Bump package version to 4.0.0 (#837)

* Bump package version to 4.0.0

* Replace references to `osp-core` with `simphony-osp`.

* Change references to master to version-specific references.

* Add knowledge-graph keyword to Python package metadata.

* Add dependency `websockets >= 9`.

* Remove release-candidate warning.

* Change formatting of README.md

Author: kysrpex

.github/pull_request_template.md

@@ -1,6 +1,6 @@
 Before submitting your pull request, please make sure that you have read and agree with the following:
-- [Code contribution guidelines](https://github.com/simphony/osp-core/blob/master/CONTRIBUTING.md#code)
-- [Code of conduct](https://github.com/simphony/osp-core/blob/master/CODE_OF_CONDUCT.md#contributor-covenant-code-of-conduct)
-- [License terms](https://github.com/simphony/osp-core/blob/master/LICENSE.md)
+- [Code contribution guidelines](https://github.com/simphony/simphony-osp/blob/v4.0.0/CONTRIBUTING.md#code)
+- [Code of conduct](https://github.com/simphony/simphony-osp/blob/v4.0.0/CODE_OF_CONDUCT.md#contributor-covenant-code-of-conduct)
+- [License terms](https://github.com/simphony/simphony-osp/blob/v4.0.0/LICENSE.md)
 
 Bear in mind that the code you contribute will share the same license terms referenced above. Do not contribute code if you do not have the rights to share it under such terms.

CONTRIBUTING.md

@@ -50,60 +50,60 @@ Thank you for considering to improve SimPhoNy. We welcome your input!
   </table>
 </div>
 
-Remember that you must adhere to the [Contributor Covenant Code of Conduct](https://github.com/simphony/osp-core/blob/master/CODE_OF_CONDUCT.md) if you decide to make a contribution.
+Remember that you must adhere to the [Contributor Covenant Code of Conduct](https://github.com/simphony/simphony-osp/blob/v4.0.0/CODE_OF_CONDUCT.md) if you decide to make a contribution.
 
 ## Issues
 
 ### Reporting bugs
 
-When you find something that is not working as it should, you can submit a bug report. This section provides guidelines on how to write your report in a way that helps [maintainers](https://github.com/simphony/osp-core/blob/master/.github/CODEOWNERS) understand the problem and reproduce it. Submitting a good bug report is a key to have issues solved quickly.
+When you find something that is not working as it should, you can submit a bug report. This section provides guidelines on how to write your report in a way that helps [maintainers](https://github.com/simphony/simphony-osp/blob/v4.0.0/.github/CODEOWNERS) understand the problem and reproduce it. Submitting a good bug report is a key to have issues solved quickly.
 
 #### Before submitting a bug report
 
 1. Consider what is the possible cause of your issue. Sometimes the source of a problem is in the least expected place. For example, it could be in the ontology that you are using, in the network connection or in the software that a SimPhoNy wrapper is interacting with.
-2. Check the [Q&A](https://github.com/simphony/osp-core/discussions/categories/q-a) section of the [discussions page](https://github.com/simphony/osp-core/discussions). Someone else might have already experienced the same issue and got an answer on how to solve it.
-3. Search for similar issues on the [issue board](https://github.com/simphony/osp-core/issues?q=is%3Aissue+sort%3Aupdated-desc+). The problem may already have been reported. If you are having issues while using a specific SimPhoNy wrapper, beware that each SimPhoNy Wrapper has its own issue board.
+2. Check the [Q&A](https://github.com/simphony/simphony-osp/discussions/categories/q-a) section of the [discussions page](https://github.com/simphony/simphony-osp/discussions). Someone else might have already experienced the same issue and got an answer on how to solve it.
+3. Search for similar issues on the [issue board](https://github.com/simphony/simphony-osp/issues?q=is%3Aissue+sort%3Aupdated-desc+). The problem may already have been reported. If you are having issues while using a specific SimPhoNy wrapper, beware that each SimPhoNy Wrapper has its own issue board.
 
 #### Submitting a bug report
 
-Bug reports should be submitted on the [SimPhoNy issue board](https://github.com/simphony/osp-core/issues?q=is%3Aissue+sort%3Aupdated-desc+).  If you suspect that the issue has its origin in the code of a specific wrapper, rather than in SimPhoNy itself, visit the issue board of the wrapper instead. To create a new report, click the green [_"New"_](https://github.com/simphony/osp-core/issues/new/choose) button.
+Bug reports should be submitted on the [SimPhoNy issue board](https://github.com/simphony/simphony-osp/issues?q=is%3Aissue+sort%3Aupdated-desc+).  If you suspect that the issue has its origin in the code of a specific wrapper, rather than in SimPhoNy itself, visit the issue board of the wrapper instead. To create a new report, click the green [_"New"_](https://github.com/simphony/simphony-osp/issues/new/choose) button.
 
 - [ ] Choose a meaningful title.
 - [ ] Describe the problem in few words.
 - [ ] Specify which version of `simphony-osp` is affected. Use `pip show simphony-osp` to find out which version you have installed. If the problem involves a wrapper, provide also the version of the wrapper.
 - [ ] Explain how to reproduce the problem, step-by-step, and include a **minimal reproducible example**. A _minimal reproducible example_ is a code snippet where the issue can be observed. Include any additional files (e.g. an ontology file) that may be needed to execute the example. Skip the example _only if it is very difficult to provide it_.
 - [ ] If the issue involves a crash or an exception, include the full error message (with the stacktrace).
 
-[Follow this link](https://github.com/simphony/osp-core/issues/740#issue-1107800007) to see an example of an accurate bug report. Providing a good bug report facilitates the work of the maintainers and enables them to solve the issue faster.
+[Follow this link](https://github.com/simphony/simphony-osp/issues/740#issue-1107800007) to see an example of an accurate bug report. Providing a good bug report facilitates the work of the maintainers and enables them to solve the issue faster.
 
 ### Proposing enhancements or suggesting new features
 
-Enhancements or new features should first be proposed on the [_"Ideas"_ section of the forum](https://github.com/simphony/osp-core/discussions/categories/ideas).
+Enhancements or new features should first be proposed on the [_"Ideas"_ section of the forum](https://github.com/simphony/simphony-osp/discussions/categories/ideas).
 
 When proposing, discussing, and designing a feature or enhancement on the forum, always aim to address the following points:
 - [ ] Motivation for the enhancement or the new feature.
 - [ ] General overview of the enhancement or the new feature. Code snippets/mock-ups of how the feature or enhancement should work and behave.
 - [ ] Estimation of the effort that implementing such enhancement or feature might involve. Technologies that could enable the implementation. This information helps the maintainers decide whether to implement a feature or enhancement, and to estimate the timeframe for a potential implementation.
 
-After this discussion phase, when the [maintainers](https://github.com/simphony/osp-core/blob/master/.github/CODEOWNERS) deem it appropriate, the discussion on the forum can be closed and an issue referencing it can be created on the [issue board](https://github.com/simphony/osp-core/issues?q=is%3Aissue+sort%3Aupdated-desc+). The goal of this procedure is to separate discussion and design from implementation efforts. The issue is now ready to be worked on. The [_code section_](#Code) explains how to contribute to solve an issue.
+After this discussion phase, when the [maintainers](https://github.com/simphony/simphony-osp/blob/v4.0.0/.github/CODEOWNERS) deem it appropriate, the discussion on the forum can be closed and an issue referencing it can be created on the [issue board](https://github.com/simphony/simphony-osp/issues?q=is%3Aissue+sort%3Aupdated-desc+). The goal of this procedure is to separate discussion and design from implementation efforts. The issue is now ready to be worked on. The [_code section_](#Code) explains how to contribute to solve an issue.
 
 ## Code
 
 Code contributions are generally aimed at fixing bugs and implementing enhancements or new features. The way to contribute code to the project are [pull requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) (PR).
 
-If you are unsure about where to start, check the issues tagged as [_newcomer task_](https://github.com/simphony/osp-core/issues?q=label%3A%22%F0%9F%91%A9%E2%80%8D%F0%9F%8E%93+newcomer+task%22+sort%3Acomments-desc). Such issues should either be simple to solve, or be a good entry point for understanding the codebase.
+If you are unsure about where to start, check the issues tagged as [_newcomer task_](https://github.com/simphony/simphony-osp/issues?q=label%3A%22%F0%9F%91%A9%E2%80%8D%F0%9F%8E%93+newcomer+task%22+sort%3Acomments-desc). Such issues should either be simple to solve, or be a good entry point for understanding the codebase.
 
 If you have a bugfix or a feature/enhancement implementation that you want to contribute, please read [this page](https://simphony.readthedocs.io/en/latest/contribute.html) to understand how the code is organized, what the meaning of the different git branches on the repository is, and what automatic checks your code will have to pass in order to be accepted. After that, just fork the repository and make a new pull request.
 
 Usually, there will be an issue associated with the specific bug to solve, or feature/enhancement to implement. Please add [closing keywords](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword) to your PR so that it becomes automatically linked to the corresponding issue.
 
-After you submit your pull request, a [maintainer](https://github.com/simphony/osp-core/blob/master/.github/CODEOWNERS) will review it. It is possible that additional work is needed before the maintainer can accept the PR. To make things smoother, please consider [allowing us to directly edit your PR](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/allowing-changes-to-a-pull-request-branch-created-from-a-fork), so that we can perform minor edits without having to wait for your feedback.
+After you submit your pull request, a [maintainer](https://github.com/simphony/simphony-osp/blob/v4.0.0/.github/CODEOWNERS) will review it. It is possible that additional work is needed before the maintainer can accept the PR. To make things smoother, please consider [allowing us to directly edit your PR](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/allowing-changes-to-a-pull-request-branch-created-from-a-fork), so that we can perform minor edits without having to wait for your feedback.
 
 Of course, even if you are not a maintainer, you are also very welcome to comment on the pull requests submitted by other community members and give feedback to them.
 
 ## Documentation
 
-If you feel that the [SimPhoNy documentation](https://simphony.readthedocs.io) is difficult to understand, we welcome your feedback and contributions! In general, changes to the documentation should be first proposed on the [_"Ideas"_ section of the forum](https://github.com/simphony/osp-core/discussions/categories/ideas).
+If you feel that the [SimPhoNy documentation](https://simphony.readthedocs.io) is difficult to understand, we welcome your feedback and contributions! In general, changes to the documentation should be first proposed on the [_"Ideas"_ section of the forum](https://github.com/simphony/simphony-osp/discussions/categories/ideas).
 
 However, in certain cases, a change in the documentation does not need to be discussed. For example, if you find a typo you can directly [create an issue](https://github.com/simphony/docs/issues/new/choose) or even a [pull request](https://github.com/simphony/docs/compare). The same applies if the documentation needs to be changed due to the implementation of enhancements or new features for SimPhoNy in a [code contribution](#code).
 
@@ -113,16 +113,16 @@ When proposing and discussing a change on the documentation, always aim to alway
 - [ ] A brief description, of the proposed changes.
 - [ ] A mock-up of the intended changes, for example the headings, a few sentences explaining the content that should be included. If the changes involve figures, please upload a sketch too.
 
-After this discussion phase, when the [maintainers](https://github.com/simphony/osp-core/blob/master/.github/CODEOWNERS) deem it appropriate, the discussion on the forum can be closed and an issue referencing it can be created on the [issue board](https://github.com/simphony/docs/issues?q=is%3Aissue+sort%3Aupdated-desc+). The goal of this procedure is to separate discussion and design from implementation efforts.
+After this discussion phase, when the [maintainers](https://github.com/simphony/simphony-osp/blob/v4.0.0/.github/CODEOWNERS) deem it appropriate, the discussion on the forum can be closed and an issue referencing it can be created on the [issue board](https://github.com/simphony/docs/issues?q=is%3Aissue+sort%3Aupdated-desc+). The goal of this procedure is to separate discussion and design from implementation efforts.
 
  The issue is now ready to be worked on. On the issue itself, the fine details and the actual contents can be more deeply discussed. Finally, a [pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) can be [submitted](https://github.com/simphony/docs/compare) to the [docs repository](https://github.com/simphony/docs/pulls?q=is%3Apr+sort%3Aupdated-desc). A maintainer will review the pull request and accept it, or request further changes if needed.
 
 ## Forum
 
-Feel free to participate on the [forum](https://github.com/simphony/osp-core/discussions)! There you may:
+Feel free to participate on the [forum](https://github.com/simphony/simphony-osp/discussions)! There you may:
 
-- Read [announcements](https://github.com/simphony/osp-core/discussions/categories/announcements) from the SimPhoNy team.
-- Have [general discussions](https://github.com/simphony/osp-core/discussions/categories/general) about SimPhoNy.
-- Propose [new features or enhancements](https://github.com/simphony/osp-core/discussions/categories/ideas). Please follow the guidelines provided on [this section](#proposing-enhancements-or-suggesting-new-features).
-- [Ask other members of the community for help](https://github.com/simphony/osp-core/discussions/categories/q-a) in a [Q&A format](https://en.wikipedia.org/wiki/Q%26A_software).
-- [Share how did you benefit from using SimPhoNy](https://github.com/simphony/osp-core/discussions/categories/show-and-tell) in your project.
+- Read [announcements](https://github.com/simphony/simphony-osp/discussions/categories/announcements) from the SimPhoNy team.
+- Have [general discussions](https://github.com/simphony/simphony-osp/discussions/categories/general) about SimPhoNy.
+- Propose [new features or enhancements](https://github.com/simphony/simphony-osp/discussions/categories/ideas). Please follow the guidelines provided on [this section](#proposing-enhancements-or-suggesting-new-features).
+- [Ask other members of the community for help](https://github.com/simphony/simphony-osp/discussions/categories/q-a) in a [Q&A format](https://en.wikipedia.org/wiki/Q%26A_software).
+- [Share how did you benefit from using SimPhoNy](https://github.com/simphony/simphony-osp/discussions/categories/show-and-tell) in your project.

README.md

@@ -15,38 +15,41 @@ SimPhoNy enables:
   transfer them among different software products using the wrappers, and query
   the knowledge graph
 
-⚠️ You are reading the README file for a _release candidate_ version of
-SimPhoNy. This version has not yet been thoroughly tested, and its
-functionality is not yet fully documented. Unless you are explicitly looking to
-try this version, please head to the
-[`master` branch](https://github.com/simphony/osp-core) of this repository to
-find the README file for the latest stable release of SimPhoNy.
-
 ## Installation
 
 SimPhoNy is available on PyPI, so it can be installed using pip
 
 `pip install simphony-osp`
 
 Detailed installation instructions can be found
-[here](https://simphony.readthedocs.io/en/v4.0.0rc4/introduction/installation.html).
+[here](https://simphony.readthedocs.io/en/v4.0.0/introduction/installation.html).
 
 ## Documentation
 
 To learn how to use SimPhoNy, check out our documentation, which is located at
-<https://simphony.readthedocs.io/en/v4.0.0rc4/>.
+<https://simphony.readthedocs.io/en/v4.0.0/>.
 
 In addition, basic usage examples to
 quickly get started are available in the
-[`examples` folder](https://github.com/simphony/osp-core/tree/v4.0.0rc4/examples).
+[`examples` folder](https://github.com/simphony/simphony-osp/tree/v4.0.0/examples).
 
-If you want to build the documentation locally, refer to our [documentation repostitory](https://github.com/simphony/docs/tree/v4.0.0rc4).
+If you want to build the documentation locally, refer to our
+[documentation repository](https://github.com/simphony/docs/tree/v4.0.0).
 
 ## Contributing
 
 If you wish to contribute to SimPhoNy, please read the
-[contributing guidelines](https://github.com/simphony/osp-core/blob/v4.0.0rc4/CONTRIBUTING.md).
+[contributing guidelines](https://github.com/simphony/simphony-osp/blob/v4.0.0/CONTRIBUTING.md).
 
 ## Acknowledgements
 
-The SimPhoNy Python package originates from the European Project [SimPhoNy](https://www.simphony-project.eu/) (Project Nr. 604005). We would like to acknowledge and thank our project partners, especially [Enthought, Inc](https://www.enthought.com/), [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.
+The SimPhoNy Python package originates from the European Project
+[SimPhoNy](https://www.simphony-project.eu/) (Project Nr. 604005). We would
+like to acknowledge and thank our project partners, especially
+[Enthought, Inc](https://www.enthought.com/),
+[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
+[simphony-common](https://github.com/simphony/simphony-common).

examples/assertional_knowledge.py

@@ -5,7 +5,7 @@
 > individuals (assertional knowledge), and ontology classes, relationships,
 > attributes and annotations (terminological knowledge).
 -- [Assertional knowledge - SimPhoNy documentation]
-   (https://simphony.readthedocs.io/en/v4.0.0rc4/usage/
+   (https://simphony.readthedocs.io/en/v4.0.0/usage/
    assertional_knowledge.html)
 
 This example focuses on accessing, editing and navigating assertional

examples/pico.py

@@ -13,7 +13,7 @@
 > are YAML configuration files that, in addition to pointing to the actual
 > ontology files, also define extra metadata.
 -- [Installing ontologies (pico) - SimPhoNy documentation]
-   (https://simphony.readthedocs.io/en/v4.0.0rc4/usage/ontologies/pico.html)
+   (https://simphony.readthedocs.io/en/v4.0.0/usage/ontologies/pico.html)
 """
 
 from simphony_osp.tools.pico import install, namespaces, packages, uninstall

examples/sessions.py

@@ -7,7 +7,7 @@
 > translates the assertional knowledge to a form that is compatible with a
 > specific simulation engine, database, data repository or file format.
 -- [Introduction (to sessions) - SimPhoNy documentation]
-   (https://simphony.readthedocs.io/en/v4.0.0rc4/usage/sessions
+   (https://simphony.readthedocs.io/en/v4.0.0/usage/sessions
    /introduction.html)
 
 This example deals, however, with sessions that are NOT connected to any
@@ -50,7 +50,7 @@
 > In SimPhoNy, all sessions are automatically “opened” when they are created.
 > The “commit” and “close” operations are controlled manually.
 -- [Introduction (to sessions) - SimPhoNy documentation]
-   (https://simphony.readthedocs.io/en/v4.0.0rc4/usage/sessions
+   (https://simphony.readthedocs.io/en/v4.0.0/usage/sessions
    /introduction.html)
 
 Note that despite the above, sessions that are not connected to a wrapper (the