From 77750e05ad1cc8bbcd649f4d873e9531fc9ce4f3 Mon Sep 17 00:00:00 2001 From: yoavnash Date: Wed, 7 Apr 2021 11:21:32 +0000 Subject: [PATCH 01/12] Create draft PR for #78 From fd51c6769a7ad8f2cc168d24307fd5d56cbe0642 Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Wed, 7 Apr 2021 13:49:01 +0200 Subject: [PATCH 02/12] Match filename with title --- docs/source/{getting_started.md => general_architecture.md} | 0 docs/source/index.md | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename docs/source/{getting_started.md => general_architecture.md} (100%) diff --git a/docs/source/getting_started.md b/docs/source/general_architecture.md similarity index 100% rename from docs/source/getting_started.md rename to docs/source/general_architecture.md diff --git a/docs/source/index.md b/docs/source/index.md index 392301e..477ef32 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -20,7 +20,7 @@ Here you can browse though the general documentation of SimPhoNy. about.md motivation.md - getting_started.md + general_architecture.md installation.md jupyter/cuds-api.ipynb jupyter/sessions_and_vars.ipynb From 89b8d4a10bfc3982efc053973e6013a6c88b31a4 Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Wed, 7 Apr 2021 13:51:01 +0200 Subject: [PATCH 03/12] Fix typo --- docs/source/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.md b/docs/source/index.md index 477ef32..7866d52 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -1,5 +1,5 @@ # Welcome to SimPhoNy docs! -Here you can browse though the general documentation of SimPhoNy. +Here you can browse through the general documentation of SimPhoNy. **Compatibility matrix** From 80a105f8ede6b66616b5f9834b0832889ec0506d Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Wed, 7 Apr 2021 20:45:13 +0200 Subject: [PATCH 04/12] Add panels --- docs/source/about.md | 12 +++++++++ docs/source/conf.py | 3 ++- docs/source/index.md | 61 ++++++++++++++++++++++++++++++++++++-------- requirements.txt | 1 + 4 files changed, 65 insertions(+), 12 deletions(-) diff --git a/docs/source/about.md b/docs/source/about.md index 2ca62e5..19ed38a 100644 --- a/docs/source/about.md +++ b/docs/source/about.md @@ -12,6 +12,18 @@ In particular, this guide will try to expose the main concepts and components. 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. +# Compatibility matrix + +```eval_rst + ============= ========== + SimPhoNy docs OSP-core + ============= ========== + 2.3.x 3.4.0-beta + 2.2.x 3.3.5-beta + 2.1.x 3.3.0-beta + ============= ========== +``` + # 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. diff --git a/docs/source/conf.py b/docs/source/conf.py index d6522b6..1ab4242 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -27,7 +27,8 @@ '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 + 'sphinx-jsonschema', # Generate JSON schema for serialized CUDS + 'sphinx_panels' # A sphinx extension for creating panels in a grid layout or as drop-downs ] master_doc = 'index' diff --git a/docs/source/index.md b/docs/source/index.md index 7866d52..8b25cb4 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -1,19 +1,58 @@ # Welcome to SimPhoNy docs! -Here you can browse through the general documentation of SimPhoNy. -**Compatibility matrix** +Here you can browse through the general documentation of SimPhoNy. ```eval_rst - ============= ========== - SimPhoNy docs OSP-core - ============= ========== - 2.3.x 3.4.0-beta - 2.2.x 3.3.5-beta - 2.1.x 3.3.0-beta - ============= ========== -``` -```eval_rst +.. panels:: + :body: text-center + + --- + **Getting Started** + + Overview, installation, and basic functionalities + + .. link-button:: about + :text: To the getting started guides + :classes: btn-outline-primary stretched-link + + --- + + **Working with Ontologies** + + s + + .. link-button:: api_ref + :text: To the development + :classes: btn-outline-primary stretched-link + --- + + **Wrapper Development** + + A deeper look into OSP-core for developing SimPhoNy wrappers + + .. link-button:: api_ref + :text: To wrapper development + :classes: btn-outline-primary stretched-link + --- + + **API Reference** + + Python API of CUDS, the *Session* classes, and other utilities + + .. link-button:: api_ref + :text: To the API reference + :classes: btn-outline-primary stretched-link + + --- + + **Tutorials** + + Walk-through tutorials on top of Jupyter Notebook + + .. link-button:: ./jupyter/ontology-interface.ipynb + :text: Ontology Interface + :classes: btn-outline-primary stretched-link .. toctree:: :caption: Introduction :maxdepth: 2 diff --git a/requirements.txt b/requirements.txt index 728f551..5c1819a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,3 +9,4 @@ ipython jupyter sphinx-jsonschema sphinx-autobuild +sphinx-panels From 0ae0288c1ee2f3dd06234f41e056c795cd3d1186 Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Wed, 7 Apr 2021 22:47:30 +0200 Subject: [PATCH 05/12] Rearrange sections --- docs/source/contact.md | 14 ++++- docs/source/index.md | 73 ++++++++++++++++++--------- docs/source/json.md | 16 ------ docs/source/{about.md => overview.md} | 14 +---- docs/source/utils.md | 14 +++++ 5 files changed, 76 insertions(+), 55 deletions(-) delete mode 100644 docs/source/json.md rename docs/source/{about.md => overview.md} (93%) diff --git a/docs/source/contact.md b/docs/source/contact.md index 4293900..d6763a4 100644 --- a/docs/source/contact.md +++ b/docs/source/contact.md @@ -5,4 +5,16 @@ 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. \ No newline at end of file +from the Materials Data Science and Informatics team, Fraunhofer IWM. + +```eval_rst +.. rubric:: Compatibility matrix + +============= ========== +SimPhoNy docs OSP-core +============= ========== +2.3.x 3.4.0-beta +2.2.x 3.3.5-beta +2.1.x 3.3.0-beta +============= ========== +``` \ No newline at end of file diff --git a/docs/source/index.md b/docs/source/index.md index 8b25cb4..5405845 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -10,28 +10,37 @@ Here you can browse through the general documentation of SimPhoNy. --- **Getting Started** - Overview, installation, and basic functionalities + Overview and main concepts, and installation guide - .. link-button:: about + .. link-button:: overview.html :text: To the getting started guides :classes: btn-outline-primary stretched-link + --- + **Usage Guide** + + Core functionalities, wrappers and more advanced features + + .. link-button:: jupyter/cuds-api.ipynb + :text: To usage guide + :classes: btn-outline-primary stretched-link + --- **Working with Ontologies** - s + Ontology overview, included ontologies, YAML ontologies and ontology querying - .. link-button:: api_ref - :text: To the development + .. link-button:: ontology_intro.html + :text: To the ontology guides :classes: btn-outline-primary stretched-link --- **Wrapper Development** - A deeper look into OSP-core for developing SimPhoNy wrappers + A deeper look into OSP-core for the purpose of development of SimPhoNy wrappers - .. link-button:: api_ref + .. link-button:: wrapper_development.html :text: To wrapper development :classes: btn-outline-primary stretched-link --- @@ -40,34 +49,45 @@ Here you can browse through the general documentation of SimPhoNy. Python API of CUDS, the *Session* classes, and other utilities - .. link-button:: api_ref + .. link-button:: api_ref.html :text: To the API reference :classes: btn-outline-primary stretched-link - + --- + **Additional Information** - **Tutorials** + License, acknowledgements, data protection, contact info and more. - Walk-through tutorials on top of Jupyter Notebook - - .. link-button:: ./jupyter/ontology-interface.ipynb - :text: Ontology Interface + .. link-button:: contribute.html + :text: To more information :classes: btn-outline-primary stretched-link + .. toctree:: - :caption: Introduction + :hidden: + :caption: Getting Started :maxdepth: 2 - about.md + overview.md motivation.md general_architecture.md installation.md + +.. toctree:: + :hidden: + :caption: Usage Guide + :maxdepth: 2 + jupyter/cuds-api.ipynb jupyter/sessions_and_vars.ipynb detailed_design.md utils.md + jupyter/multiple-wrappers.ipynb + jupyter/simlammps.ipynb + jupyter/quantum-espresso.ipynb .. toctree:: - :caption: Ontology + :hidden: + :caption: Working with Ontologies :maxdepth: 2 ontology_intro.md @@ -76,24 +96,27 @@ Here you can browse through the general documentation of SimPhoNy. owl.md jupyter/ontology-interface.ipynb - .. toctree:: - :caption: Wrappers + :hidden: + :caption: Wrapper Development + :maxdepth: 2 - jupyter/multiple-wrappers.ipynb - jupyter/simlammps.ipynb - jupyter/quantum-espresso.ipynb wrapper_development.md jupyter/wrapper_development.ipynb +.. toctree:: + :hidden: + :caption: API Reference + :maxdepth: 2 + + api_ref.md .. toctree:: - :caption: Additional + :hidden: + :caption: Additional Info :maxdepth: 2 contribute.md - api_ref.md - json.md links.md license.md Data protection diff --git a/docs/source/json.md b/docs/source/json.md deleted file mode 100644 index 2f0095e..0000000 --- a/docs/source/json.md +++ /dev/null @@ -1,16 +0,0 @@ - - -# Serialization JSON schema of CUDS objects - -When you serialize a CUDS object using the -[`serialize()` method in the utils module](api_ref.html#osp.core.utils.general.serialize), -you will get a json document as a result. -The method will traverse the hierarchical datastructure -using Depth First Traversal. -Therefore, its result is a json array composed of several flat CUDS objects. - -This array can later be deserialized using the opposite -[`deserialize`](api_ref.html#osp.core.utils.general.deserialize). - -The serialization is done via [JSON-LD](https://json-ld.org/), -with the schema used for the [OSP API in Marketplace](https://gitlab.cc-asp.fraunhofer.de/MarketPlace/osp-api). diff --git a/docs/source/about.md b/docs/source/overview.md similarity index 93% rename from docs/source/about.md rename to docs/source/overview.md index 19ed38a..ab1c6f7 100644 --- a/docs/source/about.md +++ b/docs/source/overview.md @@ -1,4 +1,4 @@ -# About +# Overview SimPhoNy is an ontology-based framework that promotes and enables interoperability between any 3rd-party software tool. Its [core functionality](https://github.com/simphony/osp-core) is an open-source python project. @@ -12,18 +12,6 @@ In particular, this guide will try to expose the main concepts and components. 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. -# Compatibility matrix - -```eval_rst - ============= ========== - SimPhoNy docs OSP-core - ============= ========== - 2.3.x 3.4.0-beta - 2.2.x 3.3.5-beta - 2.1.x 3.3.0-beta - ============= ========== -``` - # 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. diff --git a/docs/source/utils.md b/docs/source/utils.md index 8466c1a..7cb3a00 100644 --- a/docs/source/utils.md +++ b/docs/source/utils.md @@ -258,3 +258,17 @@ _Examples:_ root=city_cuds, rel=city.hasInhabitant) ``` +## Serialization JSON schema of CUDS objects + +When you serialize a CUDS object using the +[`serialize()` method in the utils module](api_ref.html#osp.core.utils.general.serialize), +you will get a json document as a result. +The method will traverse the hierarchical datastructure +using Depth First Traversal. +Therefore, its result is a json array composed of several flat CUDS objects. + +This array can later be deserialized using the opposite +[`deserialize`](api_ref.html#osp.core.utils.general.deserialize). + +The serialization is done via [JSON-LD](https://json-ld.org/), +with the schema used for the [OSP API in Marketplace](https://gitlab.cc-asp.fraunhofer.de/MarketPlace/osp-api). From 2d9f30ca8fb9714125b35dbf5507c6e36db1b548 Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Wed, 7 Apr 2021 23:19:16 +0200 Subject: [PATCH 06/12] Changes in text --- docs/source/index.md | 2 +- docs/source/jupyter/cuds-api.ipynb | 6 ++++-- docs/source/overview.md | 16 ++++------------ 3 files changed, 9 insertions(+), 15 deletions(-) diff --git a/docs/source/index.md b/docs/source/index.md index 5405845..592bc5b 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -1,6 +1,6 @@ # Welcome to SimPhoNy docs! -Here you can browse through the general documentation of SimPhoNy. +SimPhoNy is an ontology-based open-source Python-framework that promotes and enables interoperability between any 3rd-party software tool. Here you can learn more about it. ```eval_rst diff --git a/docs/source/jupyter/cuds-api.ipynb b/docs/source/jupyter/cuds-api.ipynb index cec182a..8332172 100644 --- a/docs/source/jupyter/cuds-api.ipynb +++ b/docs/source/jupyter/cuds-api.ipynb @@ -6,7 +6,9 @@ "source": [ "# Tutorial: CUDS API\n", "\n", - "This tutorial introduces the CUDS API. The code given here is based on [this](https://github.com/simphony/osp-core/blob/master/examples/api_example.py) example." + "This tutorial introduces the CUDS API. The code given here is based on [this](https://github.com/simphony/osp-core/blob/master/examples/api_example.py) example.\n", + "\n", + "Note that that this tutorial, as all others 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." ] }, { @@ -627,4 +629,4 @@ }, "nbformat": 4, "nbformat_minor": 4 -} +} \ No newline at end of file diff --git a/docs/source/overview.md b/docs/source/overview.md index ab1c6f7..28b9499 100644 --- a/docs/source/overview.md +++ b/docs/source/overview.md @@ -1,19 +1,11 @@ # Overview -SimPhoNy is an ontology-based framework that promotes and enables interoperability between any 3rd-party software tool. -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. - -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. +One of SimPhoNy’s main tasks is to convert *opaque* data, whose semantics are hidden from an external user to the system, to *transparent* data, whose semantics is understood and easily accessible by means of a common language, specified by an ontology. # Terminology -These are some of the terms used in the following sections: +The name ‘SimPhoNy’ stems from the SimPhoNy EU-project in which it was originally developed (see more details [here](https://www.simphony-project.eu/)). + +Here are some additional terms that are used throughout the documentation: 1. `API`: Application Programming Interface. A set of functions that allow the interaction with an application or system. 1. `OSP`: Open Simulation Platform. A set of common standards and related tools that form the basic environment on top of which compatible and compliant simulation workflows can be developed and run. From ce6d3d1c3a177db396ce9c251c6f79f2c8f710ea Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Thu, 8 Apr 2021 01:09:16 +0200 Subject: [PATCH 07/12] Relocate compatibility table --- docs/source/contact.md | 14 +------------- docs/source/index.md | 9 ++++----- docs/source/links.md | 21 ++++++++++++++++++++- 3 files changed, 25 insertions(+), 19 deletions(-) diff --git a/docs/source/contact.md b/docs/source/contact.md index d6763a4..94ab947 100644 --- a/docs/source/contact.md +++ b/docs/source/contact.md @@ -3,18 +3,6 @@ If you see something wrong, missing, or in need of clarification, you can direct 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 +[Jose Manuel Dominguez](mailto:jose.manuel.dominguez@iwm.fraunhofer.de) and [Yoav Nahshon](mailto:yoav.nahshon@iwm.fraunhofer.de) from the Materials Data Science and Informatics team, Fraunhofer IWM. - -```eval_rst -.. rubric:: Compatibility matrix - -============= ========== -SimPhoNy docs OSP-core -============= ========== -2.3.x 3.4.0-beta -2.2.x 3.3.5-beta -2.1.x 3.3.0-beta -============= ========== -``` \ No newline at end of file diff --git a/docs/source/index.md b/docs/source/index.md index 592bc5b..a88c893 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -10,7 +10,7 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena --- **Getting Started** - Overview and main concepts, and installation guide + Overview, main concepts, and installation guide .. link-button:: overview.html :text: To the getting started guides @@ -19,7 +19,7 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena --- **Usage Guide** - Core functionalities, wrappers and more advanced features + Core functionalities, wrappers and advanced utilities .. link-button:: jupyter/cuds-api.ipynb :text: To usage guide @@ -38,7 +38,7 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena **Wrapper Development** - A deeper look into OSP-core for the purpose of development of SimPhoNy wrappers + A deep dive into the wrapper mechanism for developing new wrappers .. link-button:: wrapper_development.html :text: To wrapper development @@ -56,7 +56,7 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena --- **Additional Information** - License, acknowledgements, data protection, contact info and more. + License, acknowledgements, data protection, contact info and more .. link-button:: contribute.html :text: To more information @@ -122,5 +122,4 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena Data protection Imprint contact.md - ``` diff --git a/docs/source/links.md b/docs/source/links.md index b38a1d1..333c48e 100644 --- a/docs/source/links.md +++ b/docs/source/links.md @@ -27,4 +27,23 @@ SimDOME Horizon 2020 H2020-NMBP-TO-IND-2018-2020 814492 INTERSECT Horizon 2020 H2020-NMBP-TO-IND-2018-2020 814487 ReaxPRO Horizon 2020 H2020-NMBP-TO-IND-2018-2020 814416 =========== ============ =========================== =============== -``` \ No newline at end of file +``` + + +# Compatibility table +The following table describes the compatibilities between of SimPhoNy docs and OSP-core. + +```eval_rst + +.. table:: + :align: center + :widths: auto + + ============= ========== + SimPhoNy docs OSP-core + ============= ========== + 2.3.x 3.4.0-beta + 2.2.x 3.3.5-beta + 2.1.x 3.3.0-beta + ============= ========== +``` From e5f0b083f991652c5e6f6bf356d6f87f60b9def5 Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Thu, 8 Apr 2021 01:10:18 +0200 Subject: [PATCH 08/12] Change title --- docs/source/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.md b/docs/source/index.md index a88c893..5aada09 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -1,4 +1,4 @@ -# Welcome to SimPhoNy docs! +# Welcome to the SimPhoNy docs! SimPhoNy is an ontology-based open-source Python-framework that promotes and enables interoperability between any 3rd-party software tool. Here you can learn more about it. From a3031b6c687f056ec0602800aec81d8a125bc57e Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Thu, 8 Apr 2021 01:14:22 +0200 Subject: [PATCH 09/12] Rename motivation section --- docs/source/{motivation.md => fundamentals.md} | 2 +- docs/source/index.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename docs/source/{motivation.md => fundamentals.md} (99%) diff --git a/docs/source/motivation.md b/docs/source/fundamentals.md similarity index 99% rename from docs/source/motivation.md rename to docs/source/fundamentals.md index 72e2c72..fce19ce 100644 --- a/docs/source/motivation.md +++ b/docs/source/fundamentals.md @@ -1,4 +1,4 @@ -## Motivation +## Fundamental concepts In this section, we will present some of the main concepts SimPhoNy was created to tackle. ### Operability There is a multitude of tools and programs out there, all with their own formats and protocols. diff --git a/docs/source/index.md b/docs/source/index.md index 5aada09..81ee990 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -68,7 +68,7 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena :maxdepth: 2 overview.md - motivation.md + fundamentals.md general_architecture.md installation.md From 5f159168793ae016443dff245d603bb4c4450d84 Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Thu, 8 Apr 2021 01:17:44 +0200 Subject: [PATCH 10/12] Rephrase --- docs/source/fundamentals.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/fundamentals.md b/docs/source/fundamentals.md index fce19ce..15fee8f 100644 --- a/docs/source/fundamentals.md +++ b/docs/source/fundamentals.md @@ -1,5 +1,5 @@ ## Fundamental concepts -In this section, we will present some of the main concepts SimPhoNy was created to tackle. +In this section we will present some of the main concepts behind SimPhoNy. ### Operability There is a multitude of tools and programs out there, all with their own formats and protocols. From 9514a5f1a2acc3bdde99134af14466bca919046e Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Thu, 8 Apr 2021 08:29:53 +0200 Subject: [PATCH 11/12] Update title --- docs/source/conf.py | 2 +- docs/source/contact.md | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 1ab4242..3f076ed 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -12,7 +12,7 @@ # -- Project information ----------------------------------------------------- project = 'SimPhoNy' # Version is given in setuptools -copyright = '2020, Materials Data Science and Informatics team at Fraunhofer IWM' +copyright = '2021, Materials Data Science and Informatics Team at Fraunhofer IWM' author = 'Materials Data Science and Informatics team at Fraunhofer IWM' # -- General configuration --------------------------------------------------- diff --git a/docs/source/contact.md b/docs/source/contact.md index 94ab947..3003224 100644 --- a/docs/source/contact.md +++ b/docs/source/contact.md @@ -5,4 +5,4 @@ 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), [Jose Manuel Dominguez](mailto:jose.manuel.dominguez@iwm.fraunhofer.de) and [Yoav Nahshon](mailto:yoav.nahshon@iwm.fraunhofer.de) -from the Materials Data Science and Informatics team, Fraunhofer IWM. +from the Materials Data Science and Informatics Team, Fraunhofer IWM. diff --git a/setup.py b/setup.py index 15b1583..dc5168d 100644 --- a/setup.py +++ b/setup.py @@ -18,7 +18,7 @@ def generate_pdf(self): setup( name=NAME, version=VERSION, - author='Materials Data Science and Informatics team at Fraunhofer IWM', + author='Materials Data Science and Informatics Team at Fraunhofer IWM', description='The SimPhoNy documentation', keywords='simphony, documentation, sphinx, Fraunhofer IWM', long_description=README_TEXT, From 58a223dd52b77301cd095b32179cb278795c8370 Mon Sep 17 00:00:00 2001 From: Yoav Nahshon Date: Fri, 9 Apr 2021 15:53:48 +0200 Subject: [PATCH 12/12] Fix phrasing --- docs/source/index.md | 8 ++++---- docs/source/overview.md | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/index.md b/docs/source/index.md index 81ee990..190ca05 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -1,6 +1,6 @@ # Welcome to the SimPhoNy docs! -SimPhoNy is an ontology-based open-source Python-framework that promotes and enables interoperability between any 3rd-party software tool. Here you can learn more about it. +SimPhoNy is an ontology-based open-source Python framework that promotes and enables interoperability between any 3rd-party software tool. Here you can learn more about it. ```eval_rst @@ -22,7 +22,7 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena Core functionalities, wrappers and advanced utilities .. link-button:: jupyter/cuds-api.ipynb - :text: To usage guide + :text: To the usage guides :classes: btn-outline-primary stretched-link --- @@ -41,7 +41,7 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena A deep dive into the wrapper mechanism for developing new wrappers .. link-button:: wrapper_development.html - :text: To wrapper development + :text: To the wrapper development guides :classes: btn-outline-primary stretched-link --- @@ -59,7 +59,7 @@ SimPhoNy is an ontology-based open-source Python-framework that promotes and ena License, acknowledgements, data protection, contact info and more .. link-button:: contribute.html - :text: To more information + :text: To get more information :classes: btn-outline-primary stretched-link .. toctree:: diff --git a/docs/source/overview.md b/docs/source/overview.md index 28b9499..2a28cb4 100644 --- a/docs/source/overview.md +++ b/docs/source/overview.md @@ -1,6 +1,6 @@ # Overview -One of SimPhoNy’s main tasks is to convert *opaque* data, whose semantics are hidden from an external user to the system, to *transparent* data, whose semantics is understood and easily accessible by means of a common language, specified by an ontology. +One of SimPhoNy’s main tasks is to convert *opaque* data, whose semantics are hidden from an external user to the system, to *transparent* data, whose semantics are understood and easily accessible by means of a common language, specified by an ontology. # Terminology The name ‘SimPhoNy’ stems from the SimPhoNy EU-project in which it was originally developed (see more details [here](https://www.simphony-project.eu/)).