diff --git a/0001-Unbundle-Random123.patch b/0001-Unbundle-Random123.patch
index d5b7d20..d4b620f 100644
--- a/0001-Unbundle-Random123.patch
+++ b/0001-Unbundle-Random123.patch
@@ -1,7 +1,7 @@
 From b5a4df18e249b9b0181698e3353b57e1063ebede Mon Sep 17 00:00:00 2001
 From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
 Date: Wed, 19 Jun 2019 18:35:39 +0100
-Subject: [PATCH 1/7] Unbundle Random123
+Subject: [PATCH 1/4] Unbundle Random123
 
 ---
  configure.ac    | 2 +-
diff --git a/0002-Unbundle-readline.patch b/0002-Unbundle-readline.patch
index b0bea03..0cccb38 100644
--- a/0002-Unbundle-readline.patch
+++ b/0002-Unbundle-readline.patch
@@ -1,7 +1,7 @@
 From 6acd994ba41f05cef28c789c9125f264f0d4e9cc Mon Sep 17 00:00:00 2001
 From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
 Date: Wed, 19 Jun 2019 18:37:49 +0100
-Subject: [PATCH 2/7] Unbundle readline
+Subject: [PATCH 2/4] Unbundle readline
 
 ---
  configure.ac    |  3 +--
diff --git a/0003-Install-ivstream-header.patch b/0003-Install-ivstream-header.patch
deleted file mode 100644
index 8dbdf2d..0000000
--- a/0003-Install-ivstream-header.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From a9e73c36d673e02d5cf946a4356d2feec04993d2 Mon Sep 17 00:00:00 2001
-From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
-Date: Wed, 19 Jun 2019 22:15:36 +0100
-Subject: [PATCH 3/7] Install ivstream header
-
----
- src/ivos/Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/ivos/Makefile.am b/src/ivos/Makefile.am
-index 03884ffc..dc21173c 100755
---- a/src/ivos/Makefile.am
-+++ b/src/ivos/Makefile.am
-@@ -8,4 +8,4 @@ SUBDIRS = InterViews OS
- 
- AM_CXXFLAGS = @MINGW_CFLAG@
- 
--EXTRA_DIST = ivstrm.h
-+include_HEADERS = ivstrm.h ivstream.h
--- 
-2.21.0
-
diff --git a/0003-Remove-duplicate-file-installation.patch b/0003-Remove-duplicate-file-installation.patch
new file mode 100644
index 0000000..d946ae5
--- /dev/null
+++ b/0003-Remove-duplicate-file-installation.patch
@@ -0,0 +1,25 @@
+From 73683d594350e10d30f65b163db7b8aafc54313b Mon Sep 17 00:00:00 2001
+From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
+Date: Sun, 23 Jun 2019 18:31:52 +0100
+Subject: [PATCH 3/4] Remove duplicate file installation
+
+---
+ src/nrniv/Makefile.am | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/nrniv/Makefile.am b/src/nrniv/Makefile.am
+index 97e9cdaf..aff9aef4 100755
+--- a/src/nrniv/Makefile.am
++++ b/src/nrniv/Makefile.am
+@@ -162,7 +162,7 @@ noinst_HEADERS = ndatclas.h nrnclass.h nrnmenu.h nrnoc2iv.h ppshape.h \
+ 	multisplitcontrol.h nvector_nrnthread.h \
+ 	bbsavestate.h nrnbbcore_write.h nrnsection_mapping.h\
+ 	nrnmusic.cpp nrndae.h matrixmap.h \
+-	structpool.h nrnhash_alt.h
++	nrnhash_alt.h
+ 
+ ## We have to play a trick on automake to get it to install the .o files in
+ ## an architecture-dependent subdirectory.  (Apparently automake's authors
+-- 
+2.21.0
+
diff --git a/0004-Build-python-bits-in-the-source-tree.patch b/0004-Build-python-bits-in-the-source-tree.patch
new file mode 100644
index 0000000..4a59dba
--- /dev/null
+++ b/0004-Build-python-bits-in-the-source-tree.patch
@@ -0,0 +1,46 @@
+From c1f3492e0ba9a985cd786fc975670c31bc2e8a4c Mon Sep 17 00:00:00 2001
+From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
+Date: Mon, 15 Jul 2019 23:43:16 +0100
+Subject: [PATCH 4/4] Build python bits in the source tree
+
+---
+ src/neuronmusic/setup.py.in | 2 +-
+ src/nrnpython/setup.py.in   | 3 +--
+ 2 files changed, 2 insertions(+), 3 deletions(-)
+
+diff --git a/src/neuronmusic/setup.py.in b/src/neuronmusic/setup.py.in
+index ddc21c68..9a91d421 100644
+--- a/src/neuronmusic/setup.py.in
++++ b/src/neuronmusic/setup.py.in
+@@ -29,6 +29,6 @@ neuronmusic_module = Extension(
+ 
+ setup(name="neuronmusic", version="@PACKAGE_VERSION@",
+     description = "NEURON+MUSIC python interface",
+-    package_dir = {'':instdir+'/share/nrn/lib/python'},
++    package_dir = {'':nrn_srcdir+'/share/nrn/lib/python'},
+     ext_modules=[neuronmusic_module]
+ )
+diff --git a/src/nrnpython/setup.py.in b/src/nrnpython/setup.py.in
+index 19bec5f2..3e2560a1 100644
+--- a/src/nrnpython/setup.py.in
++++ b/src/nrnpython/setup.py.in
+@@ -19,7 +19,6 @@ destdir = os.getenv("DESTDIR")
+ if not destdir:
+   destdir = ""
+ 
+-instdir = destdir + "@prefix@"
+ if nrn_srcdir[0] != '/' :
+     nrn_srcdir = '../../' + nrn_srcdir
+ 
+@@ -125,7 +124,7 @@ if build_rx3d:
+ 
+ setup(name="NEURON", version="@PACKAGE_VERSION@",
+       description = "NEURON bindings for python",
+-      package_dir = {'':instdir+'/share/nrn/lib/python'},
++      package_dir = {'':nrn_srcdir+'/share/lib/python'},
+       packages=packages,
+       data_files = [('neuron', [nrn_srcdir + '/share/lib/python/neuron/help_data.dat'])],
+       ext_modules=ext_modules
+-- 
+2.21.0
+
diff --git a/0004-Install-all-headers.patch b/0004-Install-all-headers.patch
deleted file mode 100644
index d051c34..0000000
--- a/0004-Install-all-headers.patch
+++ /dev/null
@@ -1,270 +0,0 @@
-From 3b8051545b49878a3f0ab917408f64e5f259b4bb Mon Sep 17 00:00:00 2001
-From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
-Date: Sun, 23 Jun 2019 18:19:28 +0100
-Subject: [PATCH 4/7] Install all headers
-
----
- src/gnu/Makefile.am             | 2 +-
- src/ivoc/Makefile.am            | 2 +-
- src/memacs/Makefile.am          | 2 +-
- src/mesch/Makefile.am           | 2 +-
- src/modlunit/Makefile.am        | 2 +-
- src/ni_pci_6229/Makefile.am     | 2 +-
- src/nmodl/Makefile.am           | 2 +-
- src/nrniv/Makefile.am           | 2 +-
- src/nrnoc/Makefile.am           | 5 +----
- src/nrnpython/Makefile.am       | 2 +-
- src/oc/Makefile.am              | 6 +-----
- src/readline/Makefile.am        | 2 +-
- src/scopmath/Makefile.am        | 3 +--
- src/sparse13/Makefile.am        | 3 +--
- src/sundials/cvodes/Makefile.am | 2 +-
- src/sundials/ida/Makefile.am    | 2 +-
- src/sundials/shared/Makefile.am | 2 +-
- src/uxnrnbbs/Makefile.am        | 2 +-
- 18 files changed, 18 insertions(+), 27 deletions(-)
-
-diff --git a/src/gnu/Makefile.am b/src/gnu/Makefile.am
-index 533cf878..27f7d682 100755
---- a/src/gnu/Makefile.am
-+++ b/src/gnu/Makefile.am
-@@ -18,7 +18,7 @@ libneuron_gnu_la_SOURCES = ACG.cpp Binomial.cpp Complex.cpp DiscUnif.cpp \
- 	Normal.cpp Poisson.cpp RNG.cpp Random.cpp RndInt.cpp SmplHist.cpp \
- 	SmplStat.cpp Uniform.cpp Weibull.cpp builtin.cpp d_avec.cpp d_vec.cpp
- 
--noinst_HEADERS = ACG.h Binomial.h Complex.h DiscUnif.h Erlang.h \
-+pkginclude_HEADERS = ACG.h Binomial.h Complex.h DiscUnif.h Erlang.h \
- 	Geom.h HypGeom.h LogNorm.h MLCG.h NegExp.h Normal.h Poisson.h RNG.h \
- 	Random.h RndInt.h SmplHist.h SmplStat.h Uniform.h Weibull.h \
- 	neuron_gnu_builtin.h d_avec.h d_defs.h d_vec.h neuron_gnu_std.h
-diff --git a/src/ivoc/Makefile.am b/src/ivoc/Makefile.am
-index 4ab2fdd2..8c0b2a6f 100755
---- a/src/ivoc/Makefile.am
-+++ b/src/ivoc/Makefile.am
-@@ -61,7 +61,7 @@ libivoc_la_SOURCES = ivoc.cpp xmenu.cpp graph.cpp rubband.cpp grmanip.cpp \
- 	ocpointer.cpp gifimage.cpp ocnoiv1.cpp grglyph.cpp mlinedit.cpp \
- 	$(sysdep_sources) ivocman1.cpp ocptrvector.cpp
- 
--noinst_HEADERS = apwindow.h axis.h bndedval.h cbwidget.h checkpnt.h \
-+pkginclude_HEADERS = apwindow.h axis.h bndedval.h cbwidget.h checkpnt.h \
- 	datapath.h dbrowser.h epsprint.h field.h fourier.h \
- 	graph.h hocmark.h idraw.h ivoc.h ivocconf.h mymath.h htlist.h \
- 	objcmd.h oc2iv.h ocbox.h ocbrowsr.h occlass.h ocdeck.h ocfile.h \
-diff --git a/src/memacs/Makefile.am b/src/memacs/Makefile.am
-index 57ae9354..c59b7bbf 100755
---- a/src/memacs/Makefile.am
-+++ b/src/memacs/Makefile.am
-@@ -16,7 +16,7 @@ libmemacs_la_SOURCES = ansi.c basic.c bind.c buffer.c display.c file.c \
- 	search.c spawn.c tcap.c termio.c window.c word.c
- 
- ## The list of header files that also have to go into the distribution.
--noinst_HEADERS = ebind.h edef.h efunc.h epath.h estruct.h redef.h intfunc.h
-+pkginclude_HEADERS = ebind.h edef.h efunc.h epath.h estruct.h redef.h intfunc.h
- 
- ## Extra stuff that should be put in a distribution but doesn't get
- ## compiled.
-diff --git a/src/mesch/Makefile.am b/src/mesch/Makefile.am
-index 0b4faae2..5cd86d22 100755
---- a/src/mesch/Makefile.am
-+++ b/src/mesch/Makefile.am
-@@ -14,5 +14,5 @@ libmeschach_la_SOURCES = arnoldi.c bdfactor.c bkpfacto.c chfactor.c \
- 	zmatio.c zmatlab.c zmatop.c zmemory.c znorm.c zqrfctr.c zschur.c \
- 	zsolve.c zvecop.c
- 
--noinst_HEADERS = err.h iter.h machine.h matlab.h matrix.h matrix2.h \
-+pkginclude_HEADERS = err.h iter.h machine.h matlab.h matrix.h matrix2.h \
- 	meminfo.h oldnames.h sparse.h sparse2.h zmatrix.h zmatrix2.h
-diff --git a/src/modlunit/Makefile.am b/src/modlunit/Makefile.am
-index 88c10563..309a6ab3 100755
---- a/src/modlunit/Makefile.am
-+++ b/src/modlunit/Makefile.am
-@@ -5,7 +5,7 @@ modlunit_SOURCES = parse1.y lex.l consist.c declare.c init.c io.c \
- 	units1.c version.c
- 
- ## The list of .h files that are needed in the distribution.
--noinst_HEADERS = extargs.h extdef.h model.h symbol.h units.h parse1.h \
-+pkginclude_HEADERS = extargs.h extdef.h model.h symbol.h units.h parse1.h \
-  macmunit.h modlunit.h
- 
- ## for building a dos version
-diff --git a/src/ni_pci_6229/Makefile.am b/src/ni_pci_6229/Makefile.am
-index 5362243b..fead6aa7 100644
---- a/src/ni_pci_6229/Makefile.am
-+++ b/src/ni_pci_6229/Makefile.am
-@@ -35,6 +35,6 @@ $(NOD)/ai.o $(NOD)/ao.o
- 
- libni6229_la_LIBADD = $(LO)
- 
--noinst_HEADERS = nrndaq.h
-+pkginclude_HEADERS = nrndaq.h
- 
- EXTRA_DIST = notes_niddk run .runinfo test1.hoc test5.hoc
-diff --git a/src/nmodl/Makefile.am b/src/nmodl/Makefile.am
-index 2d14a3b6..29281fba 100755
---- a/src/nmodl/Makefile.am
-+++ b/src/nmodl/Makefile.am
-@@ -19,7 +19,7 @@ EXTRA_DIST = cout.c lex.c nmodl.mak
- AM_YFLAGS = -d
- 
- ## The list of .h files that are needed in the distribution.
--noinst_HEADERS = extdef.h extdef2.h extdef5.h modl.h symbol.h parse1.h \
-+pkginclude_HEADERS = extdef.h extdef2.h extdef5.h modl.h symbol.h parse1.h \
- 	difeqdef.h macnmodl.h carbonnmodl.h nmodlfunc.h
- 
- 
-diff --git a/src/nrniv/Makefile.am b/src/nrniv/Makefile.am
-index 97e9cdaf..45b48b8d 100755
---- a/src/nrniv/Makefile.am
-+++ b/src/nrniv/Makefile.am
-@@ -152,7 +152,7 @@ nrniv_DEPENDENCIES = \
- 
- 
- ## Header files that must be included in the distribution:
--noinst_HEADERS = ndatclas.h nrnclass.h nrnmenu.h nrnoc2iv.h ppshape.h \
-+pkginclude_HEADERS = ndatclas.h nrnclass.h nrnmenu.h nrnoc2iv.h ppshape.h \
- 	rot3band.h rotate3d.h secbrows.h shape.h shapeplt.h singlech.h \
- 	linmod.h nrnste.h arraypool.h structpool.h \
- 	kschan.h kssingle.h nonlinz.h nrnhash.h \
-diff --git a/src/nrnoc/Makefile.am b/src/nrnoc/Makefile.am
-index 8d38192b..154d3681 100755
---- a/src/nrnoc/Makefile.am
-+++ b/src/nrnoc/Makefile.am
-@@ -101,10 +101,7 @@ hocusr.h: $(nsrc)/nrnoc/neuron.h $(nsrc)/oc/mk_hocusr_h.py $(nsrc)/nrnoc/options
- ## Header files that need to be installed:
- pkginclude_HEADERS = neuron.h md1redef.h md2redef.h section.h nrnoc_ml.h \
- 	cabvars.h membdef.h membfunc.h nrniv_mf.h nrn_ansi.h nrncvode.h \
--	options.h nrnredef.h multisplit.h multicore.h nmodlmutex.h
--
--## Header files that need to be included in the distribution but not installed:
--noinst_HEADERS = hocusr.h \
-+	options.h nrnredef.h multisplit.h multicore.h nmodlmutex.h hocusr.h \
- 	osxdlfcn.h osxdlfcn.c multicore.c \
- 	nonvintblock.h nrndae_c.h
- 
-diff --git a/src/nrnpython/Makefile.am b/src/nrnpython/Makefile.am
-index 1bf86d8c..52b452e3 100755
---- a/src/nrnpython/Makefile.am
-+++ b/src/nrnpython/Makefile.am
-@@ -27,7 +27,7 @@ libnrnpython@npy_pyver10@_la_SOURCES = nrnpython.cpp nrnpy_hoc.cpp nrnpy_nrn.cpp
- 
- librxdmath_la_SOURCES = rxdmath.c $(EXTEND)
- 
--noinst_HEADERS = nrnpython.h nrnwrap_Python.h nrnpy_reg.h \
-+pkginclude_HEADERS = nrnpython.h nrnwrap_Python.h nrnpy_reg.h \
- 	nrnpy_hoc_2.h nrnpy_hoc_3.h \
- 	nrnpy_nrn_2.h nrnpy_nrn_3.h hoccontext.h \
- 	nrnpy_utils.h rxd.h grids.h
-diff --git a/src/oc/Makefile.am b/src/oc/Makefile.am
-index 7c673b85..2e0d3640 100755
---- a/src/oc/Makefile.am
-+++ b/src/oc/Makefile.am
-@@ -62,11 +62,7 @@ oc_LDADD = libocxt.la liboc.la \
- pkginclude_HEADERS = hoc.h hoclist.h hocdec.h hocassrt.h nrnisaac.h \
- 	oc_ansi.h hocparse.h ocfunc.h ocmisc.h nrnjava.h hocgetsym.h \
- 	nrnpthread.h hoc_membf.h nrnran123.h scoplib_ansi.h nrnapi.h \
--	nrnassrt.h
--
--## Header files that need to be copied into the distribution but do not need
--## to be installed:
--noinst_HEADERS = code.h equation.h hocmodl.h hocstr.h \
-+	nrnassrt.h code.h equation.h hocmodl.h hocstr.h \
- 	profile.h redef.h parse.h mcran4.h nrnmpi.h nrnrt.h isaac64.h \
- 	nrnfilewrap.h nrn_vsscanf.c classreg.h
- 
-diff --git a/src/readline/Makefile.am b/src/readline/Makefile.am
-index 53dab988..60438d2c 100755
---- a/src/readline/Makefile.am
-+++ b/src/readline/Makefile.am
-@@ -3,7 +3,7 @@ lib_LTLIBRARIES = libreadline.la
- 
- libreadline_la_SOURCES = readline.c history.c funmap.c keymaps.c
- 
--noinst_HEADERS = chardefs.h emacs_keymap.h history.h keymaps.h \
-+pkginclude_HEADERS = chardefs.h emacs_keymap.h history.h keymaps.h \
- 	readline.h vi_keymap.h
- 
- install-exec-hook:
-diff --git a/src/scopmath/Makefile.am b/src/scopmath/Makefile.am
-index 6de7c306..de8758e0 100755
---- a/src/scopmath/Makefile.am
-+++ b/src/scopmath/Makefile.am
-@@ -14,11 +14,10 @@ libscopmath_la_SOURCES = abort.c adams.c adeuler.c adrunge.c advance.c \
- 	ssimplic_thread.c
- 
- ## Header files that need to be included in the distribution:
--noinst_HEADERS = errcodes.h f2c.h scopenv.h newton_struct.h
-+pkginclude_HEADERS = errcodes.h f2c.h scopenv.h newton_struct.h scoplib.h
- 
- EXTRA_DIST = scpmth.mak
- 
--pkginclude_HEADERS = scoplib.h
- 
- AM_CPPFLAGS = -DHOC=1
- AM_CFLAGS = @MINGW_CFLAG@ 
-diff --git a/src/sparse13/Makefile.am b/src/sparse13/Makefile.am
-index 04bcdd17..b99b98c3 100755
---- a/src/sparse13/Makefile.am
-+++ b/src/sparse13/Makefile.am
-@@ -8,9 +8,8 @@ libsparse13_la_SOURCES = spalloc.c spbuild.c spfactor.c spoutput.c \
- 	cspalloc.c cspbuild.c cspfactor.c cspoutput.c \
- 	cspsolve.c csputils.c
- 
--pkginclude_HEADERS = spmatrix.h spconfig.h cspmatrix.h cspredef.h
-+pkginclude_HEADERS = spmatrix.h spconfig.h cspmatrix.h cspredef.h spdefs.h
- 
--noinst_HEADERS = spdefs.h
- 
- 
- 
-diff --git a/src/sundials/cvodes/Makefile.am b/src/sundials/cvodes/Makefile.am
-index 5178f3b8..a88ca359 100755
---- a/src/sundials/cvodes/Makefile.am
-+++ b/src/sundials/cvodes/Makefile.am
-@@ -16,7 +16,7 @@ libcvodes_la_SOURCES = \
- 	cvodesio.c \
- 	cvspgmr.c
- 
--noinst_HEADERS = \
-+pkginclude_HEADERS = \
- 	cvband.h \
- 	cvband_impl.h \
- 	cvbandpre.h \
-diff --git a/src/sundials/ida/Makefile.am b/src/sundials/ida/Makefile.am
-index 0bf005d0..17aff4ab 100755
---- a/src/sundials/ida/Makefile.am
-+++ b/src/sundials/ida/Makefile.am
-@@ -14,7 +14,7 @@ libida_la_SOURCES = \
- 	idaio.c \
- 	idaspgmr.c
- 
--noinst_HEADERS = \
-+pkginclude_HEADERS = \
- 	idaband.h \
- 	idaband_impl.h \
- 	idabbdpre.h \
-diff --git a/src/sundials/shared/Makefile.am b/src/sundials/shared/Makefile.am
-index e1d22cc5..4d71b36c 100755
---- a/src/sundials/shared/Makefile.am
-+++ b/src/sundials/shared/Makefile.am
-@@ -25,7 +25,7 @@ libshared_la_SOURCES = band.c dense.c iterative.c \
- 	nvector.c nvector_serial.c smalldense.c spgmr.c sundialsmath.c \
- 	$(PARSRC1)
- 
--noinst_HEADERS = band.h dense.h iterative.h \
-+pkginclude_HEADERS = band.h dense.h iterative.h \
- 	nvector.h nvector_serial.h smalldense.h spgmr.h \
- 	sundialsmath.h sundialstypes.h \
- 	$(PARINC1)
-diff --git a/src/uxnrnbbs/Makefile.am b/src/uxnrnbbs/Makefile.am
-index 8bf07048..f5e10ac2 100755
---- a/src/uxnrnbbs/Makefile.am
-+++ b/src/uxnrnbbs/Makefile.am
-@@ -10,4 +10,4 @@ bin_PROGRAMS = mos2nrn
- 
- mos2nrn_SOURCES = mos2nrn.cpp
- 
--noinst_HEADERS = nrnbbs.h
-+pkginclude_HEADERS = nrnbbs.h
--- 
-2.21.0
-
diff --git a/0005-Disable-python-bits-in-install-exec-hook.patch b/0005-Disable-python-bits-in-install-exec-hook.patch
deleted file mode 100644
index 7d7df5a..0000000
--- a/0005-Disable-python-bits-in-install-exec-hook.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From ab6649fc16e0d4a4c02b0697efd25a309502478f Mon Sep 17 00:00:00 2001
-From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
-Date: Wed, 19 Jun 2019 21:45:15 +0100
-Subject: [PATCH 5/7] Disable python bits in install exec hook
-
----
- Makefile.am | 13 -------------
- 1 file changed, 13 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index 6e7b64d6..9f5c4deb 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -67,19 +67,6 @@ mswin:
- 
- endif
- 
--if BUILD_NRNPYTHON
--install-exec-hook:
--	echo "enter install-exec-hook in nrn/Makefile.am"
--	if test "@ac_pysetup@" != "no" ; then \
--		cd src/nrnpython ; \
--		$(PYTHON) setup.py install @ac_pysetup@ ;\
--	fi
--	if test "@ac_diagnose@" != "no" ; then \
--		sh bin/nrndiagnose.sh ; \
--	fi
--	echo "leave install-exec-hook in nrn/Makefile.am"
--endif
--
- ALPHADIR = hines@neuron.yale.edu:/home/htdocs/ftp/neuron/versions/alpha
- 
- if MAKE_RPMS
--- 
-2.21.0
-
diff --git a/0006-Remove-duplicate-file-installation.patch b/0006-Remove-duplicate-file-installation.patch
deleted file mode 100644
index 9b7389e..0000000
--- a/0006-Remove-duplicate-file-installation.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From 7cd0cc04b21ef57b6e7d83adfe7a13f8cbb39125 Mon Sep 17 00:00:00 2001
-From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
-Date: Sun, 23 Jun 2019 18:31:52 +0100
-Subject: [PATCH 6/7] Remove duplicate file installation
-
----
- src/nrniv/Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/nrniv/Makefile.am b/src/nrniv/Makefile.am
-index 45b48b8d..1c2e40a3 100755
---- a/src/nrniv/Makefile.am
-+++ b/src/nrniv/Makefile.am
-@@ -162,7 +162,7 @@ pkginclude_HEADERS = ndatclas.h nrnclass.h nrnmenu.h nrnoc2iv.h ppshape.h \
- 	multisplitcontrol.h nvector_nrnthread.h \
- 	bbsavestate.h nrnbbcore_write.h nrnsection_mapping.h\
- 	nrnmusic.cpp nrndae.h matrixmap.h \
--	structpool.h nrnhash_alt.h
-+	nrnhash_alt.h
- 
- ## We have to play a trick on automake to get it to install the .o files in
- ## an architecture-dependent subdirectory.  (Apparently automake's authors
--- 
-2.21.0
-
diff --git a/0007-Install-nrnmpiuse-header.patch b/0007-Install-nrnmpiuse-header.patch
deleted file mode 100644
index 7898154..0000000
--- a/0007-Install-nrnmpiuse-header.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From d6254235e7a94a8981071a7fe0504f7c215bf304 Mon Sep 17 00:00:00 2001
-From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
-Date: Sun, 23 Jun 2019 19:33:47 +0100
-Subject: [PATCH 7/7] Install nrnmpiuse header
-
----
- src/oc/Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/oc/Makefile.am b/src/oc/Makefile.am
-index 2e0d3640..de42b72a 100755
---- a/src/oc/Makefile.am
-+++ b/src/oc/Makefile.am
-@@ -64,7 +64,7 @@ pkginclude_HEADERS = hoc.h hoclist.h hocdec.h hocassrt.h nrnisaac.h \
- 	nrnpthread.h hoc_membf.h nrnran123.h scoplib_ansi.h nrnapi.h \
- 	nrnassrt.h code.h equation.h hocmodl.h hocstr.h \
- 	profile.h redef.h parse.h mcran4.h nrnmpi.h nrnrt.h isaac64.h \
--	nrnfilewrap.h nrn_vsscanf.c classreg.h
-+	nrnfilewrap.h nrn_vsscanf.c classreg.h nrnmpiuse.h
- 
- ## files that depend on the existence of parse.h
- ## this allows parallel make -j to work at the beginning when parse.h
--- 
-2.21.0
-
diff --git a/neuron.spec b/neuron.spec
index 058b639..5bbb951 100644
--- a/neuron.spec
+++ b/neuron.spec
@@ -1,8 +1,4 @@
-# This is a serial build of NEURON without Python or other bindings.
-# Both the MPI builds and Python bindings require NEURON to be already
-# installed in the system---they are build as post-installation hooks. So, we
-# first package a serial version of NEURON and then package those separately
-# after using this package as a BR
+# This is a serial build of NEURON
 %global _description %{expand:
 NEURON is a simulation environment for modeling individual neurons and networks
 of neurons. It provides tools for conveniently building, managing, and using
@@ -22,17 +18,20 @@ Please install the %{name}-devel package to compile nmodl files and so on.
 # fails somehow, disabled by default
 %bcond_with metis
 
+# Music support
+%bcond_with music
+
 # IV uses libtiff from 1995 and threfore has not been packaged yet
 %bcond_with iv
 
 Name:       neuron
 Version:    7.7.1
-Release:    6%{?dist}
+Release:    8%{?dist}
 Summary:    A flexible and powerful simulator of neurons and networks
 
 License:    GPLv3+
 URL:        http://www.neuron.yale.edu/neuron/
-Source0:    https://github.com/neuronsimulator/%{tarname}/archive/%{version}/%{name}-%{version}.tar.gz 
+Source0:    https://github.com/neuronsimulator/%{tarname}/archive/%{version}/%{name}-%{version}.tar.gz
 
 Patch0:     0001-Unbundle-Random123.patch
 # libstdc++ bundled is from 1988: seems heavily modified. Headers from there
@@ -42,12 +41,8 @@ Patch0:     0001-Unbundle-Random123.patch
 # version
 # Unbundle readline
 Patch1:     0002-Unbundle-readline.patch
-Patch2:     0003-Install-ivstream-header.patch
-Patch3:     0004-Install-all-headers.patch
-Patch4:     0005-Disable-python-bits-in-install-exec-hook.patch
-Patch5:     0006-Remove-duplicate-file-installation.patch
-Patch6:     0007-Install-nrnmpiuse-header.patch
-
+Patch2:     0003-Remove-duplicate-file-installation.patch
+Patch3:     0004-Build-python-bits-in-the-source-tree.patch
 
 # Random123 does not build on these, so neither can NEURON
 # https://github.com/neuronsimulator/nrn/issues/114
@@ -71,8 +66,6 @@ BuildRequires:  libtool
 BuildRequires:  metis-devel
 %endif
 BuildRequires:  ncurses-devel
-# Required by mk_hocusr.py
-BuildRequires:  python3
 BuildRequires:  readline-devel
 BuildRequires:  Random123-devel
 
@@ -97,9 +90,18 @@ BuildArch:  noarch
 %description doc
 Documentation for %{name}
 
+%package -n python3-%{name}
+Summary:   Python3 interface to %{name}
+Requires:  %{name}%{?_isa} = %{version}-%{release}
+BuildRequires:  python3-devel
+BuildRequires:  python3-setuptools
+BuildRequires:  python3-Cython
+
+%description -n python3-%{name} %_description
+
 
 %prep
-%autosetup -n %{tarname}-%{version} -p1 -S git
+%autosetup -n %{tarname}-%{version} -S git
 
 # Remove executable perms from source files
 find src -type f -executable ! -name "*.sh" | xargs chmod -x
@@ -146,26 +148,56 @@ popd
 %global metis_flags " "
 %endif
 
+# --disable-pytsetup simply prevents the post-exec hook where it wants to run
+# python setup.py. We do that ourselves in our two sections
 %configure %{iv_flags} %{metis_flags} \
 --with-gnu-ld --disable-pysetup \
---disable-rpm-rules --without-paranrn \
---without-nrnpython
+--with-nrnpython=%{__python3} \
+--disable-rpm-rules --without-paranrn
 
 sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool && \
 sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
 
 %make_build
-
+# For cythonisation
+%make_build -C share/lib/python
+
+# MUSIC support
+%if %{with music}
+%make_build -C src/neuronmusic
+pushd src/neuronmusic
+%{py3_build}
+popd
+%endif
 
 %install
 %make_install
-# Installs it even when we're not providing nrnpy
-rm -fv $RPM_BUILD_ROOT/%{_bindir}/*nrnpy* -f
+
+# Music support
+%if %{with music}
+pushd src/neuronmusic
+%{py3_install}
+popd
+%endif
+
+
+# Bits from the post install hook
+# It requires the libraries before to be installed, not just built, so it must
+# be done here. The only alternative is a different package that requires this,
+# but this is simpler
+
+# It can't find these somehow.
+RPM_LD_FLAGS="%{?__global_ldflags} -L$RPM_BUILD_ROOT/%{_libdir}"
+pushd src/nrnpython/
+%{py3_build}
+%{py3_install}
+popd
+
 # Remove installed libtool copy
 rm -fv $RPM_BUILD_ROOT/%{_datadir}/%{tarname}/libtool
 
 # Move to includedir
-mv $RPM_BUILD_ROOT/%{_libdir}/nrnconf.h $RPM_BUILD_ROOT/%{_includedir}/nrnconf.h
+mv $RPM_BUILD_ROOT/%{_libdir}/nrnconf.h $RPM_BUILD_ROOT/%{_includedir}/%{tarname}/nrnconf.h
 
 # Post install clean up
 # Remove stray object files
@@ -174,7 +206,8 @@ mv $RPM_BUILD_ROOT/%{_libdir}/nrnconf.h $RPM_BUILD_ROOT/%{_includedir}/nrnconf.h
 find . $RPM_BUILD_ROOT/%{_libdir}/ -name "*.o" -exec rm -f '{}' \;
 # Remove libtool archives
 find . $RPM_BUILD_ROOT/%{_libdir}/ -name "*.la" -exec rm -f '{}' \;
-
+# Remove duplicate files. These are installed in the correct python locations already
+rm -rf $RPM_BUILD_ROOT/%{_datadir}/%{tarname}/lib/python/%{name}
 
 # Rename oc to hoc to prevent conflicts with origin-client binary oc
 # rhbz: 1696118
@@ -206,6 +239,8 @@ mv $RPM_BUILD_ROOT/%{_bindir}/oc $RPM_BUILD_ROOT/%{_bindir}/hoc
 %{_bindir}/nrnoc
 %{_bindir}/nrnoc_makefile
 %{_bindir}/nrnocmodl
+%{_bindir}/nrnpyenv.sh
+%{_bindir}/set_nrnpyenv.sh
 %{_bindir}/hoc
 %{_bindir}/sortspike
 # Libs
@@ -223,10 +258,14 @@ mv $RPM_BUILD_ROOT/%{_bindir}/oc $RPM_BUILD_ROOT/%{_bindir}/hoc
 %{_libdir}/libnrnmpi.so.0
 %{_libdir}/libnrnoc.so.0.0.0
 %{_libdir}/libnrnoc.so.0
+%{_libdir}/libnrnpython.so.0.0.0
+%{_libdir}/libnrnpython.so.0
 %{_libdir}/liboc.so.0.0.0
 %{_libdir}/liboc.so.0
 %{_libdir}/libocxt.so.0.0.0
 %{_libdir}/libocxt.so.0
+%{_libdir}/librxdmath.so.0.0.0
+%{_libdir}/librxdmath.so.0
 %{_libdir}/libsparse13.so.0.0.0
 %{_libdir}/libsparse13.so.0
 %{_libdir}/libscopmath.so.0
@@ -240,6 +279,15 @@ mv $RPM_BUILD_ROOT/%{_bindir}/oc $RPM_BUILD_ROOT/%{_bindir}/hoc
 %dir %{_datadir}/%{tarname}
 %{_datadir}/%{tarname}/lib
 
+# Python bits
+%files -n python3-%{name}
+# A data file resides here
+%{python3_sitelib}/%{name}
+# The libraries are here
+%{python3_sitearch}/%{name}
+# Egg info
+%{python3_sitearch}/NEURON-7.7-py%{python3_version}.egg-info
+
 %files devel
 %license Copyright
 %doc README.md
@@ -251,24 +299,29 @@ mv $RPM_BUILD_ROOT/%{_bindir}/oc $RPM_BUILD_ROOT/%{_bindir}/hoc
 %{_libdir}/libnrniv.so
 %{_libdir}/libnrnmpi.so
 %{_libdir}/libnrnoc.so
+%{_libdir}/libnrnpython.so
 %{_libdir}/liboc.so
 %{_libdir}/libocxt.so
+%{_libdir}/librxdmath.so
 %{_libdir}/libsparse13.so
 %{_libdir}/libscopmath.so
 %{_libdir}/libivos.so
 # Bundles
 %{_libdir}/libsundials.so
 
-%{_includedir}/nrnconf.h
-%{_includedir}/ivstream.h
-%{_includedir}/ivstrm.h
-
 %files doc
 %license Copyright
 %{_datadir}/%{tarname}/examples
 %{_datadir}/%{tarname}/demo
 
 %changelog
+* Mon Jul 15 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 7.7.1-8
+- Enable Python build also
+
+* Sat Jul 13 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 7.7.1-7
+- Test a fixed python setup
+- https://github.com/neuronsimulator/nrn/issues/238#issuecomment-505191230
+
 * Sun Jun 23 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 7.7.1-6
 - Add another patch