CI actions

* add CI testing
* add CI experiments
* add badge
* fix minumal req.
* fix re-label
* fix minor msgs

.github/workflows/ci-experiment.yml

@@ -0,0 +1,88 @@
+name: CI experiments
+
+# see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
+on:  # Trigger the workflow on push or pull request, but only for the master branch
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  pytest:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [2.7, 3.6, 3.7, 3.8]
+
+    # Timeout: https://stackoverflow.com/a/59076067/4521646
+    timeout-minutes: 35
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    # Note: This uses an internal pip API and may not always work
+    # https://github.com/actions/cache/blob/master/examples.md#multiple-oss-in-a-workflow
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-py${{ matrix.python-version }}-
+
+    - name: Set py2.7 dependencies
+      if: matrix.python-version == 2.7
+      run: |
+        cp -r requirements-py27.txt requirements.txt
+
+    - name: install ImSegm
+      run: |
+        python --version
+        pip --version
+        pip install wheel --quiet
+        pip install https://github.com/Borda/pyGCO/archive/master.zip
+        pip install . --user
+        rm -rf imsegm
+        pip list
+        # create filders
+        mkdir libs
+        mkdir output
+        mkdir results
+
+    - name: ANNOTATION section
+      env:
+        DISPLAY: ""
+      run: |
+        bash handling_annotations/test_annotations.sh
+
+    - name: SEGMENTATION section
+      env:
+        DISPLAY: ""
+      run: |
+        bash experiments_segmentation/test_segmentations.sh
+
+    - name: CENTER DETECT. section
+      env:
+        DISPLAY: ""
+      run: |
+        bash experiments_ovary_centres/test_ovary_centers.sh
+
+    - name: REGION GROWING section
+      env:
+        DISPLAY: ""
+      run: |
+        bash experiments_ovary_detect/test_ovary_detect.sh
+
+    - name: remove ImSegm
+      env:
+        DISPLAY: ""
+      run: |
+        # just to not being cached
+        pip uninstall -y imsegm

.github/workflows/ci-testing.yml

@@ -0,0 +1,107 @@
+name: CI testing
+
+# see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
+on:  # Trigger the workflow on push or pull request, but only for the master branch
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  pytest:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-18.04, macOS-10.15]  # , windows-2019
+        python-version: [2.7, 3.6, 3.8]
+        requires: ['minimal', 'latest']
+        exclude:
+          - python-version: 2.7
+            requires: 'minimal'
+          - python-version: 3.8
+            requires: 'minimal'
+
+    # Timeout: https://stackoverflow.com/a/59076067/4521646
+    timeout-minutes: 35
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set py2.7 dependencies
+      if: matrix.python-version == 2.7
+      run: |
+        cp -r requirements-py27.txt requirements.txt
+        # required for matplotlib @py2
+        pip install -U backports.functools_lru_cache
+
+    - name: Set min. dependencies
+      if: matrix.requires == 'minimal'
+      run: |
+        python -c "fname = 'requirements.txt' ; req = open(fname).read().replace('>=', '==') ; open(fname, 'w').write(req)"
+        python -c "fname = 'tests/requirements.txt' ; req = open(fname).read().replace('>=', '==') ; open(fname, 'w').write(req)"
+
+    # Note: This uses an internal pip API and may not always work
+    # https://github.com/actions/cache/blob/master/examples.md#multiple-oss-in-a-workflow
+    - name: Get pip cache
+      id: pip-cache
+      run: |
+        python -c "from pip._internal.locations import USER_CACHE_DIR; print('::set-output name=dir::' + USER_CACHE_DIR)"
+
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ matrix.requires }}-${{ hashFiles('requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ matrix.requires }}-
+
+    - name: Install dependencies
+      run: |
+        pip install wheel --quiet
+        pip install --requirement requirements.txt --quiet --upgrade
+        pip install --requirement tests/requirements.txt --quiet --upgrade
+        python --version
+        pip --version
+        pip list
+        mkdir output
+        mkdir results
+      shell: bash
+
+    - name: Tests
+      env:
+        DISPLAY: ""
+      run: |
+        check-manifest
+        python setup.py check --metadata --strict
+        python setup.py install --dry-run --user
+        python setup.py build_ext --inplace
+        coverage run --source imsegm -m py.test imsegm tests --durations=25 --junitxml=junit/test-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}.xml
+        flake8 .
+
+    - name: Upload pytest test results
+      uses: actions/upload-artifact@master
+      with:
+        name: pytest-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}
+        path: junit/test-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}.xml
+      # Use always() to always run this step to publish test results when there are test failures
+      if: always()
+
+    - name: Statistics
+      if: success()
+      run: |
+        coverage report
+        coverage xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      if: success()
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: coverage.xml
+        fail_ci_if_error: false

.travis.yml

@@ -27,8 +27,8 @@ matrix:
     - dist: bionic  # Ubuntu 18.04
       python: 3.6
       env: MIN_REQUIREMENTS=1
-    - dist: bionic  # Ubuntu 18.04
-      python: 3.7
+    #- dist: bionic  # Ubuntu 18.04
+    #  python: 3.7
     - dist: bionic  # Ubuntu 18.04
       python: 3.8
 
@@ -63,7 +63,7 @@ before_script:
 script:
   - python setup.py build_ext --inplace
   # - pytest imsegm -v --doctest-modules
-  - coverage run -m py.test imsegm tests --doctest-modules --flake8
+  - coverage run --source imsegm -m py.test imsegm tests  # --flake8
   # - nosetests imsegm tests -v --exe --with-doctest --with-xunit --with-coverage --cover-package=imsegm
   - python setup.py install --dry-run
 
@@ -72,13 +72,3 @@ after_success:
   - coverage xml
   - python-codacy-coverage -r coverage.xml
   - coverage report
-  # ANNOTATION section
-  #- bash handling_annotations/test_annotations.sh
-  # SEGMENTATION section
-  #- bash experiments_segmentation/test_segmentations.sh
-  # CENTER DETECT. section
-  #- bash experiments_ovary_centres/test_ovary_centers.sh
-  # REGION GROWING section
-  #- bash experiments_ovary_detect/test_ovary_detect.sh
-  # test installed package
-  #- cd .. && python -c "import imsegm.descriptors"

README.md

@@ -5,8 +5,11 @@
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/48b7976bbe9d42bc8452f6f9e573ee70)](https://www.codacy.com/app/Borda/pyImSegm?utm_source=github.com&utm_medium=referral&utm_content=Borda/pyImSegm&utm_campaign=Badge_Grade)
 [![CircleCI](https://circleci.com/gh/Borda/pyImSegm.svg?style=svg&circle-token=a30180a28ae7e490c0c0829d1549fcec9a5c59d0)](https://circleci.com/gh/Borda/pyImSegm)
 [![CodeFactor](https://www.codefactor.io/repository/github/borda/pyimsegm/badge)](https://www.codefactor.io/repository/github/borda/pyimsegm)
+[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/Borda/pyImSegm.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/Borda/pyImSegm/context:python)
+
 [![Documentation Status](https://readthedocs.org/projects/pyimsegm/badge/?version=latest)](https://pyimsegm.readthedocs.io/en/latest/?badge=latest)
 [![Gitter](https://badges.gitter.im/pyImSegm/community.svg)](https://gitter.im/pyImSegm/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
+
 <!--
 [![Run Status](https://api.shippable.com/projects/5962ea48a125960700c197f8/badge?branch=master)](https://app.shippable.com/github/Borda/pyImSegm)
 [![Coverage Badge](https://api.shippable.com/projects/5962ea48a125960700c197f8/coverageBadge?branch=master)](https://app.shippable.com/github/Borda/pyImSegm)

circle.yml

@@ -7,7 +7,7 @@ references:
       name: Install PyPI dependences
       command: |
         sudo apt-get update -qq
-        sudo apt-get install git-lfs
+        #sudo apt-get install git-lfs
         sudo apt-get install tk-dev pkg-config python-dev python-tk
         sudo pip install --upgrade pip setuptools
         sudo pip install -r ./tests/requirements.txt
@@ -21,7 +21,7 @@ references:
       command: |
         unset DISPLAY
         mkdir output && mkdir results && mkdir test-reports
-        coverage run --source imsegm -m py.test imsegm tests -v --doctest-modules --junitxml=test-reports/pytest_junit.xml
+        coverage run --source imsegm -m py.test imsegm tests -v --junitxml=test-reports/pytest_junit.xml
         coverage report
         python setup.py check --metadata --strict
 
@@ -149,6 +149,6 @@ workflows:
       - Formatting
       - Py2-Tests
       - Py3-Tests
-      - Py2-Experiments
-      - Py3-Experiments
+      #- Py2-Experiments
+      #- Py3-Experiments
       - Build-Docs

experiments_ovary_detect/run_ellipse_cut_scale.py

@@ -87,7 +87,7 @@ def perform_stage(df_group, stage, path_images, path_out):
     stat_a = NORM_FUNC(df_group['ellipse_a'])
     stat_b = NORM_FUNC(df_group['ellipse_b'])
     norm_size = (int(stat_b), int(stat_a))
-    logging.info('normal dimension is %r' % norm_size)
+    logging.info('normal dimension is {}'.format(norm_size))
 
     path_out_stage = os.path.join(path_out, str(stage))
     if not os.path.isdir(path_out_stage):

handling_annotations/run_overlap_images_segms.py

@@ -84,7 +84,7 @@ def visualise_overlap(path_img, path_seg, path_out,
     segm_alpha = tl_visu.norm_aplha(segm_alpha)
 
     if b_relabel:
-        seg, _, _ = segmentation.relabel_sequential(seg)
+        seg, _, _ = segmentation.relabel_sequential(seg.copy())
 
     if img.ndim == 2:  # for gray images of ovary
         img = np.rollaxis(np.tile(img, (3, 1, 1)), 0, 3)

imsegm/annotation.py

@@ -279,8 +279,7 @@ def quantize_image_nearest_color(img, colors):
 
 def image_inpaint_pixels(img, valid_mask):
     assert img.shape == valid_mask.shape, \
-        'image size %r and mask size %r should be equal' \
-        % (img.shape, valid_mask.shape)
+        'image size %r and mask size %r should be equal' % (img.shape, valid_mask.shape)
     coords = np.array(np.nonzero(valid_mask)).T
     values = img[valid_mask]
     it = interpolate.NearestNDInterpolator(coords, values)

imsegm/classification.py

@@ -508,7 +508,7 @@ def feature_scoring_selection(features, labels, names=None, path_out=''):
     >>> import shutil
     >>> shutil.rmtree(path_out, ignore_errors=True)
     """
-    logging.info('Feature selection for %r', names)
+    logging.info('Feature selection for %s', names)
     features = np.array(features) if not isinstance(features, np.ndarray) else features
     labels = np.array(labels) if not isinstance(labels, np.ndarray) else labels
     logging.debug('Features: %r and labels: %r', features.shape, labels.shape)
@@ -571,7 +571,7 @@ def save_classifier(path_out, classif, clf_name, params, feature_names=None,
     'TESTINNG'
     >>> os.remove(p_clf)
     """
-    assert os.path.isdir(path_out), 'missing folder: %r' % path_out
+    assert os.path.isdir(path_out), 'missing folder: %s' % path_out
     dict_classif = {
         'params': params,
         'name': clf_name,

imsegm/graph_cuts.py

@@ -5,14 +5,15 @@
 """
 
 import logging
+from warnings import warn
 
 import numpy as np
 
 try:
     from gco import cut_general_graph
-except Exception:
-    print('WARNING: Missing Grah-Cut (GCO) library,'
-          ' please install it from https://github.com/Borda/pyGCO.')
+except ImportError:
+    warn('Missing Grah-Cut (GCO) library,'
+         ' please install it from https://github.com/Borda/pyGCO.')
 from skimage import filters
 from sklearn import metrics, preprocessing
 from sklearn import pipeline, cluster, mixture, decomposition

imsegm/region_growing.py

@@ -7,6 +7,7 @@
 """
 
 import logging
+from warnings import warn
 
 import numpy as np
 from scipy import stats, ndimage, interpolate
@@ -15,9 +16,9 @@
 
 try:
     from gco import cut_general_graph, cut_grid_graph
-except Exception:
-    print('WARNING: Missing Grah-Cut (GCO) library,'
-          ' please install it from https://github.com/Borda/pyGCO.')
+except ImportError:
+    warn('Missing Grah-Cut (GCO) library,'
+         ' please install it from https://github.com/Borda/pyGCO.')
 
 from imsegm.graph_cuts import MAX_PAIRWISE_COST, get_vertexes_edges, compute_spatial_dist
 from imsegm.labeling import histogram_regions_labels_norm

imsegm/utilities/data_io.py

@@ -173,8 +173,8 @@ def load_landmarks_csv(path_file):
     assert os.path.exists(path_file), 'missing "%s"' % path_file
     df = pd.read_csv(path_file, index_col=0)
     landmarks = df[COLUMNS_COORDS].values.tolist()
-    logging.debug(' load_landmarks_csv (%i): \n%r', len(landmarks),
-                  np.asarray(landmarks).astype(int).tolist())
+    logging.debug(' load_landmarks_csv (%i): \n%r',
+                  len(landmarks), np.asarray(landmarks).astype(int).tolist())
     return landmarks
 
 

imsegm/utilities/experiments.py

@@ -392,7 +392,7 @@ def __init__(self, wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc='',
     def __iter__(self):
         tqdm_bar = None
         if self.desc is not None:
-            desc = '%r @%i-threads' % (self.desc, self.nb_workers)
+            desc = '%s @%i-threads' % (self.desc, self.nb_workers)
             tqdm_bar = tqdm.tqdm(total=len(self), desc=desc)
 
         if self.nb_workers > 1:

requirements.txt

@@ -3,7 +3,7 @@ Cython >= 0.28  # 0.27 fails with python 3.7
 numpy >= 1.13.3  # version 1.16 breaks skimage 0.14
 scipy >= 1.0
 pandas >= 0.19
-pillow >= 2.1.0, < 7  # fail loading JPG images
+pillow >= 4.0, < 7  # fail loading JPG images
 matplotlib >= 2.0.2
 scikit-learn >= 0.18.1
 scikit-image >= 0.13.0

setup.cfg

@@ -17,6 +17,7 @@ verbose = 2
 # max-complexity = 10
 
 [tool:pytest]
+addopts = --doctest-modules
 log_cli = 1
 log_cli_level = CRITICAL
 #log_cli_format = %(message)s