddev, minmaxr, disorder)
 
 
diff --git a/histomicstk/features/compute_haralick_features.py b/histomicstk/features/compute_haralick_features.py
@@ -325,8 +325,10 @@ def compute_haralick_features(im_label, im_intensity, offsets=None,
             meanx = np.dot(n_Minus, px)
             variance = np.dot(px, np.square(n_Minus)) - np.square(meanx)
             nGLCMr = np.ravel(nGLCM)
-            Correlation = (np.dot(np.ravel(xy), nGLCMr) - np.square(meanx)) / variance
-
+            if variance:
+                Correlation = (np.dot(np.ravel(xy), nGLCMr) - np.square(meanx)) / variance
+            else:
+                Correlation = 0.0
             # computes sum of squares : variance
             SumOfSquares = variance
 
diff --git a/histomicstk/saliency/cellularity_detection_superpixels.py b/histomicstk/saliency/cellularity_detection_superpixels.py
@@ -506,7 +506,7 @@ def set_color_normalization_values(
         assert what in ('thumbnail', 'main')
 
         if ref_image_path is not None:
-            from imageio import imread
+            from imageio.v2 import imread
 
             ref_im = np.array(imread(ref_image_path, pilmode='RGB'))
             mu, sigma = lab_mean_std(ref_im)
diff --git a/histomicstk/saliency/cellularity_detection_thresholding.py b/histomicstk/saliency/cellularity_detection_thresholding.py
@@ -194,7 +194,7 @@ def find_potentially_cellular_regions(self):
         # Second, low-pass filter to dilate and smooth a bit
         self.maybe_cellular = gaussian(
             0 + (self.maybe_cellular > 0), sigma=self.cdt.cellular_step2_sigma,
-            output=None, mode='nearest', preserve_range=True)
+            out=None, mode='nearest', preserve_range=True)
 
         # find connected components
         self.maybe_cellular, _ = ndimage.label(self.maybe_cellular)
@@ -224,7 +224,7 @@ def find_top_cellular_regions(self):
         # get top n brightest regions from the largest areas
         intensity_feats.sort_values('Intensity.Mean', axis=0, inplace=True)
         discard = np.array(intensity_feats.index[:-self.cdt.cellular_top_n])
-        discard = np.in1d(top_cellular, discard).reshape(top_cellular.shape)
+        discard = np.isin(top_cellular, discard).reshape(top_cellular.shape)
         top_cellular[discard] = 0
 
         # integrate into labeled mask
@@ -614,7 +614,7 @@ def set_color_normalization_target(
         >    reinhard and macenko_pca are accepted.
 
         """
-        from imageio import imread
+        from imageioi.v2 import imread
 
         # read input image
         ref_im = np.array(imread(ref_image_path, pilmode='RGB'))
diff --git a/histomicstk/saliency/tissue_detection.py b/histomicstk/saliency/tissue_detection.py
@@ -105,7 +105,7 @@ def get_tissue_mask(
         if sigma > 0.0:
             thumbnail = gaussian(
                 thumbnail, sigma=sigma,
-                output=None, mode='nearest', preserve_range=True)
+                out=None, mode='nearest', preserve_range=True)
 
         # get threshold to keep analysis region
         try:
@@ -124,7 +124,7 @@ def get_tissue_mask(
 
     # only keep
     unique, counts = np.unique(labeled[labeled > 0], return_counts=True)
-    discard = np.in1d(labeled, unique[counts < min_size])
+    discard = np.isin(labeled, unique[counts < min_size])
     discard = discard.reshape(labeled.shape)
     labeled[discard] = 0
 
@@ -265,7 +265,7 @@ def _get_largest_regions(labeled, top_n=10):
     keep = unique[np.argsort(counts)[-top_n:]]
 
     mask = np.zeros(labeled_im.shape)
-    keep_pixels = np.in1d(labeled_im, keep)
+    keep_pixels = np.isin(labeled_im, keep)
     keep_pixels = keep_pixels.reshape(labeled_im.shape)
     mask[keep_pixels] = 1
     labeled_im[mask == 0] = 0
diff --git a/histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx b/histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx
diff --git a/setup.py b/setup.py
diff --git a/test_wheels.py b/test_wheels.py
diff --git a/tests/test_global_cell_graph_features.py b/tests/test_global_cell_graph_features.py
diff --git a/tests/test_segmentation_label.py b/tests/test_segmentation_label.py
diff --git a/tox.ini b/tox.ini
