add Streamlit demo (#31)

* streamlit demo segm
* fix Pillow ver.
* add Makefile
* move Docs CI - CircleCI > GHA
* update line length

.github/workflows/ci-experiment.yml

@@ -8,8 +8,8 @@ on:  # Trigger the workflow on push or pull request, but only for the master bra
     branches: [master]
 
 jobs:
-  pytest:
 
+  bash-expt:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -37,11 +37,6 @@ jobs:
         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

.github/workflows/docs-check.yml

@@ -0,0 +1,85 @@
+name: "Docs check"
+# https://github.com/marketplace/actions/sphinx-build
+
+on:
+- pull_request
+
+jobs:
+
+  test-docs:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@master
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      # 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: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install -y cmake pandoc
+          pip --version
+          pip install -r requirements.txt
+          pip install -r docs/requirements.txt
+          python setup.py build_ext --inplace
+          pip list
+        shell: bash
+
+      - name: Test Documentation
+        run: |
+          # First run the same pipeline as Read-The-Docs
+          cd docs
+          make doctest
+
+  make-docs:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@master
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      # 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: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake pandoc latexmk
+          sudo apt-get install -y texlive-latex-extra dvipng texlive-pictures
+          pip --version
+          pip install -r requirements.txt
+          pip install -r docs/requirements.txt
+          python setup.py build_ext --inplace
+          pip list
+        shell: bash
+
+      - name: Make Documentation
+        run: |
+          cd docs
+          make clean
+          make html --debug --jobs 2 SPHINXOPTS="-W"
+          make latexpdf
+
+      - name: Upload built docs
+        uses: actions/upload-artifact@v2
+        with:
+          name: docs-results-${{ runner.os }}-${{ matrix.python-version }}
+          path: docs/build/html/
+        if: success()

MANIFEST.in

@@ -5,13 +5,15 @@ recursive-exclude __pycache__ *.pyc *.pyo *.orig
 
 # Include the README
 include *.md
+exclude Makefile
+exclude streamlit*.py
 
 # Include the license file
 include LICENSE
 
 # Include the Requirements
 include requirements.txt
-include requirements-py27.txt
+include require-py27.txt
 
 # Include package
 recursive-include imsegm *.py *.pyx
@@ -24,7 +26,6 @@ exclude *.yml
 # Exclude testing
 exclude pytest.*
 recursive-exclude tests *
-exclude tests
 
 # Exclude experiments
 exclude */*.sh

Makefile

@@ -0,0 +1,22 @@
+.PHONY: test clean docs
+
+clean:
+	# clean all temp runs
+	rm -rf .pytest_cache
+	rm -rf ./docs/build
+	rm -rf ./docs/source/*.md
+	rm -rf ./docs/source/api
+	rm -rf ./docs/source/notebooks
+
+test: clean
+	pip install --quiet -r requirements.txt
+	pip install --quiet -r tests/requirements.txt
+
+	# run tests with coverage
+	python -m coverage run --source imsegm -m pytest imsegm tests -v
+	python -m coverage report
+
+docs: clean
+	pip install --quiet -r docs/requirements.txt
+	python setup.py build_ext --inplace
+	python -m sphinx -b html -W --keep-going docs/source docs/build

circle.yml

@@ -25,13 +25,6 @@ references:
         coverage report
         python setup.py check --metadata --strict
 
-  formatting: &formatting
-    run:
-      name: Formatting
-      command: |
-        pip install flake8 -q
-        flake8 .
-
   build_project: &build_project
    run:
      name: Building project
@@ -42,18 +35,11 @@ references:
        python setup.py build_ext --inplace
        pwd ; ls -l imsegm
 
-  install_project: &install_project
-   run:
-     name: Insatlling project
-     command: |
-       python setup.py install --user
-       rm -rf imsegm
-
   make_docs: &make_docs
    run:
      name: Make Documentation
      command: |
-       # sudo apt-get install pandoc
+       sudo apt-get install pandoc
        pyenv global 3.7.3
        python --version
        pip install -r requirements.txt
@@ -65,12 +51,6 @@ references:
        make latexpdf
 
 jobs:
-  Formatting:
-    docker:
-      - image: circleci/python:3.6
-    steps:
-      - checkout
-      - *formatting
 
   Py3-Tests:
     docker:
@@ -98,26 +78,6 @@ jobs:
       - store_artifacts:
           path: test-reports
 
-  Py3-Experiments:
-    docker:
-        - image: circleci/python:3.6
-    steps: &steps_expt
-      - checkout
-      # INSTALLATION
-      - *install_pips
-      #- run: git lfs pull
-      - *install_project
-
-      - run: mkdir libs && mkdir output && mkdir results
-      # ANNOTATION section
-      - run: bash handling_annotations/test_annotations.sh
-      # SEGMENTATION section
-      - run: bash experiments_segmentation/test_segmentations.sh
-      # CENTER DETECT. section
-      - run: bash experiments_ovary_centres/test_ovary_centers.sh
-      # REGION GROWING section
-      - run: bash experiments_ovary_detect/test_ovary_detect.sh
-
   Build-Docs:
     docker:
       - image: readthedocs/build:latest
@@ -137,8 +97,5 @@ workflows:
   version: 2
   build:
     jobs:
-      - Formatting
       - Py3-Tests
-      #- Py2-Experiments
-      #- Py3-Experiments
-      - Build-Docs
+      # - Build-Docs

docs/requirements.txt

@@ -1,7 +1,7 @@
 sphinx>=2.0, <3.0
-recommonmark  # fails with badges
 m2r  # fails with multi-line text
-nbsphinx
+myst-parser
+nbsphinx>=0.8.5
 pandoc
-docutils<0.15  # higher version breaks py2
+docutils
 ipython

docs/source/conf.py

@@ -91,8 +91,7 @@
     'sphinx.ext.napoleon',
     'sphinx.ext.autosummary',
     # 'sphinxcontrib.rsvgconverter'
-    'recommonmark',
-    # 'm2r',
+    'myst_parser',
     'nbsphinx',
 ]
 
@@ -106,6 +105,8 @@
 nbsphinx_execute = 'never'
 nbsphinx_allow_errors = True
 
+myst_update_mathjax = False
+
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
@@ -336,10 +337,11 @@ def find_source():
 
 autodoc_member_order = 'groupwise'
 autoclass_content = 'both'
-autodoc_default_flags = [
-    'members',
-    'undoc-members',
-    'show-inheritance',
-    'private-members',
-    # 'special-members', 'inherited-members'
-]
+autodoc_default_options = {
+    'members': True,
+    'undoc-members': True,
+    'private-members': True,
+    'methods': True,
+    'exclude-members': '_abc_impl',
+    'show-inheritance': True,
+}

experiments_ovary_centres/run_center_evaluation.py

@@ -159,8 +159,7 @@ def load_center_evaluate(idx_row, df_annot, path_annot, path_visu=None, col_pref
         return dict_row
 
     assert all(c in df_annot.columns for c in tl_visu.COLUMNS_POSITION_EGG_ANNOT), \
-        'some required columns %r are missing for %s' % \
-        (tl_visu.COLUMNS_POSITION_EGG_ANNOT, df_annot.columns)
+        'some required columns %r are missing for %s' % (tl_visu.COLUMNS_POSITION_EGG_ANNOT, df_annot.columns)
     mask_eggs = estimate_eggs_from_info(df_annot.loc[idx], img.shape[:2])
 
     try:

experiments_ovary_centres/run_center_prediction.py

@@ -168,8 +168,7 @@ def main(params):
     params = run_train.arg_parse_params(DEFAULT_PARAMS)
 
     params['path_classif'] = params['path_centers']
-    assert os.path.isfile(params['path_classif']), \
-        'missing classifier: %s' % params['path_classif']
+    assert os.path.isfile(params['path_classif']), 'missing classifier: %s' % params['path_classif']
 
     main(params)
 

experiments_segmentation/run_segm_slic_model_graphcut.py

@@ -320,8 +320,7 @@ def export_visual(idx_name, img, segm, debug_visual=None, path_out=None, path_vi
         fig.savefig(path_fig)
         plt.close(fig)
 
-    if path_visu is not None and os.path.isdir(path_visu) \
-            and debug_visual is not None:
+    if path_visu is not None and os.path.isdir(path_visu) and debug_visual is not None:
         path_fig = os.path.join(path_visu, str(idx_name) + '_debug.png')
         logging.debug('exporting (debug) visualization: %s', path_fig)
         fig = tl_visu.figure_segm_graphcut_debug(debug_visual)

handling_annotations/run_segm_annot_relabel.py

@@ -95,8 +95,7 @@ def relabel_folder_images(path_images, path_out, labels_old, labels_new, nb_work
     :param [int] labels_new: list of new labels
     :param int nb_workers:
     """
-    assert os.path.isdir(os.path.dirname(path_images)), \
-        'missing folder: %s' % path_images
+    assert os.path.isdir(os.path.dirname(path_images)), 'missing folder: %s' % path_images
     assert os.path.isdir(path_out), 'missing ouput folder: %s' % path_out
 
     path_imgs = sorted(glob.glob(path_images))

imsegm/graph_cuts.py

@@ -321,8 +321,7 @@ def compute_spatial_dist(centres, edges, relative=False):
     array([ 1.12,  1.57,  1.34,  1.34,  0.5 ,  0.63,  0.5 ])
     """
     assert np.max(edges) < len(centres), \
-        'max vertex %i exceed size of centres %i'\
-        % (np.max(edges), len(centres))
+        'max vertex %i exceed size of centres %i' % (np.max(edges), len(centres))
     ndim = np.max([len(c) for c in centres if c is not None])
     # replace empy segments by a empty vector
     for i, c in enumerate(centres):
@@ -510,8 +509,7 @@ def create_pairwise_matrix(gc_regul, nb_classes):
     """
     if isinstance(gc_regul, np.ndarray):
         assert gc_regul.shape[0] == gc_regul.shape[1] == nb_classes, \
-            'GC regul matrix %r should match match number of classes (%i)' \
-            % (gc_regul.shape, nb_classes)
+            'GC regul matrix %r should match match number of classes (%i)' % (gc_regul.shape, nb_classes)
         # sub_min = np.tile(np.min(gc_regul, axis=0), (gc_regul.shape[0], 1))
         pairwise = gc_regul - np.min(gc_regul)
     elif isinstance(gc_regul, list):
@@ -566,9 +564,9 @@ def insert_gc_debug_images(debug_visual, segments, graph_labels, unary_cost, edg
     debug_visual['imgs_unary_cost'] = draw_graphcut_unary_cost_segments(segments, unary_cost)
     img = debug_visual.get('slic_mean', None)
     list_centres = superpixel_centers(segments)
-    debug_visual['img_graph_edges'] = \
-        draw_graphcut_weighted_edges(segments, list_centres, edges,
-                                     edge_weights, img_bg=img)
+    debug_visual['img_graph_edges'] = draw_graphcut_weighted_edges(
+        segments, list_centres, edges, edge_weights, img_bg=img
+    )
     debug_visual['img_graph_segm'] = draw_color_labeling(segments, graph_labels)