Merge pull request #38 from simphony/dev

* Update to v3.3.9

* updated the ontology documentation

* updated entity names and imports in markdown files

* updated notebooks

* update ontology2dot image

* `nbconvert --execute` requires the jupyter_client package: `pip install jupyter_client` Fixes #16

* updated nbsphinx_kernel_name in conf.py
* updated requirements

* Add JSON schema of serialized CUDS objects to docs Fixes #21

* added missing files

* Document yaml2camelcase Fixes #25

* Updated link to RTD

* renamed openapi folder

* added CI action

* updated CI file

* added wheel to requirements

* moved wheel to CI file

* added rtd theme to req

* added pandoc

* added latexmk

* split dependencies

* split dependencies

* conf file for create-issue-branch

* updated paths

* added pico conflict notes

* added notes, hints and warning boxes

* Added wrapper_dev tutorial

* Reorganised the docs

* Reorganised wrapper section

* Update pico and installation (#34)

* updated pico uninstall all

* Updated installation notes

* Added badges (#40)

* osp-core is open source

* standalone section for installation

* added conda to installation

* removed references to pickle

* Fixed typo in tutorial

* Added note on tutorial download

* updated cuba.class references

* updated namespace import

* updated CI

* updated graph

* add vector notes, rename ontologies included

* notes on json serialisation

* added contact section, minor fixes

Co-authored-by: Matthias Urban <matthias.urban@iwm.fraunhofer.de>
Co-authored-by: Matthias Urban <42069939+urbanmatthias@users.noreply.github.com>

.github/issue-branch.yml

@@ -0,0 +1 @@
+mode: chatops

.github/workflows/ci.yml

@@ -0,0 +1,27 @@
+name: Test build
+
+on: pull_request
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+    - name: Install OS dependencies
+      run: |
+        sudo apt-get update 
+        sudo apt-get install pandoc latexmk
+        sudo apt-get install texlive-fonts-recommended texlive-latex-recommended texlive-latex-extra
+    - name: Install python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install wheel
+        pip install -r requirements.txt
+    - name: Build docs
+      run: python setup.py install

README.md

@@ -1,6 +1,9 @@
+## Build Status
+**latest** - [![Documentation latest](https://readthedocs.org/projects/simphony/badge/?version=latest)](https://simphony.readthedocs.io/en/latest/?badge=latest)  
+**dev** - [![Documentation dev](https://readthedocs.org/projects/simphony/badge/?version=dev)](https://simphony.readthedocs.io/en/latest/?badge=dev)
 
 # SimPhoNy docs
-To access the documentation, please visit: https://simphony-docs.readthedocs.io/en/latest/
+To access the documentation, please visit: https://simphony.readthedocs.io/en/latest/
 
 If you find any error or problem with the documentation, please [create an issue](https://github.com/simphony/docs/issues)
 

docs/source/about.md

@@ -1,21 +1,20 @@
 # About
+
 SimPhoNy is an ontology-based framework that promotes and enables interoperability between any 3rd-party software tool.
-Its latest version is soon to become an open-source python project.
+Its [core functionality](https://github.com/simphony/osp-core) is an open-source python project.
 The name ‘SimPhoNy’ stems from the SimPhoNy EU-project in which it was originally developed
 (See more details [here](https://www.simphony-project.eu/)). 
 One of SimPhoNy’s main tasks is to convert *opaque* data, meaning data whose semantics are hidden, to *transparent* data, that is data whose semantics is understood and easily accessible.
 
 This project aims to clarify the purpose and usage of the SimPhoNy platform through simple, short examples.
 In particular, this guide will try to expose the main concepts and components.
 
-_Contact:_ [Pablo de Andres](mailto:pablo.de.andres@iwm.fraunhofer.de), 
-[Matthias Urban](mailto:matthias.urban@iwm.fraunhofer.de) and 
-[Yoav Nahshon](mailto:yoav.nahshon@iwm.fraunhofer.de) from 
-the Materials Data Science and Informatics team, Fraunhofer IWM.
+All the tutorials in this documentation are Jupyter notebooks that can be downloaded
+by clicking on the "Edit on Github" button on the top right of the page.
 
 # License
-BSD 3-Clause 
-Copyright 2020 SimPhoNy OSP-core developers
+BSD 3-Clause  
+Copyright 2020 SimPhoNy OSP-core developers.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
@@ -44,7 +43,7 @@ These are some of the terms used in the following sections:
    1. `individual`: an instance of a class. E.g., an instance of the class 'City' can be used to represent the city of Freiburg in which case it would have the attribute 'name' with the value 'Freiburg'.
    1. `relationship`: a type of a way in which one individual relates to another. E.g., 'Has-A' which could use to form the relationship 'Freiburg (City) Has-A Dreisam (River)'.
    1. `entity`:  a general term that can refer to a class, a relationship, attribute, or an individual. E.g., 'City', 'name', 'Has-A', the Freiburg individual are all entities.
-   1. `namespace`: an ontology identifier. E.g., 'CITY_ONTOLOGY' which could be used as a namespace for the ontology that consists of the entities 'City', 'name' and 'Has-A'.
+   1. `namespace`: an ontology identifier. E.g., 'city_ontology' which could be used as a namespace for the ontology that consists of the entities 'City', 'name' and 'Has-A'.
        - Each entity is uniquely identified by its name and the namespace it is contained in. We call \<namespace name\>.\<entity name\> the `qualified entity name`.
 1. `CUDS`:  Common Universal Data Structure. A data structure that is used to uniformly represent ontology concepts in programming code.
    - CUDS exposes an API that provides CRUD (Create, Read, Update and Delete) functionalities.

docs/source/conf.py

@@ -27,6 +27,7 @@
     'nbsphinx',  # Jupyter
     'IPython.sphinxext.ipython_console_highlighting',  # Jupyter - Syntax highlight workaround
     'sphinx.ext.autosectionlabel',  # Auto-generate section labels.
+    'sphinx-jsonschema'  # Generate JSON schema for serialized CUDS
 ]
 
 master_doc = 'index'
@@ -75,3 +76,6 @@ def setup(app):
         # 'enable_auto_doc_ref': True,
     }, True)
     app.add_transform(AutoStructify)
+
+
+nbsphinx_allow_errors = True

docs/source/contact.md

@@ -0,0 +1,8 @@
+# Contact
+If you see something wrong, missing, or in need of clarification, you can directly
+create an issue in [here](https://github.com/simphony/docs/issues).
+
+Any other questions, issues or comments can be directed to [Pablo de Andres](mailto:pablo.de.andres@iwm.fraunhofer.de),
+[Matthias Urban](mailto:matthias.urban@iwm.fraunhofer.de)  and
+[Yoav Nahshon](mailto:yoav.nahshon@iwm.fraunhofer.de)
+from the Materials Data Science and Informatics team, Fraunhofer IWM.