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Neuron package with cmake build system #644

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pramodk merged 80 commits into from
May 27, 2020
Merged

Neuron package with cmake build system #644

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bf66b3a
Adding mvdtool 2.3.2, py-neurodamus, highfive/mock fix
ferdonline Dec 11, 2019
cff838b
Fixes
ferdonline Dec 12, 2019
f6e5e04
Cmake build system working and passing tests
iomaganaris Dec 11, 2019
e92a52b
[WIP] Neuron+cmake integration to Neurodamus
iomaganaris Dec 11, 2019
7f61ffd
Small fixes in neuron recipe and sim-model fixes for libnrnmech path
iomaganaris Dec 13, 2019
594b604
Added py-cython dependency in neuron
iomaganaris Dec 13, 2019
361d2c5
Made coreneuron variant False as default in neuron package
iomaganaris Dec 13, 2019
4ba499d
Added +debug variant in neuron
iomaganaris Dec 13, 2019
c3f5244
Added patch for reverting free_fast_imem to check the simstack
iomaganaris Dec 16, 2019
59dd1aa
Reverted temporary patch for neuron. Now using as preferred pure pram…
iomaganaris Dec 17, 2019
d75e8bb
Made cmake build false by default to check the autotools build system
iomaganaris Dec 17, 2019
615d079
Fixing filter_compilers
iomaganaris Dec 17, 2019
44599a4
Reverted cmake as default to test changes in filter_compilers with cmake
iomaganaris Dec 17, 2019
7de0aa3
Added dependency to py-test when python and tests are enabled
iomaganaris Dec 19, 2019
b3863fb
Clearing and fixing paths of neuron archdir
iomaganaris Dec 19, 2019
75387b5
Edit neuron and sim-model/neurodamus-core packages with new variables…
iomaganaris Dec 19, 2019
c573af2
Made cmake false by default to check the CI tests
iomaganaris Dec 19, 2019
4141964
Fixed failing asciitoh5 package with neuron_archdir
iomaganaris Dec 20, 2019
b6de35e
Reorganized functions
iomaganaris Jan 7, 2020
a1080eb
Addressed some comments from @matze. Thank you!
iomaganaris Jan 14, 2020
8740919
Fixes in versions
iomaganaris Jan 14, 2020
9e30da3
Fixed CMAKE_BUILD_TYPE when +cmake+debug
iomaganaris Jan 14, 2020
cbc1d54
Removed duplicate debug variant and rephrased debug decription accord…
iomaganaris Jan 15, 2020
37a7c3f
Small changes to filter_compilers to filter files according to the bu…
iomaganaris Jan 15, 2020
154f564
Added version 2018-10 of Neuron to the conflicting versions with cmake
iomaganaris Jan 15, 2020
0e549b2
Refactored cmake_args and cmake_enable_option a bit
iomaganaris Jan 15, 2020
9619a0c
Removed filter_compier_wrappers for files that don't exist from cmake…
iomaganaris Jan 15, 2020
d619ad4
Addressed Pramod's comments
iomaganaris Jan 16, 2020
3d17d5e
Fixed issue with ImportError: No module named site in mac os
iomaganaris Jan 16, 2020
bf0d2b1
Made '+coreneuron' default and set MPICXX_CXX
iomaganaris Jan 20, 2020
782d84d
CMake build fixes
iomaganaris Jan 20, 2020
4d04caf
Added ~cmake in older versions of neuron that exist in deployment
iomaganaris Jan 20, 2020
4d8f48f
Added coreneuron-compatible variant
iomaganaris Jan 20, 2020
b7b9194
Revert "Added coreneuron-compatible variant"
iomaganaris Jan 21, 2020
3e0935a
Install neuron+coreneuron by default and then remove CoreNeuron execu…
iomaganaris Jan 21, 2020
b8017e6
Attempt to fix issue with numpy when installing Neuron in CoreNeuron …
iomaganaris Jan 22, 2020
51bb24a
Bumped testing version to 7.8.2 to avoid reusing old archive in the CI
iomaganaris Jan 22, 2020
0c4ef2a
Set git variable in CoreNeuron spack recipe
iomaganaris Jan 24, 2020
e0d24f3
Refactored deletion of installed coreneuron binaries
iomaganaris Jan 24, 2020
678f5d6
Merge branch 'develop' into pr/neuron-cmake
iomaganaris Mar 23, 2020
994a0ba
Fixed installation after merge with develop in mac
iomaganaris Mar 23, 2020
943b319
Added mod-compatibility flag for patching mod files for coreneuron
iomaganaris Mar 24, 2020
383bfa6
Fix dylib
iomaganaris Mar 25, 2020
7a35e61
Updated neuron versions
iomaganaris Mar 25, 2020
c1691a9
flake8 fixes
iomaganaris Mar 26, 2020
f13628f
Change find to find_libraries when finding libnrnmech
iomaganaris Mar 26, 2020
e9960a0
Fix issue with clang/clang++ compiler and add conflict for neuron+bin…
iomaganaris Mar 27, 2020
3682e30
Updated Neuron version and attempt to fix Travis CI issues
iomaganaris Mar 30, 2020
b43ffce
Change % to format for string formatting
iomaganaris Mar 30, 2020
db55c6b
Fix for finding libnrnmech.so.0.0.0 with neuron~cmake
iomaganaris Mar 30, 2020
5ebc2c2
Merge branch 'develop' into pr/neuron-cmake
iomaganaris Apr 7, 2020
1296438
Update version 7.8.0c to latest master of neuron and fix patches
iomaganaris Apr 7, 2020
a64a97b
Added latest reportinglib tag
iomaganaris Apr 7, 2020
e27de53
Enable dynamic MPI with cmake
iomaganaris Apr 8, 2020
0b2f183
Fixed asciitoh5 package
iomaganaris Apr 14, 2020
8d7cd38
Updated to latest commit
iomaganaris Apr 17, 2020
18d23d3
Fix issue with py-ipykernel test
iomaganaris Apr 17, 2020
7fde90f
Revert "Fix issue with py-ipykernel test"
iomaganaris Apr 22, 2020
7168d97
Merge branch 'develop' into pr/neuron-cmake
iomaganaris Apr 22, 2020
de44676
Merge branch 'develop' into pr/neuron-cmake
iomaganaris May 1, 2020
fe42a3d
Added cmake option for building binary special
iomaganaris May 7, 2020
745fb83
Some more additions
iomaganaris May 7, 2020
142bb6d
Fixed binary option
iomaganaris May 7, 2020
0754d7f
Fix libnrnmech lib name with neuron+cmake+binary
iomaganaris May 8, 2020
95df5bf
Change binary special cmake option
iomaganaris May 8, 2020
5fa2822
Merge branch 'develop' into pr/neuron-cmake
iomaganaris May 13, 2020
8bd606d
Update neuron to latest master
iomaganaris May 13, 2020
27ccdfd
Address review comments
pramodk May 13, 2020
bb56da0
Merge branch 'develop' into pr/neuron-cmake
pramodk May 13, 2020
21b390e
flake8 fixes
pramodk May 13, 2020
abf6516
Fixed filtering of CC/CXX values in nrnmech_makefile
iomaganaris May 15, 2020
d1b11ca
Set CC/CXX env variables to mpicc/cxx in dependent environments of nrn
iomaganaris May 18, 2020
3b961d9
Change 7.8.0c to latest fix with binary special
pramodk May 26, 2020
ff01d5c
Merge branch 'develop' into pr/neuron-cmake
pramodk May 26, 2020
6d5e58a
Changes to env variables and filter file
pramodk May 26, 2020
a51b669
Set PYTHONPATH for run env
iomaganaris May 27, 2020
45a5b1a
Make flake8 happy
iomaganaris May 27, 2020
0e2f82f
Use self.spec.prefix.lib.python for PYTHONPATH
pramodk May 27, 2020
bad4624
Try removing setup_dependent_build_environment
pramodk May 27, 2020
de87f5c
use setup_dependent_run_environment as well for PYTHONPATH
pramodk May 27, 2020
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2 changes: 1 addition & 1 deletion var/spack/repos/builtin/packages/asciitoh5/package.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def install(self, spec, prefix):
include_flag = ' -I%s' % (spec['hdf5'].prefix.include)
which('nrnivmodl')('-incflags', include_flag, '-loadflags',
link_flag, 'lib/mod')
bindir = os.path.basename(spec.neuron_archdir)
bindir = os.path.basename(self.nrnivmodl_outdir)
special = join_path(bindir, 'special')
shutil.copy(special, prefix.bin)

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