Summary of changes since the last major version:
- Rebranded OSP-core to SimPhoNy-OSP. Replaced domain _simphony-project.eu_ with _simphony-osp.eu_. Renamed Python package from `osp-core` to `simphony-osp`.
- The concept of [CUDS](https://simphony.readthedocs.io/en/v3.9.0/jupyter/cuds_api.html) as a recursive container of ontology individuals controlled by the active and passive relationships defined for the ontology is no longer in the software. To transfer ontology individuals between sessions, just select them using any of the available [querying](https://simphony.readthedocs.io/en/v4.0.0/usage/sessions/index.html#sessions) methods and [add them](https://simphony.readthedocs.io/en/v4.0.0/usage/sessions/management.html) to the new session. The **same behaviour** that was available for CUDS objects can be achieved through the [`find`](https://simphony.readthedocs.io/en/v4.0.0/usage/sessions/search.html#find) function from the `simphony_osp.tools.search` module by passing the formerly defined active relationships as an argument.
- As a consequence, the syntax for defining ontology packages [has been simplified](https://simphony.readthedocs.io/en/release-4-dev/usage/ontologies/packages.html#ontology-packages).
- Sessions no longer need to be instantiated with a wrapper object in order to work with them. The wrapper object was a "root" object from which all ontology individuals in the session were be reachable, but it is no longer needed. Ontology individuals are just contained in the session and can be distributed among several [connected components](https://en.wikipedia.org/wiki/Connected_component). Therefore cannot be "orphan" ontology individuals anymore (since they can always be accessed) and sessions do not need to be "pruned" anymore.
- There is now a strict separation in the code between the interface to [terminological](https://simphony.readthedocs.io/en/v4.0.0/usage/terminological_knowledge.html) and [assertional knowledge](https://simphony.readthedocs.io/en/v4.0.0/usage/assertional_knowledge.html), the [sessions](https://simphony.readthedocs.io/en/v4.0.0/usage/sessions/index.html) (where terminological and assertional knowledge lives), RDF graphs (the data structure where sessions store ontology entities encoded as RDF) and [wrappers](https://simphony.readthedocs.io/en/v4.0.0/developers/wrappers.html). This architectural change addresses or renders several issues outdated (a few, but not the only examples are #210, 422, 438, 551, 624, 669).
- Dropped support for YAML ontologies.
- [Index notation](https://simphony.readthedocs.io/en/v4.0.0/usage/assertional_knowledge.html#Using-the-index-operator-[]) for managing relationships, attributes and annotations.
- Non-functional ontology attributes are now supported.
- Any attribute can be assigned to any ontology individual (not restricted to classes declared in the domain's attribute).
- Support for [annotation properties](https://www.w3.org/TR/owl2-syntax/#Annotation_Properties), which are accessed normally from the [namespace object](https://simphony.readthedocs.io/en/v4.0.0/usage/terminological_knowledge.html#Namespace-objects:-accessing-entities).
- Support for [RDFS vocabularies](https://simphony.readthedocs.io/en/v4.0.0/usage/ontologies/supported_formats.html#supported-formats).
- It is no longer necessary to specify whether entities from ontology namespaces should be accessed by label or by prefix. It is simply possible to access them using both at all times, and all labels in all languages can be used.
- SQLite and SQLAlchemy wrappers are now based on `rdflib-sqlalchemy`.
- The [Wrapper API](https://simphony.readthedocs.io/en/v4.0.0/developers/wrappers.html) has been unified and simplified. There is now just one wrapper abstract class. Extra methods have been added to make lower-level implementations possible and improve file handling.
- Introduced [SimPhoNy operations](https://simphony.readthedocs.io/en/v4.0.0/developers/operations.html), which are actions linked to specific ontology classes.
- Sessions can now actually hold both T-Box and A-Boxes (even though users are meant to use them only to store A-Boxes). The T-Box that is used to describe an A-Box can be different for each session (although by default it is a T-Box containing the ontologies installed with `pico`). This feature replaces the former namespace registry.
- `ontology2dot` and `cuds2dot` are now a single tool, called `semantic2dot`. `semantic2dot` can mix plots of A-Boxes and T-Boxes. Several T-Boxes can be simultaneously plotted. `semantic2dot` also shows plots directly in Jupyter notebooks without the need to save them to a file first.
- [SKOS](https://simphony.readthedocs.io/en/release-4-dev/usage/ontologies/ontologies_included.html#simple-knowledge-organization-system-skos) is now bundled with SimPhoNy.
- The fixed-length string custom data type has been removed.
- The custom vector data type has been enhanced and is also now serialized to an RDF literal as bytes using b85 encoding. There is a single vector data type regardless of the vector's shape or length.
- Ontology individuals imported from a file keep their custom IRIs (issue 758).
- Support for Python 3.6 dropped.
- Most of the code features type-hinting now.
- Improved [RDF import and export](https://simphony.readthedocs.io/en/v4.0.0/usage/sessions/import_export.html) features.
- The label attribute of ontology individuals now refers to their `rdfs:label` and is configurable.
- The transport layer now works at the triple level.
- All user-facing tools have been moved to the `simphony_osp.tools` module.
- The City ontology has been migrated to OWL.
- The schema validation feature is no longer available, will likely be replaced in the future by SCHACL.
- Files are now managed through SimPhoNy operations, and can be uploaded and downloaded on-demand. Files have been better integrated in the Wrapper API.
- Session locking feature: sessions can be set as default using the `with` statement without needing to close them afterwards.
- Removed Dockerfile.
For a detailed list of all changes since the last major version, check the [commit history](https://github.com/simphony/osp-core/compare/f792734...v4.0.0) since the last commit common to this and the previous major release.