add sphinx docs

* reformat version & doc
* add read-the-doc
* auto api-doc
* add ipynb examples
* add github templates
* ignore tests
* drop 3-party packages
* reformat module desc.
* link source-code

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Contributor Covenant Code of Conduct
+
+> A code of conduct is a set of rules outlining the social norms and rules and responsibilities of, or proper practices for, an individual, party or organization
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all project spaces, and it also applies when an individual is representing the project or its community in public spaces. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at TBA. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,38 @@
+# Description
+
+Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
+
+Fixes # (issue)
+
+## Type of change
+
+Please delete options that are not relevant.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+# How Has This Been Tested?
+
+Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
+
+- [ ] Test A
+- [ ] Test B
+
+**Test Configuration**:
+* Firmware version:
+* Hardware:
+* Toolchain:
+* SDK:
+
+# Checklist:
+
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Any dependent changes have been merged and published in downstream modules

.gitignore

@@ -28,4 +28,7 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
-.hypothesis/
+.hypothesis/
+
+# Documentation
+docs/build

.readthedocs.yml

@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.6
+  install:
+    - requirements: requirements.txt
+    - requirements: docs/requirements.txt

.shippable.yml

@@ -40,7 +40,7 @@ install:
   - mkdir libs
 
   - pip install -r requirements.txt
-  - pip install "nose>=1.3.7" coverage codecov "pytest>=3.0.5" flake8
+  - pip install -r requirements-dev.txt
   - pip list
 
 script:

.travis.yml

@@ -31,9 +31,8 @@ before_install:
 
 install:
   - mkdir libs
-
   - pip install -r requirements.txt
-  - pip install nose coverage codecov pytest codacy-coverage check-manifest flake8
+  - pip install -r requirements-dev.txt
   - pip list
 
 before_script:

MANIFEST.in

@@ -11,6 +11,7 @@ include LICENSE
 
 # Include the Requirements
 include requirements.txt
+exclude requirements-*.txt
 
 # Include package
 recursive-include imsegm *.py *.pyx

README.md

@@ -5,24 +5,25 @@
 [![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)
-[![Coverage Badge](https://api.shippable.com/projects/5962ea48a125960700c197f8/coverageBadge?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)
 <!--
+[![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)
 -->
 
 ---
 
 ## Superpixel segmentation with GraphCut regularisation
 
-Image segmentation is widely used as an initial phase of many image processing tasks in computer vision and image analysis. Many recent segmentation methods use superpixels because they reduce the size of the segmentation problem by order of magnitude. Also,  features on superpixels are much more robust than features on pixels only. We use spatial regularisation on superpixels to make segmented regions more compact. The segmentation pipeline comprises (i) computation of superpixels; (ii) extraction of descriptors such as colour and texture; (iii) soft classification, using a standard classifier for supervised learning, or the Gaussian Mixture Model for unsupervised learning; (iv) final segmentation using Graph Cut. We use this segmentation pipeline on real-world applications in medical imaging (see a sample [images](./data_images)). We also show that [unsupervised segmentation](./notebooks/segment-2d_slic-fts-model-gc.ipynb) is sufficient for some situations, and provides similar results to those obtained using [trained segmentation](notebooks/segment-2d_slic-fts-classif-gc.ipynb).
+Image segmentation is widely used as an initial phase of many image processing tasks in computer vision and image analysis. Many recent segmentation methods use superpixels because they reduce the size of the segmentation problem by order of magnitude. Also,  features on superpixels are much more robust than features on pixels only. We use spatial regularisation on superpixels to make segmented regions more compact. The segmentation pipeline comprises (i) computation of superpixels; (ii) extraction of descriptors such as colour and texture; (iii) soft classification, using a standard classifier for supervised learning, or the Gaussian Mixture Model for unsupervised learning; (iv) final segmentation using Graph Cut. We use this segmentation pipeline on real-world applications in medical imaging (see a sample [images](./data_images)). We also show that [unsupervised segmentation](notebooks/segment-2d_slic-fts-clust-gc.ipynb) is sufficient for some situations, and provides similar results to those obtained using [trained segmentation](notebooks/segment-2d_slic-fts-classif-gc.ipynb).
 
 ![schema](figures/schema_slic-fts-clf-gc.jpg)
 
 **Sample ipython notebooks:**
 * [Supervised segmentation](notebooks/segment-2d_slic-fts-classif-gc.ipynb) requires training annotation
-* [Unsupervised segmentation](notebooks/segment-2d_slic-fts-model-gc.ipynb) just asks for expected number of classes
+* [Unsupervised segmentation](notebooks/segment-2d_slic-fts-clust-gc.ipynb) just asks for expected number of classes
 * **partially annotated images** with missing annotation is marked by a negative number
 
 **Illustration**
@@ -339,6 +340,6 @@ pip install --user git+https://github.com/Borda/morph-snakes.git
 ## References
 
 For complete references see [BibTex](docs/references.bib).
-1. Borovec J., Svihlik J., Kybic J., Habart D. (2017). **Supervised and unsupervised segmentation using superpixels, model estimation, and Graph Cut.** SPIE Journal of Electronic Imaging 26(6), 061610, [DOI: 10.1117/1.JEI.26.6.061610](http://doi.org/10.1117/1.JEI.26.6.061610).
+1. Borovec J., Svihlik J., Kybic J., Habart D. (2017). **Supervised and unsupervised segmentation using superpixels, model estimation, and Graph Cut.** SPIE Journal of Electronic Imaging 26(6), 061610. [DOI: 10.1117/1.JEI.26.6.061610](http://doi.org/10.1117/1.JEI.26.6.061610).
 1. Borovec J., Kybic J., Nava R. (2017) **Detection and Localization of Drosophila Egg Chambers in Microscopy Images.** In: Wang Q., Shi Y., Suk HI., Suzuki K. (eds) Machine Learning in Medical Imaging. MLMI 2017. LNCS, vol 10541. Springer, Cham. [DOI: 10.1007/978-3-319-67389-9_3](http://doi.org/10.1007/978-3-319-67389-9_3).
-1. Borovec J., Kybic J., Sugimoto, A. (2017). **Region growing using superpixels with learned shape prior.** SPIE Journal of Electronic Imaging 26(6),  061611, [DOI: 10.1117/1.JEI.26.6.061611](http://doi.org/10.1117/1.JEI.26.6.061611).
+1. Borovec J., Kybic J., Sugimoto, A. (2017). **Region growing using superpixels with learned shape prior.** SPIE Journal of Electronic Imaging 26(6),  061611. [DOI: 10.1117/1.JEI.26.6.061611](http://doi.org/10.1117/1.JEI.26.6.061611).

circle.yml

@@ -9,7 +9,7 @@ references:
         sudo apt-get update
         sudo apt-get install tk-dev pkg-config python-dev python-tk
         sudo pip install --upgrade pip setuptools
-        sudo pip install nose coverage pytest pytest-cov flake8
+        sudo pip install -r requirements-dev.txt
         sudo pip install -U backports.functools_lru_cache  # required for matplotlib @py2
         pip install -r requirements.txt --user
         pip list
@@ -32,6 +32,15 @@ references:
        pip --version ; pip freeze
        python setup.py build_ext --inplace
 
+  make_docs: &make_docs
+   run:
+     name: Make Documentation
+     command: |
+       sudo apt-get install pandoc
+       sudo pip install -r docs/requirements.txt
+       # sphinx-apidoc -o ./docs/source ./imsegm **/tests/* --force --follow-links
+       cd docs; make html
+
 jobs:
   Py2:
     docker:
@@ -44,6 +53,8 @@ jobs:
       - *build_project
       # TESTING
       - *test_coverage
+      # DOCUMENTATION
+      - *make_docs
 
       # ANNOTATION section
       - run: bash handling_annotations/test_annotations.sh

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/requirements.txt

@@ -0,0 +1,5 @@
+sphinx>=1.4
+recommonmark  # fails with badges
+m2r  # fails with multi-line text
+nbsphinx
+pandoc