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diff --git a/python-kappy.spec b/python-kappy.spec new file mode 100644 index 0000000..6d5a5b1 --- /dev/null +++ b/python-kappy.spec @@ -0,0 +1,510 @@ +%global _empty_manifest_terminate_build 0 +Name: python-kappy +Version: 4.1.2 +Release: 1 +Summary: Wrapper to interact with the Kappa tool suite +License: LGPLv3 +URL: https://github.com/Kappa-Dev/KappaTools.git +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/76/75/b0f141d0a57d44f330fe855fc466a40116f97b2d884b7a8b28aa71a616b4/kappy-4.1.2.tar.gz +BuildArch: noarch + +Requires: python3-requests +Requires: python3-future +Requires: python3-nose + +%description +<img +src="https://rawgithub.com/Kappa-Dev/KaSim/master/man/img/KaSim-Logo.svg" +alt="KaSim logo" title="Stochastic Kappa Simulator" align="right" height="90"/> +# KappaTools + +[](https://travis-ci.com/Kappa-Dev/KappaTools) +[](https://gitter.im/Kappa-Dev/KaSim?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) + +KaSim is a stochastic simulator for rule-based models written in Kappa. KaSa is +a static analyser for Kappa models. + +Kappy is a python library to launch and analyse runs and outputs of +Kappa models. + +## User manual +See [documentation page on kappalanguage.org](https://kappalanguage.org/documentation). + +Kappy [API +documentation is online](https://kasim.readthedocs.io/en/latest/kappy.html). + +The latex sources of the "older" reference manual (and KaSa one) are +available in the `man/` directory. To compile the manuel, in addition of +a decent LaTeX distribution you need +[gnuplot](http://www.gnuplot.info/) and +[graphviz](http://www.graphviz.org/) to generate images (make sure +that `dot` is in the PATH of your OS). To generate the pdf of the +manual type + +`make doc` + +## Installation + +### Core tools + +[Released versions](https://github.com/Kappa-Dev/KaSim/releases) come with +binaries for MacOS, Windows and Debian derivatives (as Ubuntu). [Nightly +builds](https://tools.kappalanguage.org/nightly-builds/) of the master branch +are built for these platforms by the continuous integration tools. + +If you want or need your own build, + - Install [opam](https://opam.ocaml.org/doc/Install.html) (the OCaml + package manager) and initialize it (by issuing `opam init`) + - In the source directory, install all the dependencies by `opam install --deps-only .` + - `dune build` + +You can be more fine grained if you only need the command-line tools +(and therefore could install less dependencies) by doing `opam install +--deps-only kappa-binaries` followed by `make all` + +If nothing worked for you so far. Well, you're pretty much on your +own... Kappa tools depend upon the OCaml native compiler version +4.05.0 or above as well as _dune_, _findlib_, _Lwt_ (>= 2.6.0), _Re_, +_Fmt_, _Logs_ and _Yojson_ libraries. Find any way to install them and +you'll be only a `make all` away from getting Kappa binaries... + +### Kappy + +You should be able to `pip install kappy`. + +- Under MacOS and linux (and if you're not using a python version so + cutting edge that we haven't notice its release yet), _wheels_ that + contain the core binaries should be available. +- For other platforms/python versions, you need to get kappa agents by + yourself thanks to the *opam* package manager by `opam install + kappa-binaries kappa-agents` (or use an externaly hosted REST API) +- In order to develop in kappy and run all its tests, you need to + follow the "get your own build section" above as well as install + _requests_ (and _future_). + +## Usage + +### KaSim + +In order to run a simulation for 100 time units printing observables values +every 0.5 time unit, type + +`bin/KaSim kappa_file_1 ... kappa_file_n -l 100 -p 0.5 -o data_file` + +This will produce a data file of 200 point containing the +trajectory that was produced during the simulation. + +Type: + +`bin/KaSim --help` + +for a complete list of options. + +### Kappy + +Do: + +```python +import kappy +client = kappy.KappaRest("http\://url_of/the_server","project_name") +``` + +to get a kappa client that uses the REST API hosted by +*http://url_of/the_server* and deals with project *project_name*. + +or do: + +```python +import kappy +client = kappy.KappaStd() +``` + +to get a kappa client that uses a kappa agent installed locally. Add a +string argument specifing the `path/to/KaSimAgent` to use a specific agent. + +A minimal example of usage is: + +```python +model = "\ +%agent: A(x[x.A]) \ +%var: n_0 100 \ +%var: k_on 1e-2 \ +'rule' A(x[.]), A(x[.]) <-> A(x[1]), A(x[1]) @ k_on, 1 \ +%plot: |A(x[.])| \ +%init: n_0 A()" +client.add_model_string(model) +client.project_parse() +sim_params = kappy.SimulationParameter(pause_condition="[T] > 100",plot_period=1) +client.simulation_start(sim_params) +client.wait_for_simulation_stop() +results = client.simulation_plot() +client.simulation_delete() +# Rerun with some overwritten values for algebraic variables +client.project_parse(k_on=5e-2,n_0=500) +client.simulation_start(sim_params) +client.wait_for_simulation_stop() +results' = client.simulation_plot() +client.shutdown() +``` + +## Tests + +Launch the core/integration tests by `make check`. + +Regenerate the reference files if you've changed something in the +outputs by `make build-tests` + +Launch python tests by `nosetests` (after having followed the "Get +your own build" section). + + + + +%package -n python3-kappy +Summary: Wrapper to interact with the Kappa tool suite +Provides: python-kappy +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-kappy +<img +src="https://rawgithub.com/Kappa-Dev/KaSim/master/man/img/KaSim-Logo.svg" +alt="KaSim logo" title="Stochastic Kappa Simulator" align="right" height="90"/> +# KappaTools + +[](https://travis-ci.com/Kappa-Dev/KappaTools) +[](https://gitter.im/Kappa-Dev/KaSim?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) + +KaSim is a stochastic simulator for rule-based models written in Kappa. KaSa is +a static analyser for Kappa models. + +Kappy is a python library to launch and analyse runs and outputs of +Kappa models. + +## User manual +See [documentation page on kappalanguage.org](https://kappalanguage.org/documentation). + +Kappy [API +documentation is online](https://kasim.readthedocs.io/en/latest/kappy.html). + +The latex sources of the "older" reference manual (and KaSa one) are +available in the `man/` directory. To compile the manuel, in addition of +a decent LaTeX distribution you need +[gnuplot](http://www.gnuplot.info/) and +[graphviz](http://www.graphviz.org/) to generate images (make sure +that `dot` is in the PATH of your OS). To generate the pdf of the +manual type + +`make doc` + +## Installation + +### Core tools + +[Released versions](https://github.com/Kappa-Dev/KaSim/releases) come with +binaries for MacOS, Windows and Debian derivatives (as Ubuntu). [Nightly +builds](https://tools.kappalanguage.org/nightly-builds/) of the master branch +are built for these platforms by the continuous integration tools. + +If you want or need your own build, + - Install [opam](https://opam.ocaml.org/doc/Install.html) (the OCaml + package manager) and initialize it (by issuing `opam init`) + - In the source directory, install all the dependencies by `opam install --deps-only .` + - `dune build` + +You can be more fine grained if you only need the command-line tools +(and therefore could install less dependencies) by doing `opam install +--deps-only kappa-binaries` followed by `make all` + +If nothing worked for you so far. Well, you're pretty much on your +own... Kappa tools depend upon the OCaml native compiler version +4.05.0 or above as well as _dune_, _findlib_, _Lwt_ (>= 2.6.0), _Re_, +_Fmt_, _Logs_ and _Yojson_ libraries. Find any way to install them and +you'll be only a `make all` away from getting Kappa binaries... + +### Kappy + +You should be able to `pip install kappy`. + +- Under MacOS and linux (and if you're not using a python version so + cutting edge that we haven't notice its release yet), _wheels_ that + contain the core binaries should be available. +- For other platforms/python versions, you need to get kappa agents by + yourself thanks to the *opam* package manager by `opam install + kappa-binaries kappa-agents` (or use an externaly hosted REST API) +- In order to develop in kappy and run all its tests, you need to + follow the "get your own build section" above as well as install + _requests_ (and _future_). + +## Usage + +### KaSim + +In order to run a simulation for 100 time units printing observables values +every 0.5 time unit, type + +`bin/KaSim kappa_file_1 ... kappa_file_n -l 100 -p 0.5 -o data_file` + +This will produce a data file of 200 point containing the +trajectory that was produced during the simulation. + +Type: + +`bin/KaSim --help` + +for a complete list of options. + +### Kappy + +Do: + +```python +import kappy +client = kappy.KappaRest("http\://url_of/the_server","project_name") +``` + +to get a kappa client that uses the REST API hosted by +*http://url_of/the_server* and deals with project *project_name*. + +or do: + +```python +import kappy +client = kappy.KappaStd() +``` + +to get a kappa client that uses a kappa agent installed locally. Add a +string argument specifing the `path/to/KaSimAgent` to use a specific agent. + +A minimal example of usage is: + +```python +model = "\ +%agent: A(x[x.A]) \ +%var: n_0 100 \ +%var: k_on 1e-2 \ +'rule' A(x[.]), A(x[.]) <-> A(x[1]), A(x[1]) @ k_on, 1 \ +%plot: |A(x[.])| \ +%init: n_0 A()" +client.add_model_string(model) +client.project_parse() +sim_params = kappy.SimulationParameter(pause_condition="[T] > 100",plot_period=1) +client.simulation_start(sim_params) +client.wait_for_simulation_stop() +results = client.simulation_plot() +client.simulation_delete() +# Rerun with some overwritten values for algebraic variables +client.project_parse(k_on=5e-2,n_0=500) +client.simulation_start(sim_params) +client.wait_for_simulation_stop() +results' = client.simulation_plot() +client.shutdown() +``` + +## Tests + +Launch the core/integration tests by `make check`. + +Regenerate the reference files if you've changed something in the +outputs by `make build-tests` + +Launch python tests by `nosetests` (after having followed the "Get +your own build" section). + + + + +%package help +Summary: Development documents and examples for kappy +Provides: python3-kappy-doc +%description help +<img +src="https://rawgithub.com/Kappa-Dev/KaSim/master/man/img/KaSim-Logo.svg" +alt="KaSim logo" title="Stochastic Kappa Simulator" align="right" height="90"/> +# KappaTools + +[](https://travis-ci.com/Kappa-Dev/KappaTools) +[](https://gitter.im/Kappa-Dev/KaSim?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) + +KaSim is a stochastic simulator for rule-based models written in Kappa. KaSa is +a static analyser for Kappa models. + +Kappy is a python library to launch and analyse runs and outputs of +Kappa models. + +## User manual +See [documentation page on kappalanguage.org](https://kappalanguage.org/documentation). + +Kappy [API +documentation is online](https://kasim.readthedocs.io/en/latest/kappy.html). + +The latex sources of the "older" reference manual (and KaSa one) are +available in the `man/` directory. To compile the manuel, in addition of +a decent LaTeX distribution you need +[gnuplot](http://www.gnuplot.info/) and +[graphviz](http://www.graphviz.org/) to generate images (make sure +that `dot` is in the PATH of your OS). To generate the pdf of the +manual type + +`make doc` + +## Installation + +### Core tools + +[Released versions](https://github.com/Kappa-Dev/KaSim/releases) come with +binaries for MacOS, Windows and Debian derivatives (as Ubuntu). [Nightly +builds](https://tools.kappalanguage.org/nightly-builds/) of the master branch +are built for these platforms by the continuous integration tools. + +If you want or need your own build, + - Install [opam](https://opam.ocaml.org/doc/Install.html) (the OCaml + package manager) and initialize it (by issuing `opam init`) + - In the source directory, install all the dependencies by `opam install --deps-only .` + - `dune build` + +You can be more fine grained if you only need the command-line tools +(and therefore could install less dependencies) by doing `opam install +--deps-only kappa-binaries` followed by `make all` + +If nothing worked for you so far. Well, you're pretty much on your +own... Kappa tools depend upon the OCaml native compiler version +4.05.0 or above as well as _dune_, _findlib_, _Lwt_ (>= 2.6.0), _Re_, +_Fmt_, _Logs_ and _Yojson_ libraries. Find any way to install them and +you'll be only a `make all` away from getting Kappa binaries... + +### Kappy + +You should be able to `pip install kappy`. + +- Under MacOS and linux (and if you're not using a python version so + cutting edge that we haven't notice its release yet), _wheels_ that + contain the core binaries should be available. +- For other platforms/python versions, you need to get kappa agents by + yourself thanks to the *opam* package manager by `opam install + kappa-binaries kappa-agents` (or use an externaly hosted REST API) +- In order to develop in kappy and run all its tests, you need to + follow the "get your own build section" above as well as install + _requests_ (and _future_). + +## Usage + +### KaSim + +In order to run a simulation for 100 time units printing observables values +every 0.5 time unit, type + +`bin/KaSim kappa_file_1 ... kappa_file_n -l 100 -p 0.5 -o data_file` + +This will produce a data file of 200 point containing the +trajectory that was produced during the simulation. + +Type: + +`bin/KaSim --help` + +for a complete list of options. + +### Kappy + +Do: + +```python +import kappy +client = kappy.KappaRest("http\://url_of/the_server","project_name") +``` + +to get a kappa client that uses the REST API hosted by +*http://url_of/the_server* and deals with project *project_name*. + +or do: + +```python +import kappy +client = kappy.KappaStd() +``` + +to get a kappa client that uses a kappa agent installed locally. Add a +string argument specifing the `path/to/KaSimAgent` to use a specific agent. + +A minimal example of usage is: + +```python +model = "\ +%agent: A(x[x.A]) \ +%var: n_0 100 \ +%var: k_on 1e-2 \ +'rule' A(x[.]), A(x[.]) <-> A(x[1]), A(x[1]) @ k_on, 1 \ +%plot: |A(x[.])| \ +%init: n_0 A()" +client.add_model_string(model) +client.project_parse() +sim_params = kappy.SimulationParameter(pause_condition="[T] > 100",plot_period=1) +client.simulation_start(sim_params) +client.wait_for_simulation_stop() +results = client.simulation_plot() +client.simulation_delete() +# Rerun with some overwritten values for algebraic variables +client.project_parse(k_on=5e-2,n_0=500) +client.simulation_start(sim_params) +client.wait_for_simulation_stop() +results' = client.simulation_plot() +client.shutdown() +``` + +## Tests + +Launch the core/integration tests by `make check`. + +Regenerate the reference files if you've changed something in the +outputs by `make build-tests` + +Launch python tests by `nosetests` (after having followed the "Get +your own build" section). + + + + +%prep +%autosetup -n kappy-4.1.2 + +%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-kappy -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 31 2023 Python_Bot <Python_Bot@openeuler.org> - 4.1.2-1 +- Package Spec generated |