Simphony-osp

Critical bugfix release:

- `rdflib-jsonld` has been tombstoned. The latest version `0.6.2` removes all functionality. The developers recommend to use `0.5.0`, but it cannot be installed with `setuptools >= 58`. Luckily, version `0.6.1` is still functional and compatible with `setuptools >= 58`, so this is the version required now by OSP-core.
- `websockets 10` has been released, introducing breaking changes and dropping support for Python 3.6. Thus, for now the requirement `websockets < 10` is enforced.

Critical bugfix release:

- Fixed error affecting default, mutable attributes (issue 679).
- Fixed error when installing ontologies on Windows (issue 684).

Critical bugfix release:

- `rdflib==6.0.0` has been released, but `osp-core==3.5.4` is incompatible with it. The python package manager _pip_ was installing `rdflib==6.0.0` by default, making new installs unusable. This has now been fixed.
- Fixed regression that broke the `ontology2dot` tool.

**REMARK:** This release is **incompatible** with `rdflib==6.0.0`, which was released just a few days afterwards (see issue 677). Right now, the simplest solution is `pip install rdflib==5.0.0`.

- Added benchmarks, integrated with the CI, which publishes the results automatically [here](https://simphony.github.io/osp-core/dev/bench/index.html).
- Support for [OWL `hasValue`](https://www.w3.org/TR/owl-ref/#hasValue-def) property restrictions. The values are not enforced, but are set as defaults for new CUDS's attributes.
- Fixed bug when removing CUDS objects directly connected to the wrapper object (they were not removed).
- Added a new type conversion feature to the SPARQL queries. By default, `SparqlResult` (result) objects return `SparqlBindingSet` (row) objects when iterated, that in turn return rdflib's URIRefs or Literals when queried (e.g. `row['queriedvariable']`). Now `SparqlResult` objects are callable, like `result(irivariable='cuds', literalvariable=float)`, where each keyword argument can be either `'cuds'` or a callable. This makes the `SparqlResult` object return `SparqlBindingSet` objects that return CUDS objects or python objects when queried, making post-query operations simpler, such as getting a dataframe from the query results.
- Files fetched by the transport session are no longer prepended with the CUDS object's uid. The uid will be added within parentheses after the name, **only if** there is a name conflict.
- Fixed bug that showed wrong values for the `path` attribute of file CUDS.
- Other changes and bug fixes (see the [full changelog](https://github.com/simphony/osp-core/compare/v3.5.3.1-beta...v3.5.4-beta)).

- Fixed a bug in the pico ontology installation tool that showed the namespaces `xml, rdf, rdfs, xsd, owl` as installed even though they were not.
- CUDS objects (ontology individuals) can now have a custom IRI, instead of one from the OSP-core namespace. Just use the `iri` keyword argument when calling the ontology class to create the CUDS object, e.g. `city.Citizen(name='Klaus', age=55, iri='http://example.org/London#Klaus')`. However, in order to achieve optimal performance it is recommended to continue using the OSP-core namespace, as in such case OSP-core only has to store and handle an _uuid_, instead of an _iri_, which is usually far longer.
- The namespace objects now support [IPython tab completion](https://ipython.readthedocs.io/en/stable/interactive/tutorial.html#tab-completion) (click [here](https://user-images.githubusercontent.com/43052541/120196144-cfbd5a80-c21f-11eb-85dc-36fbbfde5808.png) to see an example). See [the docs](https://simphony.readthedocs.io/en/latest/jupyter/ontology_interface.html#Accessing-entities:-the-namespace-object) for more details.
- Added basic SPARQL support. It works on the core session (although with performance issues specific to the core session) and on all triple store wrapper sessions (it's mandatory to implement the support when creating one). Just import `sparql` from `osp.core.utils` and use it to perform the queries. See [the docs](https://simphony.readthedocs.io/en/dev/api_ref.html#osp.core.utils.sparql) for more details on how to make queries (or just run `help(sparql)` on the Python interpreter).
- Improved the RDF import and export support. All import and export functionalities (including single cuds import/export and json-ld import/export) have been integrated into two utility functions: [`import_cuds`](https://simphony.readthedocs.io/en/latest/api_ref.html#osp.core.utils.import_cuds) and [`export_cuds`](https://simphony.readthedocs.io/en/latest/api_ref.html#osp.core.utils.export_cuds). Check out the [new tutorial](https://simphony.readthedocs.io/en/latest/jupyter/import_export.html) on import and export capabilities for more details.
- Other changes and bug fixes (see the [full changelog](https://github.com/simphony/osp-core/compare/v3.5.2-beta...v3.5.3.1-beta)).

- Support for importing RDF files!
- Support for OWL restrictions and compositions. Now they have their own classes: `Composition` and `Restriction`. They can be accessed through the `axioms` attribute of an ontology class.
- Several performance improvements. CUDS objects instantiated within a with statement applied to a session are now directly created in such session.
- Some, mostly internal changes on how ontology entities are referenced in namespaces. User facing change: now, two entities cannot have the same label in the same ontology file. This prevents ambiguous references to entities.
- Other changes and bug fixes (see the [full changelog](https://github.com/simphony/osp-core/compare/v3.5.1-beta...v3.5.2-beta)).