Port to SimPhoNy v4

* Rename SimLammps to SimLAMMPS.

* Upgrade wrapper logic to the SimPhoNy v4 API.

* Update examples to the SimPhoNy v4 API.

* Port the SimLAMMPS ontology to OWL, as SimPhoNy v4 dropped support for YAML ontologies.

* Change directory structure.

* Update `README.md`. Update copyright year, change contact point to SimPhoNy mailing list, remove compatibility table (this information is on `setup.py`), change installation section, change docker section, remove directory structure section.

* Update LICENSE (changed to GPLv2).

* Rename package to `simphony-osp-simlammps`. Add classifiers and additional fields in `setup.py`. Do not use `packageinfo.py`, which has been deleted. Update entry points in `setup.py`.

* Add @pablo-de-andres and @kysrpex as CODEOWNERS.

* Use `pre-commit in the repository`.

* Remove `gitlab-ci.yml`.

* Add GitHub CI, including tests with tox for Python 3.7-3.10.

* Update dockerfile, change maintainer to `simphony@fraunhofer.iwm.de`. Delete `Dockerfile copy`.

* Revision of wrapper files: change mentions of "CUDS" to "ontology individual" or similar terms. Add type hints to most functions. Remove type hints from the docstrings.

* Removed copyright notice on `utils.py` as it is already on the `README.md`, and will be in the license file once one is provided.

* Add a consistency check on `commit` before modifying the LAMMPS data structures, to avoid leaving them on an inconsistent state if the commit fails or if the user sets a state that leads to inconsistencies.

* Change domain simphony-project.eu to simphony-osp.eu.

.github/CODEOWNERS

@@ -0,0 +1,4 @@
+# follows the same pattern as .gitignore files
+# file/mask username1/email1 ... usernameN/emailN
+
+* @pablo-de-andres @kysrpex

.github/workflows/ci.yml

@@ -0,0 +1,41 @@
+name: CI
+
+on: pull_request
+
+jobs:
+  PEP8:
+    runs-on: self-hosted
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Flake8
+        run: flake8 . --ignore=E203,W503 --docstring-convention=google
+
+      # Includes isort, black and other checks, see `.pre-commit.config.yaml`.
+      - name: pre-commit
+        run: pre-commit run --all-files
+
+  complexity:
+    runs-on: self-hosted
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Radon
+        run: |
+          radon cc -s -a .,
+          radon mi -s .
+
+  security:
+    runs-on: self-hosted
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Bandit
+        run: bandit -r osp --skip B101
+
+  testing:
+    runs-on: self-hosted
+    steps:
+      - uses: actions/checkout@v3
+      - name: tox
+        run: tox

.pre-commit-config.yaml

@@ -1,31 +1,30 @@
----
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-json
+      - id: check-yaml
+      - id: pretty-format-json
+        args:
+        - --autofix
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
 
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.1.0
-      hooks:
-          - id: check-json
-          - id: check-yaml
-          - id: pretty-format-json
-            args:
-            - --autofix
-          - id: end-of-file-fixer
-          - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args: [--line-length, "79"]
+        additional_dependencies: ['click==8.0.4']
 
-    - repo: https://github.com/psf/black
-      rev: 22.1.0
-      hooks:
-          - id: black
-            additional_dependencies: ['click==8.0.4']
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        args: [--profile, black, --filter-files]
 
-    - repo: https://github.com/pycqa/isort
-      rev: 5.10.1
-      hooks:
-          - id: isort
-            args: [--profile, black, --filter-files]
-
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v2.31.1
-      hooks:
-          - id: pyupgrade
-            args: [--py38-plus]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.1
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]

Dockerfile

@@ -1,5 +1,5 @@
 FROM python:3.9
-LABEL maintainer="pablo.de.andres@fraunhofer.iwm.de"
+LABEL maintainer="simphony@fraunhofer.iwm.de"
 
 # Install requirements
 RUN apt-get update && \
@@ -15,7 +15,7 @@ RUN cmake  -C ../cmake/presets/basic.cmake -D BUILD_SHARED_LIBS=on -D LAMMPS_EXC
     cmake --install .
 
 # Install osp-core
-RUN pip install osp-core
+RUN pip install simphony-osp
 
 # Install simlammps
 WORKDIR /simphony/wrappers/simlammps

README.md

@@ -1,74 +1,75 @@
-# Simlammps
-[![pipeline status](https://gitlab.cc-asp.fraunhofer.de/simphony/wrappers/simlammps/badges/master/pipeline.svg)](https://gitlab.cc-asp.fraunhofer.de/simphony/wrappers/simlammps/commits/master)
-[![coverage report](https://gitlab.cc-asp.fraunhofer.de/simphony/wrappers/simlammps/badges/master/coverage.svg)](https://gitlab.cc-asp.fraunhofer.de/simphony/wrappers/simlammps/commits/master)
+# SimLAMMPS
 
-Wrapper for LAMMPS developed by the SimPhoNy group at Fraunhofer IWM
+SimLAMMPS is a SimPhoNy wrapper that enables the use of the LAMMPS molecular 
+dynamics simulation engine on the SimPhoNy Open Simulation Platform.
 
-Copyright (c) 2014-2019, Adham Hashibon and Materials Informatics Team at Fraunhofer IWM.
-All rights reserved.
-Redistribution and use are limited to the scope agreed with the end user.
-No parts of this software may be used outside of this context.
-No redistribution is allowed without explicit written permission.
+**Disclaimer**: We are **not** affiliated nor associated with the 
+[authors of LAMMPS](https://docs.lammps.org/Intro_authors.html).
 
-Contact: [Pablo de Andres](mailto:pablo.de.andres@iwm.fraunhofer.de)
-
-## Requirements
+## Installation
 
-The SimLammps wrapper is built on top of the [OSP core](https://github.com/simphony/osp-core) package.
-The following table describes the version compatibility between these two packages.
+This wrapper requires a working LAMMPS installation. If you are running
+Ubuntu or CentOS, you are lucky, as we have prepared a
+script that can install it for you.
+```
+    ./install_engine.sh
+```
 
-|__SimLammps__|__OSP core__|
-|:-----------:|:----------:|
-|    3.4.x    | 3.5.x-beta |
-|    3.3.x    | 3.3.4-beta |
-|    3.2.x    | 3.3.0-beta |
-|    3.1.x    | 3.2.x-beta |
-|    3.0.x    | 3.1.x-beta |
-|    2.0.0    |    2.0.x   |
-|    0.0.1    |    1.x.x   |
+If you are running a different distribution or operating system, you will
+have to install it yourself. Please make sure that LAMMPS is installed before 
+proceeding.
 
-The releases of OSP core are available [here](https://github.com/simphony/osp-core/releases).
+The next step is to install the wrapper itself. SimLAMMPS is available on PyPI,
+so it can be installed using the
+[`pip` package manager](https://pip.pypa.io/en/stable/), you can do so by 
+running:
 
-## Installation
-If LAMMPS is not installed in the system, you can install it by running in your console:
-```
-    ./install_engine
+```shell
+    pip install simphony-osp-simlammps
 ```
 
-If osp-core is not in the system, install it before:
-```
-    pip install git+https://github.com/simphony/osp-core.git
-```
+Finally, the wrapper requires a specific ontology to operate. Download the 
+[ontology file](https://github.com/simphony/simlammps/blob/v4.0.0/simphony_osp_simlammps/simlammps.ttl)
+and 
+[ontology package](https://github.com/simphony/simlammps/blob/v4.0.0/simphony_osp_simlammps/simlammps.yml),
+then install the latter with the following command:
 
-__NOTE:__ Until a proper, stable version of the ontology with all the entities is available in OSP Core, a toy ontology for temporary usage is provided.
 ```
-    # to install the simlammps ontology
-    pico install simlammps/simlammps.ontology.yml
+    pico install simlammps.yml
 ```
 
-The package requires python 3 (tested for 3.7), installation is based on `setuptools`:
-```
-    # build and install simlammps
-    pip install .
-```
+**Note:** The provided ontology is not connected to any 
+top-level ontology, therefore its scope is limited to this wrapper. 
 
-## Documentation
-All information about SimPhoNy and its wrappers is available in the [SimPhoNy docs](https://simphony.readthedocs.io)
+### Docker
 
-The LAMMPS engine documentation can be visited [here](https://lammps.sandia.gov/).
-
-## Directory structure
-- osp/wrappers/simlammps -- simlammps wrapper files.
-- tests -- unittesting of the code.
-- examples -- examples of usage.
-
-## Docker
-We have prepared a Dockerfile with all the necessary requirements.
-Since osp-core is not public yet, a username and password are necessary to clone it.
-This is all simplified via a script called `docker_install.sh`
+Alternatively, you can run the wrapper from a Docker image. We have
+prepared a Dockerfile with all the necessary requirements.
 ```shell
     # Build it
     docker build -t simphony/simlammps .
-    # Run it (console entypoint)
+    # Run it (console entrypoint)
     docker run -ti --rm --entrypoint=/bin/bash simphony/simlammps
 ```
+
+
+## Documentation
+
+All information about SimPhoNy is available on the
+[SimPhoNy documentation](https://simphony.readthedocs.io/en/v4.0.0rc3). Check out the
+[examples folder](https://github.com/simphony/simlammps/blob/v4.0.0/examples)
+for examples on how to use SimLAMMPS itself.
+
+The LAMMPS engine documentation is available [here](https://lammps.sandia.gov/).
+
+## License
+
+Copyright (c) 2014-2022, Fraunhofer-Gesellschaft zur Förderung der angewandten
+Forschung e.V. acting on behalf of its Fraunhofer IWM.
+
+SimLAMMPS is distributed under the terms of the
+[GNU Public License Version 2](https://github.com/simphony/simlammps/blob/v4.0.0/LICENSE)
+as required 
+[by the license terms of LAMMPS itself](https://docs.lammps.org/Intro_opensource.html).
+
+Contact: [SimPhoNy](mailto:simphony@iwm.fraunhofer.de)