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Prepare SimPhoNy v4 rc1 for publication in PyPI (#798)
* Remove `.gitmodules` file * Update `MANIFEST.in` * Update year in `LICENSE.md` * Change `simphony-osp` version number to 4.0.0-rc1 * Run tests also for Python 3.9 and 3.10 * Update dockerfile to use `python:3.10`, change maintainer to SimPhoNy mailing list. * Remove unneeded packages in tox test environment * Include owl ontology files in MANIFEST.in * Improve metadata on setup.py * Change description * Change homepage * Add more keywords * Add chassifiers, maintainer, license * Remove setup_requires * Reorder items in setup.py * Update README.md
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| FROM ubuntu:18.04 | ||
| LABEL org.opencontainers.image.authors="pablo.de.andres@fraunhofer.iwm.de, jose.manuel.dominguez@iwm.fraunhofer.de, yoav.nahshon@iwm.fraunhofer.de" | ||
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| RUN apt-get update && \ | ||
| apt-get install -y python3.7 python3-pip | ||
| RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.6 1 | ||
| RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.7 2 | ||
| RUN update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 2 | ||
| RUN python -m pip install --upgrade pip | ||
| FROM python:3.10 | ||
| LABEL org.opencontainers.image.authors="simphony@fraunhofer.iwm.de" | ||
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| ADD . /simphony/simphony-osp | ||
| RUN pip install /simphony/simphony-osp |
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| include packageinfo.py | ||
| include osp/core/ontology/docs/*.yml | ||
| include osp/core/ontology/docs/*.xml | ||
| include osp/core/ontology/docs/*.ttl | ||
| include osp/core/ontology/docs/EMMO/emmo-inferred.owl | ||
| include simphony_osp/ontology/files/*.yml | ||
| include simphony_osp/ontology/files/*.ttl | ||
| include simphony_osp/ontology/files/*.xml | ||
| include simphony_osp/ontology/files/*.owl |
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| [](https://simphony.readthedocs.io/en/latest/?badge=latest) | ||
|  | ||
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| ## Note | ||
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| For applications where performance is important, we recommend v3.4.2 | ||
| The performance optimizations will be done as a next step to v3.5.X | ||
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| # OSP core | ||
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| Native implementation of the core cuds object and the class generation | ||
| by the SimPhoNy team at Fraunhofer IWM. Builds up on the previous | ||
| version, simphony-common (SimPhoNy, EU FP7 Project (Nr. 604005) | ||
| www.simphony-project.eu) | ||
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| ## Requirements | ||
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| - PyYaml (on Windows, use <https://stackoverflow.com/a/33673823>) for parsing yaml files | ||
| - numpy for vector attributes of cuds | ||
| - websockets for the transport layer | ||
| - requests for sending CUDS to a server | ||
| - tox to run unittests | ||
| - unittest2 to run unittests | ||
| - pympler for the performance test | ||
| - responses for unittesting requests | ||
| # SimPhoNy | ||
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| 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 | ||
| on the domain of materials science. | ||
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| SimPhoNy enables: | ||
| - Visualization and exploration of | ||
| [OWL ontologies](https://www.w3.org/TR/2012/REC-owl2-primer-20121211/) and | ||
| [RDFS Vocabularies](https://www.w3.org/TR/rdf-schema/) | ||
| - _Wrappers_: interfaces between ontologies and software products or digital | ||
| objects | ||
| - Manipulation of ontology-based data: work with ontology individuals, | ||
| transfer them among different software products using the wrappers, and query | ||
| the knowledge graph | ||
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| ⚠️ 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. | ||
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| ## Installation | ||
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| See [https://simphony.readthedocs.io/en/latest/installation.html](https://simphony.readthedocs.io/en/latest/installation.html). | ||
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| ## Visualization of ontologies | ||
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| We provide the tool `ontology2dot` to visualize your ontologies. You can visualize installed namespaces together with non-installed yaml files (requires Graphviz https://graphviz.gitlab.io/): | ||
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| ```sh | ||
| ontology2dot <installed-namespace-1> ... <installed-namespace-n> <path/to/ontology-1.yml> ... <path/to/ontology-m.yml> | ||
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| # Alternative | ||
| python -m simphony_osp.tools.ontology2dot <installed-namespace-1> ... <installed-namespace-n> <path/to/ontology-1.yml> ... <path/to/ontology-m.yml> | ||
| ``` | ||
| SimPhoNy is available on PyPI, so it can be installed using pip | ||
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| You can use parameter `-g` to group the namespaces. Use `-o` to change the filename of the resulting png file. | ||
| `pip install simphony-osp` | ||
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| ## Testing | ||
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| Testing is done using tox (`pip install tox`): | ||
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| ```sh | ||
| # run tests automatically in different environments | ||
| tox | ||
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| # run tests in your current environment (you must manually install unittest2, responses for that) | ||
| python -m unittest -v | ||
| ``` | ||
| Detailed installation instructions can be found | ||
| [here](https://simphony.readthedocs.io/en/latest/installation.html). | ||
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| ## Documentation | ||
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| Our documentation is located at <https://simphony.readthedocs.io>. | ||
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| If you want to build the documentation locally, refer to our [documentation repostitory](https://github.com/simphony/docs). | ||
| To learn how to use SimPhoNy, check out our documentation, which is located at | ||
| <https://simphony.readthedocs.io>. | ||
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| ### Examples | ||
| In addition, basic usage examples to | ||
| quickly get started are available in the | ||
| [`examples` folder](https://github.com/simphony/osp-core/tree/release/4/dev/examples). | ||
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| Further examples can be found in the /examples folder. There the usage of wrappers is explained. | ||
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| ## Troubleshooting | ||
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| If installation fails, try to install the dependencies one by one before installing simphony-osp. | ||
| The dependencies are listed at the top of this readme file. | ||
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| On Windows, unittests can fail when you use a virtual environment. | ||
| For testing the transport layer, we start a transport layer server using pythons subprocess package. | ||
| It can happen, that the started subprocess does not pick up the correct virtual environment, causing the server to crash and the corresponding tests to fail. | ||
| From our experience, this will not happen if you use the virtual environements of conda. | ||
| If you want to build the documentation locally, refer to our [documentation repostitory](https://github.com/simphony/docs). | ||
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| ### Directory structure | ||
| ## Contributing | ||
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| - osp/core -- The source code | ||
| - tools -- various tools to work with simphony-osp. | ||
| - ontology -- the parser and generation of the entities and classes. | ||
| - yml -- The supplied ontology files | ||
| - session -- Different abstract classes for wrappers. | ||
| - examples -- examples of usage. | ||
| - tests -- unittesting of the code | ||
| If you wish to contribute to SimPhoNy, please read the | ||
| [contributing guidelines](https://github.com/simphony/osp-core/blob/release/4/dev/CONTRIBUTING.md). | ||
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| ## Acknowledgements | ||
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| 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 OSP-core, 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 https://github.com/simphony/simphony-common. |
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| [tox] | ||
| envlist = py37,py38 | ||
| envlist = py37,py38,py39,py310 | ||
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| [testenv] | ||
| deps = | ||
| unittest2 | ||
| pympler | ||
| responses | ||
| coverage | ||
| requests | ||
| commands = | ||
| coverage run -m unittest -v | ||
| coverage report --omit=tests/*,.eggs/*,osp/core/ontology/docs/EMMO/* --skip-covered | ||
| coverage report --omit=tests/*,.eggs/* --skip-covered |