build fixes in master that should get cherry-picked into release/7.8.1

[nrnhines]

Need to cherry-pick from the following items from git rebase -i release/7.8.1.
(the commits that will NOT be included for release will be ticked off)

• e341499 Observer list iteration bug when iteration removed items. (Observer list iteration bug when iteration removed items. #666)
• 3ea6c3d Skip stub libraries from OSX (Skip stub libraries from OSX #670)
• 9641b2e re-introduce toplinks (cf html2.py) (re-introduce toplinks (cf html2.py) [closes #668] #674)
• 7c567ba Adamjhn gridswarning (Adamjhn gridswarning #675)
• bf3a292 Pointer can be dereferenced only if non-NULL. (Pointer can be dereferenced only if non-NULL. #676)
• 78fd391 Fix warn (Fix warn #678)
• 1f8b2f8 separate nbconvert target (separate nbconvert target #679)
• ddf47c7 Avoid system directories into rpath (Avoid system directories into rpath via nrnivmodl #681)
• 9782fcc NRN_ENABLE_SHARED=OFF builds static library (for GPU support) (NRN_ENABLE_SHARED=OFF builds static library (for GPU support) #682)
• 9a08d10 Look for corenrn_embedded_run instead of corenrn_version for CoreNEURON (Look for corenrn_embedded_run instead of corenrn_version for CoreNEURON #683)
• 71eda9d Build error fix for Random123 on IBM Power9 system with PGI compiler (Build error fix for Random123 on IBM Power9 system with PGI compiler #684)
• a77db57 ion style error (ion style error #685)
• f698710 Bug fix for library name extensions (Bug fix for library name extensions #687)
• f2d9679 CMake - consolidate docs building target (CMake - consolidate docs building target #691)
• 0681c0f Cmakeuserdoc (Cmakeuserdoc #690)
• cbabda2 callback for returning spikes from CORENEURON (callback for returning spikes from CORENEURON #692)
• f067494 catch if too many arguments to SectionList.append (catch if too many arguments to SectionList.append #694)
• 6d2aa05 Update CoreNEURON submodule to latest master (Update CoreNEURON submodule to latest master #696)
• 677b1da bugfix: Stop rxd keeping section alive and fix CVode/nseg change problem. ( bugfix: Stop rxd keeping section alive and fix CVode/nseg change problem. #693)
• 7ab735f Sped up rxd tests by reducing model sizes and moved the test data into a submodule. (Sped up rxd tests by reducing model sizes and moved the test data into a submodule. #701)
• da76365 temporary workaround since pep425tags no longer available from wheel 0.35 (temporary workaround since pep425tags no longer available from wheel 0.35 #703)
• b804df5 referencing and unrefrerencing NEURON objects
• b72c244 clarification about ref counts for nrnpy_po2ho
• dbeb52b added info on how to get a Vect* argument
• d1ba505 Test of FOR_NETCONS (Test of FOR_NETCONS #695)
• 1759767 Avoid using xcrun on non-osx platforms (Avoid using xcrun on non-osx platforms #710)
• 6f4ae45 CoreNEURON GPU build integration improvements (CoreNEURON GPU build integration improvements #707)
• 1a7d97c Avoid rare duplication of RangeVarPlot points due to recursion. (Avoid rare duplication of RangeVarPlot points due to recursion. #720)
• 19cb091 RangeVarPlot enhancements (RangeVarPlot enhancements #706)
• 03400bf Callback from CoreNEURON to help transfer data to NEURON. (Callback from CoreNEURON to help transfer data to NEURON. #717)
• db70778 nrnbbcore_write code re-organisation (nrnbbcore_write code re-organisation  #722)
• 5a765ce Allow signal handlers to print backtrace
• b3f0a08 Added conftest variable and fixed minor issues
• 07ad326 Added C++ demangling
• 0b11dc7 Add backward-cpp for better backtraces
• 40b3c35 Removed homegrown code
• 623bdc4 Added back simple backtraces
• e6ea6cf Added backtrace line parsing for linux
• 601ef33 Fixes in build system
• 72ace5d Link cmake_doc/options.rst (Link cmake_doc/options.rst #738)
• f560830 Set Python_ADDITIONAL_VERSIONS cmake property (Set Python_ADDITIONAL_VERSIONS cmake property #737)
• a42fae5 _semi_compile raises Exception if bad state (_semi_compile raises Exception if bad state #715)
• 1101017 bugfix: Distribute mulitcompartment reaction fluxes in MPI. (bugfix: Distribute mulitcompartment reaction fluxes in MPI. #728)
• b212594 If a netcon_srcgid is negative, need to determine the thread. (If a netcon_srcgid is negative, need to determine the thread. #735)
• e1194ee sysconfig provenance requires major.minor in libpython name. (sysconfig provenance requires major.minor in libpython name. #744)
• 42ff857 ${IV_DIR}/lib/cmake is place to find CMake configuration files. (${IV_DIR}/lib/cmake is place to find CMake configuration files. #721)
• b3b29cc Fix some ctest errors. (Fix some ctest errors. #752)
• 5feec90 Fix error in rxd test when using python2. (Fix error in rxd test when using python2. #757)
• 04fd8b4 Some usage doc info about NRN_ENABLE_TESTS. (Some usage doc info about NRN_ENABLE_TESTS. #755)
• ea6e034 Update CoreNEURON submodule to latest release v0.22 (Update CoreNEURON submodule to latest release v0.22 #766)
• acdd898 Some PROP_PY_INDEX dependent fragments need #if USE_PYTHON wrapper. (Some PROP_PY_INDEX dependent fragments need #if USE_PYTHON wrapper. #772)
• fc74b85 Avoid "NEURON model internal structures are out of date" error while running NEURON (Avoid "NEURON model internal structures are out of date" error while running NEURON #774)
• 8570e8e Update SCMGuide.md (Update SCMGuide.md: fix numbered lists #777)
• 48287ca autotools: -with-paranrn: CXX loses the -std=c++11 flag. (autotools: -with-paranrn: CXX loses the -std=c++11 flag. #778)
• 6aff783 Dynam units (Dynam units #746)
• 9f15e51 Print CMake version as part of CI build (Print CMake version as part of CI build #779)
• 86ce417 One of the neurondemo examples unnecessarily assigned to FARADAY. (One of the neurondemo examples unnecessarily assigned to FARADAY. #783)
• ce417f7 Remove scipy from rxd tests. (Remove scipy from rxd tests. #764)
• c17998b Fix loop to conform to C standard
• 14f0a76 Fixes and improvements thanks to @pramodk's comments
• 65393ef Binprog wheel (Binprog wheel #765)
• 609e1d9 Simpler fixup of neurondemo libnrnmech.so for relative libnrniv.dylib (Simpler fixup of neurondemo libnrnmech.so for relative libnrniv.dylib #787)
• 4963240 Support for building NEURON on windows under Azure CI with installer (Support for building NEURON on windows under Azure CI with installer #572)
• d74533f Axon attach (Axon attach #781)
• af2ad86 Nrnunit assign (Nrnunit assign #790)
• 69241d8 h.cas() calling chk_access cannot handle the possible hoc_execerror. (h.cas() calling chk_access cannot handle the possible hoc_execerror. #773)
• d4116fa Try to unref hoc object if constructor fails after Object* created. (Try to unref hoc object if constructor fails after Object* created. #762)
• 7254be1 find_library in FindPythonLibsNew.cmake needs prior unset of PYTHON_LIBRARY (find_library in FindPythonLibsNew.cmake needs prior unset of PYTHON_L… #758)
• ef5bc82 modlunit units.c space not allocated. (modlunit units.c space not allocated. #792)
• 6663076 don't attempt to parse stacktrace on _WIN32
• 26651ec Return type from -4 to 1
• 45483fb Added a few useful comments
• a640445 MPI_Abort if hoc_execerror from python and nhost > 1. (MPI_Abort if hoc_execerror from python and nhost > 1. #796)
• eff5ee2 also run rxd tests for osx autotools job (also run rxd tests for osx autotools job #795)
• ebe8605 contributing points to neuron development topics (contributing points to neuron development topics #804)
• f6105de Use early numpy wheel for each neuron wheel. (Use early numpy wheel for each neuron wheel. #801)
• 8a0c5e3 Wheel distribution compiles cython files with -O2 despite long compil… (Wheel distribution compiles cython files with -O2 despite long compil… #798)
• cc84503 CMake option to toggle new/legacy for dynamic units (CMake option to toggle new/legacy for dynamic units #805)
• 94147e5 Check consistency of units selection for NEURON and CoreNEURON. (Check consistency of units selection for NEURON and CoreNEURON. #793)
• cccff14 nhost_world() does not have to be a multiple of the subworld size. (nhost_world() does not have to be a multiple of the subworld size. #803)
• 140f046 Test modlunit (Test modlunit #794)
• 36983d1 Publish windows installer as artifact on Azure CI (Publish windows installer as artifact on Azure CI #808)
• 2387a2b travis quickly return for Azure CI changes (travis quickly return for Azure CI changes #809)
• 9552a68 Windows does not have dlfcn.h (Windows does not have dlfcn.h #811)
• 6e84138 Update coreneuron to the last version (Update coreneuron to the last version #818)
• 8f2aaaa nrniv -python windows gui event loop not started (nrniv -python windows gui event loop not started #817)
• 3cbcaf0 fix azure test installer task + make it more robust (fix azure test installer task + make it more robust #821)
• 22a6f40 Remove hasattr check for _voltage_dependent in rates and reactions to avoid unnecessary recursion.$
• a03d70e Windows Installer Test via Github Actions (Windows Installer Test via Github Actions #822)
• 20c2d56 Use early version of cmake for CI. (Use early version of cmake for CI. #812)
• e68a690 Windows anaconda3 2020 without path. Figure out the python path. (Windows anaconda3 2020 without path. Figure out the python path. #824)
• 68ae199 macos wheel for Python3.9 (macos wheel for Python3.9 #834)
• 0491235 Add timeout for Windows Github Actions CI (Add timeout for Windows Github Actions CI #835)
• 961dd9b fix issue Undefined hoc procedure causes segfault from python. #836 (fix issue #836 #837)
• 8302621 Enable Python 3.9 manylinux1 wheel (Enable Python 3.9 manylinux1 wheel #838)
• d87f34b For mac pgk -DNRN_ENABLE_INTERNAL_READLINE=ON (For mac pgk -DNRN_ENABLE_INTERNAL_READLINE=ON #841)
• c072040 Fix compilation issue with latest PGI compiler (Fix compilation issue with latest PGI compiler #832)
• 879baf2 Fix/newobj error (Fix/newobj error #833)
• da2acc5 Github Actions - NEURON CI (Github Actions - NEURON CI #848)
• 12f644b Documentation deployment with GitHub Actions (documentation deployment #849)
• e6334e5 nrnversion fails when not in git (nrnversion fails when not in git #831)
• 894edb6 Build modlunit and nocmodl with debug flags. (Build modlunit and nocmodl with debug flags. #852)
• 210611a Windows CIs: use curl to get NSIS 3.05 (Windows CIs: use curl to get NSIS 3.05 #856)
• a8e0a9c nsis curl cmd: set retries + remove resume option (nsis curl cmd: set retries + remove resume option #857)
• 564ae67 Dblunits (Dblunits #853)
• 41ec0b2 nrnivmodl under cmake no longer uses symbolic links. (nrnivmodl under cmake no longer uses symbolic links. #850)

[pramodk]

@nrnhines : this looks like a bit long list. I wonder if we should reduce it to minimal as we are planning 8.0 alpha soon anyway.
e.g. going from 7.8.1 to 7.8.2, I would't include Dblunits (#853) which changes the result.

cc: @alexsavulescu

[alexsavulescu]

A fair amount of commits are non-relevant release wise. #853 would normally imply 7.9 or even 8.0, so I agree with @pramodk it should be left out. If 8.0.alpha is very soon, we can target a few specific changesets for 7.8.2.

[nrnhines]

That is the entire list to select from. The selection would hopefully be a dozen or so. The difficulty i had today was that many of the items could not be cherry picked without manual attention. I think I'll try to (automatically) reduce the list to just those which cherry-pick successfully and then figure out the desired selection from that.

[nrnhines]

The 22 selected for cherry picking are

e341499
3ea6c3d
bf3a292
ddf47c7
71eda9d
a77db57
f698710
da76365
1759767
1a7d97c
f560830
e1194ee
acdd898
ef5bc82
a640445
f6105de
8f2aaaa
e68a690
68ae199
8302621
d87f34b
41ec0b2

[nrnhines]

Manual operations required by the cherry pick are

e341499 skip
3ea6c3d skip
bf3a292 
ddf47c7
71eda9d
a77db57
f698710
da76365 skip
1759767
1a7d97c
f560830 resolve
e1194ee
acdd898
ef5bc82 resolve
a640445 resolve
f6105de resolve
8f2aaaa
e68a690
68ae199 skip
8302621 skip
d87f34b skip
41ec0b2 resolve

[nrnhines]

@adamjhn Just list the extra changes to cherry-pick for rxd here. Thanks. ... I'm seeing

677b1da
a42fae5
1101017
5feec90
22a6f40

the manual operations required were

677b1da resolve
a42fae5
1101017 resolve
5feec90
22a6f40

[nrnhines]

to avoid compile errors, rxd cherry-pick requires 7c567ba so reset and move branch to cherry-master-7.8.1-2 . Compilation was
successful with

7c567ba
677b1da
a42fae5
1101017 resolve
5feec90
22a6f40

also, for successful compilation, modlunit/units.c had to be reverted back to b6e02bc