%global checkout_date 20200807

%global debug_package %{nil}

Name:           neuroConstruct
Version:        1.7.2
Release:        5%{?dist}
Summary:        Biophysically detailed neuronal modelling in 3D

# jython: CNRI and BSD and ASL and MIT
# neuroConstruct: GPLv2+
# jogl: BSD
# joal: BSD
# jocl: BSD
# gluegen: BSD
License:        GPLv2+ and ASL 2.0 and BSD and MIT and Python and CNRI
URL:            http://www.neuroconstruct.org/

# Using the pre-built jar
Source0:        https://github.com/NeuralEnsemble/neuroConstruct/releases/download/v%{version}/neuroConstruct_%{version}.zip

Requires:       java-headless
Requires:       javapackages-filesystem

Provides:       bundled(jneuroml2) = 2.0.0
Provides:       bundled(jneuroml) = 0.8.3
Provides:       bundled(lems) = 0.8.3
Provides:       bundled(junit) = 4.8.1
# Version not provided
Provides:       bundled(jhdf5)
Provides:       bundled(jython) = 2.7b3
# all part of j3d?
Provides:       bundled(j3d) = 1.6.0-pre9
Provides:       bundled(joal) = 2.1.2
Provides:       bundled(jogl) = 2.1.2
Provides:       bundled(jocl) = 2.1.2
Provides:       bundled(gluegen) = 2.1.2
# jython bundles these
Provides:       bundled(antlr) = 3.1.3
Provides:       bundled(asm) = 4.0
Provides:       bundled(commons-compress) = 1.8.1
Provides:       bundled(guava) = 17.0
Provides:       bundled(icu4j) = 52_1
Provides:       bundled(jarjar) = 1.4
Provides:       bundled(jffi) = 1.2.6
Provides:       bundled(jline) = 1.0
Provides:       bundled(jnr-constants) = 0.8.4
Provides:       bundled(jnr-ffi) = 0.7.0
Provides:       bundled(jnr-netdb) = 1.1.1
Provides:       bundled(jnr-posix) = 2.4.0
Provides:       bundled(junit) = 4.10
Provides:       bundled(libreadline-java) = 0.8
Provides:       bundled(mysql-connector) = 5.1.6
Provides:       bundled(netty) = 4.0.20
Provides:       bundled(postgresql-java) = 8.3-603
Provides:       bundled(servlet-api) = 2.5
Provides:       bundled(xercesImpl) = 2.11.0
Provides:       bundled(xml-apis) = 2.11.0
Provides:       bundled(mockrunner) = 0.4.1
Provides:       bundled(cpptasks) = 1.0b5


%description
This is neuroConstruct, software for developing 3D networks for biologically realistic neuronal simulations.
Some of the key features of neuroConstruct are:

- neuroConstruct can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in single cell or network models, or more abstract cells can also be built manually.
- Creation of networks of conductance based neurons positioned in 3D
- Complex connectivity patterns between cell groups can be specified for the networks
- Simulation scripts can be generated for NEURON, GENESIS, MOOSE, PSICS and PyNN based simulators (note: not every project can be generated for every simulator)
- Biophysically realistic cellular mechanisms (synapses/channel mechanisms) can be imported from native script files (*.mod or *.g) or created from templates using ChannelML
- Automatic generation of code to record simulation data and visualisation/analysis of data in neuroConstruct
- Recorded simulation runs can be viewed and managed through the Simulation Browser interface
- A Python based scripting interface can be used to control model generation and execution, allowing multiple simulations to be run for cell and network model optimisation

This package includes the pre-built Jar file along with the necessary dependencies.

%prep
%autosetup -n %{name}_%{version}
# Fix the path
sed -i 's|^export NC_HOME.*|export NC_HOME="%{_javadir}/%{name}/"|' nCenv.sh

%build
# Nothing to do here

%install
# Put stuff in the right place
install -p -m 0644 -D -T %{name}_%{version}.jar %{buildroot}/%{_javadir}/%{name}/%{name}_%{version}.jar

# scripts
install -p -m 0755 -D -T nC.sh %{buildroot}/%{_bindir}/nC.sh
install -p -m 0755 -D -T nCenv.sh %{buildroot}/%{_bindir}/nCenv.sh

# everything is hard-coded to go into the NC_HOME dir
cp -rv jNeuroMLJar %{buildroot}/%{_javadir}/%{name}/
rm -rfv lib/hdf5/win*
find lib -name "*windows*" -delete
find lib -name "*Windows*" -delete
find lib -name "*macosx*" -delete
find lib -name "*Darwin*jar" -delete
find lib -name "*ppc*jar" -delete
find lib -name "*s390x*jar" -delete
find lib -name "*sparc*jar" -delete
find lib -name "*FreeBSD*jar" -delete
find lib -name "*OpenBSD*jar" -delete
find lib -name "*SunOS*jar" -delete
cp -rv lib %{buildroot}/%{_javadir}/%{name}/
cp -rv nCexamples %{buildroot}/%{_javadir}/%{name}/
cp -rv templates %{buildroot}/%{_javadir}/%{name}/
cp -rv NeuroML2 %{buildroot}/%{_javadir}/%{name}/

# Do this separately because some bits are to go into docs in the files section
install -p -m 0755 -d %{buildroot}/%{_javadir}/%{name}/docs/
cp -rv docs/XML %{buildroot}/%{_javadir}/%{name}/docs/

install -p -m 0755 -d %{buildroot}/%{_datadir}/%{name}
cp -rv matlabOctave %{buildroot}/%{_datadir}/%{name}/

# Remove unneeded stuff
rm -rf *.sh *.bat tests testProjects src *.xml docs/website

%files
%license licence.txt
%{_javadir}/%{name}
%{_bindir}/nC.sh
%{_bindir}/nCenv.sh
%{_datadir}/%{name}
%doc docs/helpdocs
%doc pythonnC

%changelog
* Fri Sep 18 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.7.2-5
- Include more files needed at runtime
- List bundled jars
- Remove unneeded jars

* Thu Sep 17 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.7.2-3
- Add docs to package
- Update licenses

* Thu Sep 17 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.7.2-2
- Remove noarch: build fails on F31 and F32

* Thu Sep 17 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.7.2-1
- Initial build