update CI

* drop Shippable
* try git LFS
* update init info
* fix pkg setup
* fix yaml load

.gitattributes

@@ -1 +1,7 @@
-*.ipynb linguist-vendored
+*.ipynb linguist-vendored
+# Used by Git-LFS
+# *.png filter=lfs diff=lfs merge=lfs -text
+# *.jpg filter=lfs diff=lfs merge=lfs -text
+# *.jpeg filter=lfs diff=lfs merge=lfs -text
+# *.tif filter=lfs diff=lfs merge=lfs -text
+# *.tiff filter=lfs diff=lfs merge=lfs -text

.travis.yml

@@ -54,12 +54,12 @@ after_success:
   - python-codacy-coverage -r coverage.xml
   - coverage report
   # ANNOTATION section
-  - bash handling_annotations/test_annotations.sh
+  #- bash handling_annotations/test_annotations.sh
   # SEGMENTATION section
-  - bash experiments_segmentation/test_segmentations.sh
+  #- bash experiments_segmentation/test_segmentations.sh
   # CENTER DETECT. section
-  - bash experiments_ovary_centres/test_ovary_centers.sh
+  #- bash experiments_ovary_centres/test_ovary_centers.sh
   # REGION GROWING section
-  - bash experiments_ovary_detect/test_ovary_detect.sh
+  #- bash experiments_ovary_detect/test_ovary_detect.sh
   # test installed package
-  - cd .. && python -c "import imsegm.descriptors"
+  #- cd .. && python -c "import imsegm.descriptors"

README.md

@@ -4,11 +4,11 @@
 [![codecov](https://codecov.io/gh/Borda/pyImSegm/branch/master/graph/badge.svg?token=BCvf6F5sFP)](https://codecov.io/gh/Borda/pyImSegm)
 [![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)
-[![Run Status](https://api.shippable.com/projects/5962ea48a125960700c197f8/badge?branch=master)](https://app.shippable.com/github/Borda/pyImSegm)
 [![CodeFactor](https://www.codefactor.io/repository/github/borda/pyimsegm/badge)](https://www.codefactor.io/repository/github/borda/pyimsegm)
 [![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)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Borda/pyImSegm/master?filepath=notebooks)
 -->

circle.yml

@@ -6,19 +6,21 @@ references:
     run:
       name: Install PyPI dependences
       command: |
-        sudo apt-get update
+        sudo apt-get update -qq
+        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
         sudo pip install -U backports.functools_lru_cache  # required for matplotlib @py2
         pip install -r requirements.txt --user
-        pip list
+        pip --version ; pip list
 
   test_coverage: &test_coverage
     run:
       name: Testing and Formating
       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
         python setup.py check -m -s
         flake8 . --ignore=E402,E731 --max-line-length=100
@@ -27,11 +29,16 @@ references:
    run:
      name: Building project
      command: |
-       mkdir libs && mkdir output && mkdir results && mkdir test-reports
        gcc --version ; python --version ; pwd ; ls -l
-       pip --version ; pip freeze
        python setup.py build_ext --inplace
 
+  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
@@ -42,29 +49,21 @@ references:
        cd docs; make html
 
 jobs:
-  Py2:
+  Py3-Tests:
     docker:
-      - image: circleci/python:2.7
-    steps: &steps
+      - image: circleci/python:3.6
+    steps: &steps_test
       - checkout
       # INSTALLATION
       - *install_pips
+      #- run: git lfs pull
       # BUILDING
       - *build_project
       # TESTING
       - *test_coverage
       # DOCUMENTATION
       - *make_docs
 
-      # 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
-
       # PASSING
       - run:
           name: Finalise
@@ -77,14 +76,41 @@ jobs:
       - store_artifacts:
           path: test-reports
 
-  Py3:
+  Py3-Experiments:
     docker:
-      - image: circleci/python:3.6
-    steps: *steps
+        - 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
+
+  Py2-Tests:
+    docker:
+      - image: circleci/python:2.7
+    steps: *steps_test
+
+  Py2-Experiments:
+    docker:
+      - image: circleci/python:2.7
+    steps: *steps_expt
 
 workflows:
   version: 2
   build:
     jobs:
-      - Py2
-      - Py3
+      - Py2-Tests
+      - Py3-Tests
+      - Py2-Experiments
+      - Py3-Experiments

docs/source/conf.py

@@ -30,7 +30,7 @@
 
 # export the documentation
 with open('intro.rst', 'w') as fp:
-    intro = imsegm.__doc__.replace(os.linesep + ' ', '')
+    intro = imsegm.__long_doc__.replace(os.linesep + ' ', '')
     fp.write(m2r.convert(intro))
     # fp.write(imsegm.__doc__)
 

imsegm/__init__.py

@@ -16,8 +16,9 @@
 __author_email__ = '[email protected]'
 __license__ = 'BSD 3-clause'
 __homepage__ = 'https://borda.github.io/pyImSegm'
-__copyright__ = 'Copyright (c) 2014-2019, Jiri Borovec.'
-__doc__ = """# Image segmentation - general superpixel segmentation & region growing
+__copyright__ = 'Copyright (c) 2014-2019, %s.' % __author__
+__doc__ = 'Image segmentation - general superpixel segmentation & region growing'
+__long_doc__ = "# %s" % __doc__ + """
 
 This package is aiming at (un/semi)supervised segmentation on superpixels with
  computing some basic colour and texture features. This general segmentation

imsegm/utilities/experiments.py

@@ -152,15 +152,15 @@ def create_experiment_folder(params, dir_name, stamp_unique=True, skip_load=True
     >>> p = {'path_out': '.'}
     >>> p = create_experiment_folder(p, 'my_test', False, skip_load=True)
     >>> pd.Series(p).sort_index()  #doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
-    computer                   (...
+    computer                   [...
     path_exp      ./my_test_EXAMPLE
     path_out                      .
     dtype: object
     >>> p = create_experiment_folder(p, 'my_test', False, skip_load=False)
     >>> shutil.rmtree(p['path_exp'], ignore_errors=True)
     >>> p = create_experiment_folder(p, 'my_test', stamp_unique=True)
     >>> pd.Series(p).sort_index()  #doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
-    computer                         (...
+    computer                         [...
     path_exp    ./my_test_EXAMPLE_...-...
     path_out                            .
     dtype: object
@@ -175,9 +175,11 @@ def create_experiment_folder(params, dir_name, stamp_unique=True, skip_load=True
         if os.path.isdir(path_expt):
             logging.warning('particular out folder already exists')
             path_expt += ':' + str(uuid.uuid4().hex)
+
     logging.info('creating experiment folder "{}"'.format(path_expt))
     if not os.path.exists(path_expt):
         os.mkdir(path_expt)
+
     # loading confing if it exists
     path_config = os.path.join(path_expt, CONFIG_YAML)
     if os.path.exists(path_config) and not skip_load:
@@ -186,8 +188,9 @@ def create_experiment_folder(params, dir_name, stamp_unique=True, skip_load=True
         params = load_config_yaml(path_config)
         params.update({k: params_in[k] for k in params_in if 'path' in k})
         logging.info('loaded following PARAMETERS: %s', string_dict(params))
+
     # extending parameters bu this run
-    params.update({'computer': os.uname(), 'path_exp': path_expt})
+    params.update({'computer': list(os.uname()), 'path_exp': path_expt})
     # export experiment config
     logging.debug('saving params to file "%s"', CONFIG_YAML)
     save_config_yaml(path_config, params)
@@ -456,7 +459,7 @@ def load_config_yaml(path_config):
     >>> os.remove(p_conf)
     """
     with open(path_config, 'r') as fp:
-        config = yaml.load(fp)
+        config = yaml.safe_load(fp)
     return config
 
 

setup.py

@@ -77,7 +77,7 @@ def _parse_requirements(file_path):
     long_description=imsegm.__doc__,
     long_description_content_type='text/markdown',
 
-    packages=['imsegm'],
+    packages=['imsegm', 'imsegm.utilities'],
     cmdclass={'build_ext': BuildExt},
     ext_modules=[
         Extension('imsegm.features_cython',