Bump version to 4.0.0 (#244)

* Bump version to 4.0.0

* Update README.md

* Remove release-candidate warning

Author: kysrpex

README.md

@@ -1,20 +1,18 @@
-## Build Status
+# SimPhoNy documentation
 
-**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)
+To access the documentation, please visit:
+[https://simphony.readthedocs.io](https://simphony.readthedocs.io/en/v4.0.0/).
 
-# SimPhoNy docs
+If you find any error or problem with the documentation,
+please [create an issue](https://github.com/simphony/docs/issues).
 
-To access the documentation, please visit: [https://simphony.readthedocs.io](https://simphony.readthedocs.io).
-
-If you find any error or problem with the documentation, please [create an issue](https://github.com/simphony/docs/issues).
-
-## Local Rendering
+## Local rendering
 
 ### HTML
 
-A server will start, generate the docs and listen for changes in the source files.
-This can be done by using docker or installing the development environment directly on the you machine. Next are installation guides for Docker and Linux OS.
+Start a server, generate the docs and listen for changes in the source files.
+This can be done by using docker or installing the development environment
+directly on your machine. Next are installation guides for Docker and Linux.
 
 #### Docker
 
@@ -59,7 +57,8 @@ The documentation will be available on
 
 ### PDF (LaTeX)
 
-To generate a PDF of the documentation, simply run (from the root project folder):
+To generate a PDF of the documentation, simply run (from the root project
+folder):
 
 ```sh
 make -C docs latexpdf

docs/contribute.md

@@ -23,12 +23,12 @@ It might be useful to become familiar with them:
 
 There are 3 main categories of repos:
 
-- The [_SimPhoNy_ repository](https://github.com/simphony/osp-core/tree/v4.0.0rc4)
+- The [_SimPhoNy_ repository](https://github.com/simphony/simphony-osp/tree/v4.0.0)
   contains the nucleus of SimPhoNy, the base on which the wrappers build.
 - Each _wrapper_ will be in its own repository on GitHub or GitLab,
   mimicking
   [wrapper_development](https://github.com/simphony/wrapper-development).
-- [_docs_](https://github.com/simphony/docs/tree/v4.0.0rc4)
+- [_docs_](https://github.com/simphony/docs/tree/v4.0.0)
   holds the source for this documentation.
 
 There are also 4 types of branches:
@@ -100,21 +100,21 @@ workflow, and the different commits used to synchronise them:
   [Flake8](https://github.com/pycqa/flake8) tool. The validation is also
   enforced on the repository by the
   [continuous integration](contribute.md#continuous-integration). Click
-  [here](https://github.com/simphony/osp-core/blob/master/.github/workflows/ci.yml#L12)
+  [here](https://github.com/simphony/simphony-osp/blob/v4.0.0/.github/workflows/ci.yml#L12)
   to see the specific options with which Flake8 is launched.
 - All Python code should be reformatted with
   [black](https://github.com/psf/black) and
   [isort](https://github.com/PyCQA/isort). The use of said tools is
   enforced by the
   [continuous integration](contribute.md#continuous-integration). Therefore,
   we strongly recommend that you use the
-  [configuration file](https://github.com/simphony/osp-core/blob/master/.pre-commit-config.yaml)
+  [configuration file](https://github.com/simphony/simphony-osp/blob/v4.0.0/.pre-commit-config.yaml)
   bundled with the repository to
   [install](https://pre-commit.com/#installation) the
   [pre-commit framework](https://pre-commit.com/), that automates the task
   using git pre-commit hooks.
 - A few
-  [other style conventions](https://github.com/simphony/osp-core/blob/master/.pre-commit-config.yaml)
+  [other style conventions](https://github.com/simphony/simphony-osp/blob/v4.0.0/.pre-commit-config.yaml)
   are also enforced by the continuous integration through
   [pre-commit](https://pre-commit.com/) (such as empty lines at the end of
   text files). If you decide not to use it, the CI will let you know what
@@ -132,11 +132,11 @@ workflow, and the different commits used to synchronise them:
 - Code style conventions are enforced through the use of Flake8, black, isort,
   and various
   [pre-commit](https://pre-commit.com/)
-  [hooks](https://github.com/simphony/osp-core/blob/master/.pre-commit-config.yaml).
+  [hooks](https://github.com/simphony/simphony-osp/blob/v4.0.0/.pre-commit-config.yaml).
 - Tests are automatically run for all pull requests.
 - For the OSP-core code, benchmarks are run after every merge to `dev`.
   Benchmark results are available
-  [here](https://simphony.github.io/osp-core/dev/bench/index.html). The CI
+  [here](https://simphony.github.io/simphony-osp/dev/bench/index.html). The CI
   will report a failure when a benchmark is 50% slower than in the previous
   run, in addition to automatically commenting on the commit.
 

docs/developers/wrappers.md

@@ -314,4 +314,4 @@ the server with small amounts of large exchanges of information.
 This page is meant to offer a mid-level view on what SimPhoNy Wrappers are
 and how do they work. If you are interested in developing one, you may find a
 template for building and packaging a wrapper in the
-[wrapper development repository](https://github.com/simphony/wrapper-development/tree/v4.0.0rc5).
+[wrapper development repository](https://github.com/simphony/wrapper-development/tree/v4.0.0).

docs/index.md

@@ -1,12 +1,5 @@
 # Welcome to the SimPhoNy documentation!
 
-```{note}
-⚠️ You are reading the documentation of a release candidate version of
-SimPhoNy. The documentation for the latest
-stable version of SimPhoNy can be found
-[here](https://simphony.readthedocs.io/en/latest/).
-```
-
 The SimPhoNy Open Simulation Platform is a framework that aims to achieve
 interoperability between software such as simulation engines, databases and
 data repositories using a knowledge graph as the common language. It is focused

docs/introduction/installation.md

@@ -7,7 +7,7 @@ required. SimPhoNy is
 installed using the [`pip` package manager](https://pip.pypa.io/en/stable/).
 
 ```shell
-pip install osp-core
+pip install simphony-osp
 ```
 
 ## Wrapper installation
@@ -23,7 +23,7 @@ instructions.
 ## Developers
 
 If you are a developer or an advanced user, you might be interested in
-installing OSP-core from source.
+installing SimPhoNy from source.
 
 ```shell
 git clone https://github.com/simphony/simphony-osp.git

docs/introduction/quickstart.ipynb

@@ -15,7 +15,7 @@
    "source": [
     "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n",
     "    \n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v4.0.0rc4?filepath=docs%2Fintroduction%2Fquickstart.ipynb \"Click to run this tutorial yourself!\")\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v4.0.0?filepath=docs%2Fintroduction%2Fquickstart.ipynb \"Click to run this tutorial yourself!\")\n",
     "    \n",
     "</figure>\n",
     "\n",

docs/links.md

@@ -6,7 +6,7 @@ SimPhoNy:
 
 - [GitLab's SimPhoNy group](https://gitlab.cc-asp.fraunhofer.de/simphony)
 - [GitHub's SimPhoNy group](https://github.com/simphony)
-- [SimPhoNy repository](https://github.com/simphony/osp-core)
+- [SimPhoNy repository](https://github.com/simphony/simphony-osp)
 - [wrappers](https://gitlab.cc-asp.fraunhofer.de/simphony/wrappers)
 - [wrapper development](https://github.com/simphony/wrapper-development)
 
@@ -18,7 +18,7 @@ Technologies used:
 
 # Acknowledgements
 
-SimPhoNy OSP-core and wrappers development is supported by the following Grants:
+SimPhoNy is supported by the following grants:
 
 ```{eval-rst}
 =============  ============  ===============================   ==================
@@ -44,4 +44,5 @@ We would like to acknowledge and thank our project partners, especially
 [Centre Internacional de Mètodes Numèrics a l'Enginyeria (CIMNE)](https://cimne.com/)
 and the [University of Jyväskylä](https://www.jyu.fi/en), for their important
 contributions to some of the core concepts of SimPhoNy, which were originally
-demonstrated under the project https://github.com/simphony/simphony-common.
+demonstrated under the project
+[simphony-common](https://github.com/simphony/simphony-common).

docs/usage/assertional_knowledge.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n",
     "\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v4.0.0rc4?filepath=docs%2Fusage%2Fassertional_knowledge.ipynb \"Click to run this tutorial yourself!\")\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v4.0.0?filepath=docs%2Fusage%2Fassertional_knowledge.ipynb \"Click to run this tutorial yourself!\")\n",
     "    \n",
     "</figure>"
    ]
@@ -138,7 +138,7 @@
     "<div class=\"admonition note\">\n",
     "<div class=\"admonition-title\" style=\"font-weight: bold\"><div style=\"display: inline-block\">Note</div></div>\n",
     "\n",
-    "At the moment, it is not possible to instantiate multi-class individuals. We [are aware of this issue](https://github.com/simphony/osp-core/issues/669), and planning to include this functionality in a future minor release.\n",
+    "At the moment, it is not possible to instantiate multi-class individuals. We [are aware of this issue](https://github.com/simphony/simphony-osp/issues/669), and planning to include this functionality in a future minor release.\n",
     "\n",
     "Until this is fixed, the suggested workaround is to instantiate an ontology individual of any class and change the classes _a posteriori_, just as shown below.\n",
     "    \n",

docs/usage/sessions/import_export.ipynb

@@ -15,7 +15,7 @@
    "source": [
     "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n",
     "    \n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v4.0.0rc4?filepath=docs%2Fusage%2Fsessions%2Fimport_export.ipynb \"Click to run this tutorial yourself!\")\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v4.0.0?filepath=docs%2Fusage%2Fsessions%2Fimport_export.ipynb \"Click to run this tutorial yourself!\")\n",
     "    \n",
     "</figure>\n",
     "\n",

docs/usage/sessions/introduction.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n",
     "\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v4.0.0rc4?filepath=docs%2Fusage%2Fsessions%2Fintroduction.ipynb \"Click to run this tutorial yourself!\")\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v4.0.0?filepath=docs%2Fusage%2Fsessions%2Fintroduction.ipynb \"Click to run this tutorial yourself!\")\n",
     "    \n",
     "</figure>"
    ]