diff options
| author | CoprDistGit <infra@openeuler.org> | 2023-05-15 04:27:27 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-15 04:27:27 +0000 |
| commit | 28518606b5d6683a394248d032b4b8cd2b63f114 (patch) | |
| tree | 9a500b00c8d67b6786c99f5a30acf09ba7ff285c | |
| parent | 658de7534541344680461424527fcbc94ee9028d (diff) | |
automatic import of python-vivarium-core
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-vivarium-core.spec | 300 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 302 insertions, 0 deletions
@@ -0,0 +1 @@ +/vivarium-core-1.5.5.tar.gz diff --git a/python-vivarium-core.spec b/python-vivarium-core.spec new file mode 100644 index 0000000..a874fa9 --- /dev/null +++ b/python-vivarium-core.spec @@ -0,0 +1,300 @@ +%global _empty_manifest_terminate_build 0 +Name: python-vivarium-core +Version: 1.5.5 +Release: 1 +Summary: Engine for composing and simulating computational biology models with the Vivarium interface. +License: MIT +URL: https://github.com/vivarium-collective/vivarium-core +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/ed/82/e3f5bd9a5a24bce1e857b31c67371759d2a66dcbb82455e604e07a97e131/vivarium-core-1.5.5.tar.gz +BuildArch: noarch + + +%description +# Vivarium Core + +[](https://pypi.org/project/vivarium-core/) +[](https://vivarium-core.readthedocs.io/en/latest/) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pylint.yml?query=branch%3Amaster) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pytest.yml?query=branch%3Amaster) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/mypy.yml?query=branch%3Amaster) + + +Vivarium Core provides a process interface and simulation engine for composing +and executing integrative multi-scale models. + +## Getting Started + +Vivarium Core is available on PyPI [here](https://pypi.org/project/vivarium-core/), and can be installed as a python library like this: + +```console +$ pip install vivarium-core +``` + +To get started using Vivarium Core, see our +[documentation](https://vivarium-core.readthedocs.io/en/latest/getting_started.html) +and [tutorial +notebooks](https://vivarium-core.readthedocs.io/en/latest/tutorials/index.html). + +If you want to contribute to Vivarium Core, see our [contribution +guidelines](https://github.com/vivarium-collective/vivarium-core/blob/master/CONTRIBUTING.md). + +## Concept + +Computational systems biology requires software for multi-algorithmic model +composition, which allows many modeling efforts to be extended, combined, and +simulated together. We need an "interface protocol" -- analogous to TCP/IP for +the Internet -- which allows diverse pieces of simulation software to connect, +communicate, and synchronize seamlessly into large, complex, and open-ended +networks that anyone can contribute to. + +Vivarium addresses the challenges of model reuse and multi-scale integration by +explicitly separating the interface that connects models from the frameworks that +implement them. Vivarium's modular interface makes individual simulation tools into +modules that can be wired together in composite multi-scale models, parallelized +across multiple CPUs, and run with Vivarium's discrete-event simulation engine. + +The figure below illustrates the key terminology of Vivarium's interface. +* (**a**) A *Process*, shown as a rectangular flowchart symbol, is a modular model that contains parameters, +an update function, and ports. +* (**b**) A *Store*, shown as the flowchart symbol for a database, holds the state variables and schemas that +determine how to handle updates. +* (**c**) *Composites* are bundles of Processes and Stores wired together by a bipartite network called a *Topology*, +with Processes connecting to Stores through their ports. +* (**d**) *Compartments* are Stores with inner sub-Stores and Processes. Processes can connect across compartments via +boundary stores. +* (**e**) Compartments are embedded in a *Hierarchy* -- depicted as a place network with discrete layers, +with outer compartments shown above and inner compartments below. + +<p align="center"> + <img src="https://github.com/vivarium-collective/vivarium-core/blob/master/doc/_static/interface.png?raw=true" width="500"> +</p> + + +## License + +Copyright (C) 2019-2022 The Vivarium Authors + +Licensed under the Apache License, Version 2.0 (the "License"); you may +not use this project except in compliance with the License. You may +obtain a copy of the License at +http://www.apache.org/licenses/LICENSE-2.0. + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +See [`LICENSE.txt`](https://github.com/vivarium-collective/vivarium-core/blob/master/LICENSE.txt) for a copy of the full license, and see +[`AUTHORS.md`](https://github.com/vivarium-collective/vivarium-core/blob/master/AUTHORS.md) for a list of the Vivarium Authors. + +%package -n python3-vivarium-core +Summary: Engine for composing and simulating computational biology models with the Vivarium interface. +Provides: python-vivarium-core +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-vivarium-core +# Vivarium Core + +[](https://pypi.org/project/vivarium-core/) +[](https://vivarium-core.readthedocs.io/en/latest/) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pylint.yml?query=branch%3Amaster) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pytest.yml?query=branch%3Amaster) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/mypy.yml?query=branch%3Amaster) + + +Vivarium Core provides a process interface and simulation engine for composing +and executing integrative multi-scale models. + +## Getting Started + +Vivarium Core is available on PyPI [here](https://pypi.org/project/vivarium-core/), and can be installed as a python library like this: + +```console +$ pip install vivarium-core +``` + +To get started using Vivarium Core, see our +[documentation](https://vivarium-core.readthedocs.io/en/latest/getting_started.html) +and [tutorial +notebooks](https://vivarium-core.readthedocs.io/en/latest/tutorials/index.html). + +If you want to contribute to Vivarium Core, see our [contribution +guidelines](https://github.com/vivarium-collective/vivarium-core/blob/master/CONTRIBUTING.md). + +## Concept + +Computational systems biology requires software for multi-algorithmic model +composition, which allows many modeling efforts to be extended, combined, and +simulated together. We need an "interface protocol" -- analogous to TCP/IP for +the Internet -- which allows diverse pieces of simulation software to connect, +communicate, and synchronize seamlessly into large, complex, and open-ended +networks that anyone can contribute to. + +Vivarium addresses the challenges of model reuse and multi-scale integration by +explicitly separating the interface that connects models from the frameworks that +implement them. Vivarium's modular interface makes individual simulation tools into +modules that can be wired together in composite multi-scale models, parallelized +across multiple CPUs, and run with Vivarium's discrete-event simulation engine. + +The figure below illustrates the key terminology of Vivarium's interface. +* (**a**) A *Process*, shown as a rectangular flowchart symbol, is a modular model that contains parameters, +an update function, and ports. +* (**b**) A *Store*, shown as the flowchart symbol for a database, holds the state variables and schemas that +determine how to handle updates. +* (**c**) *Composites* are bundles of Processes and Stores wired together by a bipartite network called a *Topology*, +with Processes connecting to Stores through their ports. +* (**d**) *Compartments* are Stores with inner sub-Stores and Processes. Processes can connect across compartments via +boundary stores. +* (**e**) Compartments are embedded in a *Hierarchy* -- depicted as a place network with discrete layers, +with outer compartments shown above and inner compartments below. + +<p align="center"> + <img src="https://github.com/vivarium-collective/vivarium-core/blob/master/doc/_static/interface.png?raw=true" width="500"> +</p> + + +## License + +Copyright (C) 2019-2022 The Vivarium Authors + +Licensed under the Apache License, Version 2.0 (the "License"); you may +not use this project except in compliance with the License. You may +obtain a copy of the License at +http://www.apache.org/licenses/LICENSE-2.0. + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +See [`LICENSE.txt`](https://github.com/vivarium-collective/vivarium-core/blob/master/LICENSE.txt) for a copy of the full license, and see +[`AUTHORS.md`](https://github.com/vivarium-collective/vivarium-core/blob/master/AUTHORS.md) for a list of the Vivarium Authors. + +%package help +Summary: Development documents and examples for vivarium-core +Provides: python3-vivarium-core-doc +%description help +# Vivarium Core + +[](https://pypi.org/project/vivarium-core/) +[](https://vivarium-core.readthedocs.io/en/latest/) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pylint.yml?query=branch%3Amaster) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pytest.yml?query=branch%3Amaster) +[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/mypy.yml?query=branch%3Amaster) + + +Vivarium Core provides a process interface and simulation engine for composing +and executing integrative multi-scale models. + +## Getting Started + +Vivarium Core is available on PyPI [here](https://pypi.org/project/vivarium-core/), and can be installed as a python library like this: + +```console +$ pip install vivarium-core +``` + +To get started using Vivarium Core, see our +[documentation](https://vivarium-core.readthedocs.io/en/latest/getting_started.html) +and [tutorial +notebooks](https://vivarium-core.readthedocs.io/en/latest/tutorials/index.html). + +If you want to contribute to Vivarium Core, see our [contribution +guidelines](https://github.com/vivarium-collective/vivarium-core/blob/master/CONTRIBUTING.md). + +## Concept + +Computational systems biology requires software for multi-algorithmic model +composition, which allows many modeling efforts to be extended, combined, and +simulated together. We need an "interface protocol" -- analogous to TCP/IP for +the Internet -- which allows diverse pieces of simulation software to connect, +communicate, and synchronize seamlessly into large, complex, and open-ended +networks that anyone can contribute to. + +Vivarium addresses the challenges of model reuse and multi-scale integration by +explicitly separating the interface that connects models from the frameworks that +implement them. Vivarium's modular interface makes individual simulation tools into +modules that can be wired together in composite multi-scale models, parallelized +across multiple CPUs, and run with Vivarium's discrete-event simulation engine. + +The figure below illustrates the key terminology of Vivarium's interface. +* (**a**) A *Process*, shown as a rectangular flowchart symbol, is a modular model that contains parameters, +an update function, and ports. +* (**b**) A *Store*, shown as the flowchart symbol for a database, holds the state variables and schemas that +determine how to handle updates. +* (**c**) *Composites* are bundles of Processes and Stores wired together by a bipartite network called a *Topology*, +with Processes connecting to Stores through their ports. +* (**d**) *Compartments* are Stores with inner sub-Stores and Processes. Processes can connect across compartments via +boundary stores. +* (**e**) Compartments are embedded in a *Hierarchy* -- depicted as a place network with discrete layers, +with outer compartments shown above and inner compartments below. + +<p align="center"> + <img src="https://github.com/vivarium-collective/vivarium-core/blob/master/doc/_static/interface.png?raw=true" width="500"> +</p> + + +## License + +Copyright (C) 2019-2022 The Vivarium Authors + +Licensed under the Apache License, Version 2.0 (the "License"); you may +not use this project except in compliance with the License. You may +obtain a copy of the License at +http://www.apache.org/licenses/LICENSE-2.0. + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +See [`LICENSE.txt`](https://github.com/vivarium-collective/vivarium-core/blob/master/LICENSE.txt) for a copy of the full license, and see +[`AUTHORS.md`](https://github.com/vivarium-collective/vivarium-core/blob/master/AUTHORS.md) for a list of the Vivarium Authors. + +%prep +%autosetup -n vivarium-core-1.5.5 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-vivarium-core -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 1.5.5-1 +- Package Spec generated @@ -0,0 +1 @@ +149aa7c778c52cc5eab2d70d30bbc20b vivarium-core-1.5.5.tar.gz |