diff options
| author | CoprDistGit <infra@openeuler.org> | 2023-05-17 02:59:53 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-17 02:59:53 +0000 |
| commit | 7c21eedf50514d8a1ff6aa2f135707f005333819 (patch) | |
| tree | ca9a6166d5ca2b007eb3d553e35cbf5e54c377a8 | |
| parent | 4a6a2efcc5c16bd55f02718f92d80e88e3f370ae (diff) | |
automatic import of python-pylems
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-pylems.spec | 380 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 382 insertions, 0 deletions
@@ -0,0 +1 @@ +/PyLEMS-0.6.2.tar.gz diff --git a/python-pylems.spec b/python-pylems.spec new file mode 100644 index 0000000..01aae7f --- /dev/null +++ b/python-pylems.spec @@ -0,0 +1,380 @@ +%global _empty_manifest_terminate_build 0 +Name: python-PyLEMS +Version: 0.6.2 +Release: 1 +Summary: A Python library for working with the Low Entropy Model Specification language (LEMS) +License: LGPL +URL: https://github.com/LEMS/pylems +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/b2/ad/7c440cb5dfea6bf6ceae226ed27e04d9ec75a8151f2c6b307e6c51357219/PyLEMS-0.6.2.tar.gz +BuildArch: noarch + +Requires: python3-lxml +Requires: python3-typing + +%description +## PyLEMS + +[](https://github.com/LEMS/pylems/actions/workflows/ci.yml) +[](https://github.com/LEMS/pylems/actions/workflows/examples.yml) +[](https://pylems.readthedocs.io/en/latest/?badge=latest) + + +A LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2 models (see [here](https://docs.neuroml.org/Userdocs/Software/pyLEMS.html)). + +For more about PyLEMS see: + +Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig Gleeson, +**libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience** +[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00038/abstract), doi: 10.3389/fninf.2014.00038 + +_**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_ + +For more details on LEMS see: + +Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver, +**LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2**, +[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00079/abstract), doi: 10.3389/fninf.2014.00079 + + +### Installation + +A stable version of PyLEMS is [available on PyPI](https://pypi.python.org/pypi/PyLEMS) using [pip](https://pip.pypa.io/en/latest/installing.html): + + pip install pylems + +To install as root: + + sudo pip install pylems + +Alternatively, you can obtain the latest version with + + git clone https://github.com/LEMS/pylems.git + cd pylems + git checkout development # optional + sudo python setup.py install + +### Usage as a LEMS model simulator + + pylems [options] LEMS_file + +**Options** + +- -I/-include path - Adds a directory to the model file include search path + + +### Examples + + +**NeuroML examples (from https://github.com/NeuroML/NeuroML2/tree/development/NeuroML2CoreTypes)** + +- Example 0 -- Working +- Example 1 -- Working +- Example 2 -- Working +- Example 3 -- Working +- Example 4 -- Not working (Unsupported in PyLEMS: KSChannel) +- Example 5 -- Working +- Example 6 -- Working +- Example 7 -- Working +- Example 8 -- Working +- Example 9 -- Working +- Example 10 -- Working +- Example 11 -- Working +- Example 12 -- Not working (Unsupported in PyLEMS: Property) +- Example 13 -- Working +- Example 14 -- Not working (Unsupported in PyLEMS: Property) +- Example 15 -- Working +- Example 16 -- Working (apart from spikeArray) +- Example 17 -- Working +- Example 18 -- Working + + +**LEMS examples (in directory examples)** + +- example1.xml -- Working +- example2.xml -- Working +- example3.xml -- Working +- example4.xml -- Not working (Unsupported in PyLEMS: KSChannel) +- example5.xml -- Not working (Unsupported in PyLEMS: KSChannel) +- example6.xml -- Working +-- TODO: Rest of examples require an update to the `<Simulation>` element, + i.e. use `<Simulation...>` not `<SimulationSet...>`, to work in PyLEMS + + +**LEMS elements that do not work** + +- KSChannel +- Property +- XPath based parameters - PathParameter +- Assertions + +**Tasks TODO** + +- Implement flattening +- Decouple events from runnables +- Improve dimension-checking on expressions. + +This code is distributed under the terms of the GNU Lesser General Public License. + + +%package -n python3-PyLEMS +Summary: A Python library for working with the Low Entropy Model Specification language (LEMS) +Provides: python-PyLEMS +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-PyLEMS +## PyLEMS + +[](https://github.com/LEMS/pylems/actions/workflows/ci.yml) +[](https://github.com/LEMS/pylems/actions/workflows/examples.yml) +[](https://pylems.readthedocs.io/en/latest/?badge=latest) + + +A LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2 models (see [here](https://docs.neuroml.org/Userdocs/Software/pyLEMS.html)). + +For more about PyLEMS see: + +Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig Gleeson, +**libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience** +[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00038/abstract), doi: 10.3389/fninf.2014.00038 + +_**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_ + +For more details on LEMS see: + +Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver, +**LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2**, +[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00079/abstract), doi: 10.3389/fninf.2014.00079 + + +### Installation + +A stable version of PyLEMS is [available on PyPI](https://pypi.python.org/pypi/PyLEMS) using [pip](https://pip.pypa.io/en/latest/installing.html): + + pip install pylems + +To install as root: + + sudo pip install pylems + +Alternatively, you can obtain the latest version with + + git clone https://github.com/LEMS/pylems.git + cd pylems + git checkout development # optional + sudo python setup.py install + +### Usage as a LEMS model simulator + + pylems [options] LEMS_file + +**Options** + +- -I/-include path - Adds a directory to the model file include search path + + +### Examples + + +**NeuroML examples (from https://github.com/NeuroML/NeuroML2/tree/development/NeuroML2CoreTypes)** + +- Example 0 -- Working +- Example 1 -- Working +- Example 2 -- Working +- Example 3 -- Working +- Example 4 -- Not working (Unsupported in PyLEMS: KSChannel) +- Example 5 -- Working +- Example 6 -- Working +- Example 7 -- Working +- Example 8 -- Working +- Example 9 -- Working +- Example 10 -- Working +- Example 11 -- Working +- Example 12 -- Not working (Unsupported in PyLEMS: Property) +- Example 13 -- Working +- Example 14 -- Not working (Unsupported in PyLEMS: Property) +- Example 15 -- Working +- Example 16 -- Working (apart from spikeArray) +- Example 17 -- Working +- Example 18 -- Working + + +**LEMS examples (in directory examples)** + +- example1.xml -- Working +- example2.xml -- Working +- example3.xml -- Working +- example4.xml -- Not working (Unsupported in PyLEMS: KSChannel) +- example5.xml -- Not working (Unsupported in PyLEMS: KSChannel) +- example6.xml -- Working +-- TODO: Rest of examples require an update to the `<Simulation>` element, + i.e. use `<Simulation...>` not `<SimulationSet...>`, to work in PyLEMS + + +**LEMS elements that do not work** + +- KSChannel +- Property +- XPath based parameters - PathParameter +- Assertions + +**Tasks TODO** + +- Implement flattening +- Decouple events from runnables +- Improve dimension-checking on expressions. + +This code is distributed under the terms of the GNU Lesser General Public License. + + +%package help +Summary: Development documents and examples for PyLEMS +Provides: python3-PyLEMS-doc +%description help +## PyLEMS + +[](https://github.com/LEMS/pylems/actions/workflows/ci.yml) +[](https://github.com/LEMS/pylems/actions/workflows/examples.yml) +[](https://pylems.readthedocs.io/en/latest/?badge=latest) + + +A LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2 models (see [here](https://docs.neuroml.org/Userdocs/Software/pyLEMS.html)). + +For more about PyLEMS see: + +Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig Gleeson, +**libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience** +[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00038/abstract), doi: 10.3389/fninf.2014.00038 + +_**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_ + +For more details on LEMS see: + +Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver, +**LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2**, +[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00079/abstract), doi: 10.3389/fninf.2014.00079 + + +### Installation + +A stable version of PyLEMS is [available on PyPI](https://pypi.python.org/pypi/PyLEMS) using [pip](https://pip.pypa.io/en/latest/installing.html): + + pip install pylems + +To install as root: + + sudo pip install pylems + +Alternatively, you can obtain the latest version with + + git clone https://github.com/LEMS/pylems.git + cd pylems + git checkout development # optional + sudo python setup.py install + +### Usage as a LEMS model simulator + + pylems [options] LEMS_file + +**Options** + +- -I/-include path - Adds a directory to the model file include search path + + +### Examples + + +**NeuroML examples (from https://github.com/NeuroML/NeuroML2/tree/development/NeuroML2CoreTypes)** + +- Example 0 -- Working +- Example 1 -- Working +- Example 2 -- Working +- Example 3 -- Working +- Example 4 -- Not working (Unsupported in PyLEMS: KSChannel) +- Example 5 -- Working +- Example 6 -- Working +- Example 7 -- Working +- Example 8 -- Working +- Example 9 -- Working +- Example 10 -- Working +- Example 11 -- Working +- Example 12 -- Not working (Unsupported in PyLEMS: Property) +- Example 13 -- Working +- Example 14 -- Not working (Unsupported in PyLEMS: Property) +- Example 15 -- Working +- Example 16 -- Working (apart from spikeArray) +- Example 17 -- Working +- Example 18 -- Working + + +**LEMS examples (in directory examples)** + +- example1.xml -- Working +- example2.xml -- Working +- example3.xml -- Working +- example4.xml -- Not working (Unsupported in PyLEMS: KSChannel) +- example5.xml -- Not working (Unsupported in PyLEMS: KSChannel) +- example6.xml -- Working +-- TODO: Rest of examples require an update to the `<Simulation>` element, + i.e. use `<Simulation...>` not `<SimulationSet...>`, to work in PyLEMS + + +**LEMS elements that do not work** + +- KSChannel +- Property +- XPath based parameters - PathParameter +- Assertions + +**Tasks TODO** + +- Implement flattening +- Decouple events from runnables +- Improve dimension-checking on expressions. + +This code is distributed under the terms of the GNU Lesser General Public License. + + +%prep +%autosetup -n PyLEMS-0.6.2 + +%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-PyLEMS -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 17 2023 Python_Bot <Python_Bot@openeuler.org> - 0.6.2-1 +- Package Spec generated @@ -0,0 +1 @@ +659609637713dd136881f4b523dd06ac PyLEMS-0.6.2.tar.gz |
