Merge pull request #2 from simphony/v2.2.0-dev

v2.2.0

.readthedocs.yml

@@ -0,0 +1,20 @@
+# 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
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+  - epub
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: requirements.txt

LICENSE

@@ -0,0 +1,12 @@
+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:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,13 +1,12 @@
-[![pipeline status](https://gitlab.cc-asp.fraunhofer.de/simphony/documentation/badges/master/pipeline.svg)](https://gitlab.cc-asp.fraunhofer.de/simphony/documentation/commits/master)
 
 # SimPhoNy docs
-To access the documentation, please visit: http://simphony.pages.fraunhofer.de/documentation/latest
+To access the documentation, please visit: https://simphony-docs.readthedocs.io/en/latest/
 
-If you find any error or problem with the documentation, please [create an issue](https://gitlab.cc-asp.fraunhofer.de/simphony/documentation/issues)
+If you find any error or problem with the documentation, please [create an issue](https://github.com/simphony/docs/issues)
 
 ## Local installation
 First, some requirements have to be manually installed:
-- [osp-core](https://gitlab.cc-asp.fraunhofer.de/simphony/osp-core)
+- [osp-core](https://github.com/simphony/osp-core)
 - pandoc
 - LaTeX requirements
   ```shell
@@ -21,7 +20,7 @@ First, some requirements have to be manually installed:
 
 If you want to render the documentation locally, you can run:
 ```
-python3 setup.py build_sphinx
+python3 setup.py install
 ```
 
 This will render the html and generate a LaTeX pdf (in `docs/build/latex/SimPhoNy_docs.pdf`).

docs/source/about.md

@@ -1,5 +1,8 @@
 # About
-SimPhoNy is an ontology-based framework that promotes and enables interoperability between any 3rd-party software tool. It’s latest version is soon to become 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/)). 
+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.
+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.
@@ -10,6 +13,20 @@ _Contact:_ [Pablo de Andres](mailto:pablo.de.andres@iwm.fraunhofer.de),
 [Yoav Nahshon](mailto:yoav.nahshon@iwm.fraunhofer.de) from 
 the Materials Data Science and Informatics team, Fraunhofer IWM.
 
+# License
+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:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
 # Terminology
 These are some of the terms used in the following sections:
 1. `API`: Application Programming Interface. A set of functions that allow the interaction with an application or system.

docs/source/api_ref.md

@@ -1,5 +1,5 @@
 # API Reference
-This document is for developers of osp-core, it contians the API functions
+This document is for developers of OSP-core, it contains the API functions
 
 ## Cuds class
 ```eval_rst

docs/source/conf.py

@@ -16,7 +16,6 @@
 author = 'Materials Data Science and Informatics team at Fraunhofer IWM'
 
 # -- General configuration ---------------------------------------------------
-
 extensions = [
     'recommonmark',  # md
     'sphinx.ext.autodoc',  # API ref
@@ -30,7 +29,10 @@
     'sphinx.ext.autosectionlabel',  # Auto-generate section labels.
 ]
 
+master_doc = 'index'
+
 plantuml = 'java -jar lib/plantuml.jar'
+plantuml_output_format = 'svg_img'
 
 templates_path = ['_templates']
 
@@ -46,18 +48,6 @@
 html_favicon = '_static/img/simphony_favicon.png'
 html_logo = '_static/img/simphony_logo_light.png'
 html_static_path = ['_static']
-html_js_files = [
-    'version_links.js',
-]
-
-html_context = {
-    "gitlab_host": "gitlab.cc-asp.fraunhofer.de",
-    "display_gitlab": True, # Integrate Gitlab
-    "gitlab_user": "simphony", # Username
-    "gitlab_repo": "documentation", # Repo name
-    "gitlab_version": "master", # Version
-    "conf_py_path": "/docs/source/", # Path in the checkout to the docs root
-}
 
 
 # -- Options for LaTeX output -------------------------------------------------

docs/source/conversion_owl_to_yaml.md

@@ -9,7 +9,7 @@ converted to YAML.
 - We use owlready2 for the conversion. Therefore, the ontology
 must be in one of the following formats: RDF/XML, OWL/XML, NTriples.
 - Make sure you ran the reasoner and exported the inferred axioms.
-- OSP core must be installed
+- OSP-core must be installed
 
 ## Conversion
 
@@ -34,15 +34,15 @@ The document doc/working_with_emmo.md explains how you can get the EMMO.
      --namespace NAMESPACE, -n NAMESPACE
                            The namespace for the resulting YAML file in UPPERCASE
      --conversion_options_file CONVERSION_OPTIONS_FILE, -c CONVERSION_OPTIONS_FILE
-                           Path to a file explaining how the ontology should be transformed, s.t. it is compatible with osp-core
+                           Path to a file explaining how the ontology should be transformed, s.t. it is compatible with OSP-core
      --version VERSION, -v VERSION
                            The version string for the resulting YAML file
      --output-file OUTPUT_FILE, -o OUTPUT_FILE
                            Where the output file should be saved
    ```
 
 2. You have to specify the owl input file and the namespace,
-   with which the entities in the owl file should be accessible in OSP core:
+   with which the entities in the owl file should be accessible in OSP-core:
 
    ```sh
    $ owl2yml -n MY_NAMESPACE path/to/owlfile.owl
@@ -61,7 +61,7 @@ The document doc/working_with_emmo.md explains how you can get the EMMO.
    ```
 
 5. It is recommended that you extend the ontology,
-   such that it is easier to use with OSP core.
+   such that it is easier to use with OSP-core.
    For that you have to create a yaml file in
    the following format:
 
@@ -84,7 +84,7 @@ The document doc/working_with_emmo.md explains how you can get the EMMO.
 
    - You can specify a default relationship with the `default_rel` keyword.
      You have to provide the IRI of the relationship.
-     In OSP core, when you add one CUDS objects to another without specifying a relationship, this relationship will be used.
+     In OSP-core, when you add one CUDS objects to another without specifying a relationship, this relationship will be used.
 
    - CUDS objects are containers conceptually.
      Therefore, you need to specify which relationships encode a containment in a CUDS objects.