diff --git a/brain/circuit.h b/brain/circuit.h index 57aa915..69cb0ee 100644 --- a/brain/circuit.h +++ b/brain/circuit.h @@ -127,9 +127,9 @@ class Circuit */ BRAIN_API Strings getElectrophysiologyTypeNames() const; - /** @return \if pybind A Nx4 numpy array with the \else The \endif - * local to world transformations of the given cells in the - * iteration + /** @return \if pybind A Nx4x4 numpy array with the \else The \endif + * local to world transformations of the given cells in their + * iteration order. */ BRAIN_API Matrix4fs getTransforms(const GIDSet& gids) const; diff --git a/brain/python/circuit.cpp b/brain/python/circuit.cpp index 9505c8e..c6d616b 100644 --- a/brain/python/circuit.cpp +++ b/brain/python/circuit.cpp @@ -192,70 +192,71 @@ SynapsesWrapper Circuit_getProjectedSynapses( } void export_Circuit() +// clang-format off { - bp::class_ circuitWrapper( - "Circuit", DOXY_CLASS(brain::Circuit), bp::no_init); - bp::scope circuitScope = circuitWrapper; +bp::class_ circuitWrapper( + "Circuit", DOXY_CLASS(brain::Circuit), bp::no_init); - bp::enum_("Coordinates") - .value("global_", Circuit::Coordinates::global) - .value("local", Circuit::Coordinates::local); +bp::scope circuitScope = circuitWrapper; - const auto selfarg = bp::arg("self"); +bp::enum_("Coordinates") + .value("global_", Circuit::Coordinates::global) + .value("local", Circuit::Coordinates::local); - // Do not modify whitespace on DOXY_FN lines +const auto selfarg = bp::arg("self"); - circuitWrapper - .def("__init__", bp::make_constructor(Circuit_initFromURI), - DOXY_FN(brain::Circuit::Circuit(const URI&))) - .def("gids", Circuit_getAllGIDs, (selfarg), - DOXY_FN(brain::Circuit::getGIDs() const)) - .def("gids", Circuit_getGIDs, (selfarg, bp::arg("target")), - DOXY_FN(brain::Circuit::getGIDs(const std::string&) const)) - .def("random_gids", Circuit_getRandomTargetGIDs, - (selfarg, bp::arg("fraction"), bp::arg("target")), - DOXY_FN(brain::Circuit::getRandomGIDs(float, const std::string&) - const)) - .def("random_gids", Circuit_getRandomGIDs, - (selfarg, bp::arg("fraction")), - DOXY_FN(brain::Circuit::getRandomGIDs(float) const)) - .def("morphology_uris", Circuit_getMorphologyURIs, - (selfarg, bp::arg("gids")), - DOXY_FN(brain::Circuit::getMorphologyURIs)) - .def("load_morphologies", Circuit_loadMorphologies, - (selfarg, bp::arg("gids"), bp::arg("coords")), - DOXY_FN(brain::Circuit::loadMorphologies)) - .def("positions", Circuit_getPositions, (selfarg, bp::arg("gids")), - DOXY_FN(brain::Circuit::getPositions)) - .def("morphology_types", Circuit_getMorphologyTypes, - (selfarg, bp::arg("gids")), - DOXY_FN(brain::Circuit::getMorphologyTypes)) - .def("morphology_type_names", Circuit_getMorphologyTypeNames, (selfarg), - DOXY_FN(brain::Circuit::getMorphologyTypeNames)) - .def("electrophysiology_types", Circuit_getElectrophysiologyTypes, - (selfarg, bp::arg("gids")), - DOXY_FN(brain::Circuit::getElectrophysiologyTypes)) - .def("electrophysiology_type_names", - Circuit_getElectrophysiologyTypeNames, (selfarg), - DOXY_FN(brain::Circuit::getElectrophysiologyTypeNames)) - .def("transforms", Circuit_getTransforms, (selfarg, bp::arg("gids")), - DOXY_FN(brain::Circuit::getTransforms)) - .def("rotations", Circuit_getRotations, (selfarg, bp::arg("gids")), - DOXY_FN(brain::Circuit::getRotations)) - .def("num_neurons", &Circuit::getNumNeurons, (selfarg), - DOXY_FN(brain::Circuit::getNumNeurons)) - .def("afferent_synapses", Circuit_getAfferentSynapses, - (selfarg, bp::arg("gids"), - bp::arg("prefetch") = SynapsePrefetch::none), - DOXY_FN(brain::Circuit::getAfferentSynapses)) - .def("efferent_synapses", Circuit_getEfferentSynapses, - (selfarg, bp::arg("gids"), - bp::arg("prefetch") = SynapsePrefetch::none), - DOXY_FN(brain::Circuit::getEfferentSynapses)) - .def("projected_synapses", Circuit_getProjectedSynapses, - (selfarg, bp::arg("preGids"), bp::arg("postGIDs"), - bp::arg("prefetch") = SynapsePrefetch::none), - DOXY_FN(brain::Circuit::getProjectedSynapses)); +// Do not modify whitespace on DOXY_FN lines +circuitWrapper + .def("__init__", bp::make_constructor(Circuit_initFromURI), + DOXY_FN(brain::Circuit::Circuit(const URI&))) + .def("gids", Circuit_getAllGIDs, (selfarg), + DOXY_FN(brain::Circuit::getGIDs() const)) + .def("gids", Circuit_getGIDs, (selfarg, bp::arg("target")), + DOXY_FN(brain::Circuit::getGIDs(const std::string&) const)) + .def("random_gids", Circuit_getRandomTargetGIDs, + (selfarg, bp::arg("fraction"), bp::arg("target")), + DOXY_FN(brain::Circuit::getRandomGIDs(float, const std::string&) const)) + .def("random_gids", Circuit_getRandomGIDs, + (selfarg, bp::arg("fraction")), + DOXY_FN(brain::Circuit::getRandomGIDs(float) const)) + .def("morphology_uris", Circuit_getMorphologyURIs, + (selfarg, bp::arg("gids")), + DOXY_FN(brain::Circuit::getMorphologyURIs)) + .def("load_morphologies", Circuit_loadMorphologies, + (selfarg, bp::arg("gids"), bp::arg("coords")), + DOXY_FN(brain::Circuit::loadMorphologies)) + .def("positions", Circuit_getPositions, (selfarg, bp::arg("gids")), + DOXY_FN(brain::Circuit::getPositions)) + .def("morphology_types", Circuit_getMorphologyTypes, + (selfarg, bp::arg("gids")), + DOXY_FN(brain::Circuit::getMorphologyTypes)) + .def("morphology_type_names", Circuit_getMorphologyTypeNames, (selfarg), + DOXY_FN(brain::Circuit::getMorphologyTypeNames)) + .def("electrophysiology_types", Circuit_getElectrophysiologyTypes, + (selfarg, bp::arg("gids")), + DOXY_FN(brain::Circuit::getElectrophysiologyTypes)) + .def("electrophysiology_type_names", + Circuit_getElectrophysiologyTypeNames, (selfarg), + DOXY_FN(brain::Circuit::getElectrophysiologyTypeNames)) + .def("transforms", Circuit_getTransforms, (selfarg, bp::arg("gids")), + DOXY_FN(brain::Circuit::getTransforms)) + .def("rotations", Circuit_getRotations, (selfarg, bp::arg("gids")), + DOXY_FN(brain::Circuit::getRotations)) + .def("num_neurons", &Circuit::getNumNeurons, (selfarg), + DOXY_FN(brain::Circuit::getNumNeurons)) + .def("afferent_synapses", Circuit_getAfferentSynapses, + (selfarg, bp::arg("gids"), + bp::arg("prefetch") = SynapsePrefetch::none), + DOXY_FN(brain::Circuit::getAfferentSynapses)) + .def("efferent_synapses", Circuit_getEfferentSynapses, + (selfarg, bp::arg("gids"), + bp::arg("prefetch") = SynapsePrefetch::none), + DOXY_FN(brain::Circuit::getEfferentSynapses)) + .def("projected_synapses", Circuit_getProjectedSynapses, + (selfarg, bp::arg("preGids"), bp::arg("postGIDs"), + bp::arg("prefetch") = SynapsePrefetch::none), + DOXY_FN(brain::Circuit::getProjectedSynapses)); } +// clang-format on } diff --git a/doc/python/python tutorial.ipynb b/doc/python/python tutorial.ipynb index a785bd8..af33dbf 100644 --- a/doc/python/python tutorial.ipynb +++ b/doc/python/python tutorial.ipynb @@ -18,7 +18,7 @@ "\n", "Before you start you have to make sure that you have the Python module available in your environemnt. In the Blue Brain clusters you have two possibilities depending on the Python version you want to use:\n", "* For Python 3.4: ```module load BBP/viz/latest```\n", - "* For Python 2.7: ```module load memcache/bbpviz nix/viz/brion/2.0 nix/python2.7-full```" + "* For Python 2.7: ```module load memcache/bbpviz nix/viz/brion nix/python/2.7-full```" ] }, { diff --git a/doc/python/python_tutorial.rst b/doc/python/python_tutorial.rst index 333fad2..781822d 100644 --- a/doc/python/python_tutorial.rst +++ b/doc/python/python_tutorial.rst @@ -26,7 +26,7 @@ available in your environemnt. In the Blue Brain clusters you have two possibilities depending on the Python version you want to use: * For Python 3.4: ``module load BBP/viz/latest`` - * For Python 2.7: ``module load memcache/bbpviz nix/viz/brion/2.0 nix/python2.7-full`` + * For Python 2.7: ``module load memcache/bbpviz nix/viz/brion nix/python/2.7-full`` .. code:: python