Merge remote-tracking branch 'origin/master'

.github/ISSUE_TEMPLATE/release-patch.md

@@ -22,31 +22,32 @@ Pre-release
 Sanity checks
 ---
 - [ ] After cherrypicks PR is merged, make sure GitHub, Azure and CircleCI builds pass for `release/x.y` branch
-- [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the `release/x.y` branch; see [nrn-build-ci guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow) 
+- [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the `release/x.y` branch; see [nrn-build-ci guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow)
 - [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
 - [ ] Run BBP Simulation Stack & other relevant tests
-- [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 
 
 Releasing
 ---
 - [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release and  will contain the full-src-package and the Windows installer at the end of the release workflow.
-- [ ] Create, test and upload manual artifacts 
+- [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
+- [ ] Create, test and upload manual artifacts
   - [ ] MacOS package installer (manual task, ask Michael)
   - [ ] arm64 wheels (manual task, check with Alex or Pramod)
   - [ ] aarch64 wheels (use existing `release/x.y-aarch64` branch for this, see [guide](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-circleci))
 - [ ] Publish the `x.y.z` wheels on PyPI; see [wheel publishing instructions](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure)
 - [ ] Once wheels are published, activate the `x.y.z` tag on ReadTheDocs
 - [ ] Rename the Windows installer in the GitHub release to match the new version and the supported python versions (i.e. `nrn-8.2.2.w64-mingw-py-37-38-39-310-311-setup.exe`)
-- [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox) 
+- [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox)
 
 
 Post-release
 ---
 - [ ] Deactivate ReadTheDocs build for `release/x.y`
-- [ ] Go to [ReadTheDocs advanced settings](https://readthedocs.org/dashboard/nrn/advanced/) and set `Default version` to `x.y.z` 
+- [ ] Go to [ReadTheDocs advanced settings](https://readthedocs.org/dashboard/nrn/advanced/) and set `Default version` to `x.y.z`
 - [ ] Let people know :rocket:
 - [ ] Cherrypick changelog and installer links to `master`
+- [ ] Update the changelog for the release on GitHub
 
 
 Changelog

.github/ISSUE_TEMPLATE/release.md

@@ -17,10 +17,9 @@ Pre-release
 Sanity checks
 ---
 - [ ] Create `release/x.y` branch and make sure GitHub, Azure and CircleCI builds pass
-- [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the respective Azure build; see [Azure drop guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow) 
+- [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the respective Azure build; see [Azure drop guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow)
 - [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
 - [ ] Run BBP Simulation Stack & other relevant tests
-- [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 
 
 Releasing
@@ -30,6 +29,7 @@ Releasing
 - [ ] Update `docs/index.rst` accordingly with the new `.pkg` and `.exe` links for `PKG installer` and `Windows Installer`
 - [ ] Run the ReadTheDocs build again for `release-x.y`, make sure the build passes and inspect the Changelog page.
 - [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release and  will contain the full-src-package and the Windows installer at the end of the release workflow.
+- [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 - [ ] Create, test and upload manual artifacts
   - [ ] MacOS package installer (manual task, ask Michael)
   - [ ] arm64 wheels (manual task, check with Alex or Pramod)
@@ -44,12 +44,13 @@ Releasing
 Post-release
 ---
 - [ ] To mark the start of a new development cycle, tag `master` as follows:
-  - minor version: `x.(y+1).dev` 
+  - minor version: `x.(y+1).dev`
   - major version: `(x+1).0.dev`
 - [ ] Deactivate ReadTheDocs build for `release/x.y`
-- [ ] Go to [ReadTheDocs advanced settings](https://readthedocs.org/dashboard/nrn/advanced/) and set `Default version` to `x.y.z` 
+- [ ] Go to [ReadTheDocs advanced settings](https://readthedocs.org/dashboard/nrn/advanced/) and set `Default version` to `x.y.z`
 - [ ] Let people know :rocket:
 - [ ] Cherrypick changelog and installer links to `master`
+- [ ] Update the changelog for the release on GitHub
 
 Changelog
 ======

CONTRIBUTING.md

@@ -26,7 +26,7 @@ favor of Python. The hoc code itself is in the nrn repository and also should no
 
 There are several NEURON-related repositories hosted elsewhere which also encourage contributions. Each of these will have its own *Contributing* document.
 1. [NMODL](https://github.com/BlueBrain/nmodl) -- improved method for compiling and porting *.mod* files using *abstract syntax trees*
-1. [CoreNEURON](https://github.com/BlueBrain/CoreNeuron) -- an optimized NEURON for running on high performance computers (HPCs)
+1. [CoreNEURON](https://github.com/neuronsimulator/nrn/tree/master/src/coreneuron) -- an optimized NEURON for running on high performance computers (HPCs)
 1. [NetPyNE](https://github.com/Neurosim-lab/netpyne) -- multiscale modeling tool for developing, simulating and analyzing networks which include complex cells, potentially
 with detailed molecular-modeling.
 1. [NetPyNE-UI](https://github.com/MetaCell/NetPyNE-UI) -- graphical user interface for NetPyNE

build_osx_wheels.sh

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+
+# This script assumes that you have the prerequisites already installed
+# See https://nrn.readthedocs.io/en/latest/install/python_wheels.html#installing-macos-prerequisites
+#
+# If you want the script to check the nrniv output (for version string checking), set the following environment variable
+# Note that this will require manual intervention during script execution
+#
+# export INTERACTIVE_OK=yes
+
+set -x
+
+export BREW_PREFIX=$(brew --prefix)
+export PATH=/opt/homebrew/opt/bison/bin:/opt/homebrew/opt/flex/bin:$PATH
+
+export NRN_RELEASE_UPLOAD=false
+export NRN_NIGHTLY_UPLOAD=false
+export NEURON_NIGHTLY_TAG=""
+
+export SKIP_EMBEDED_PYTHON_TEST=true
+
+if [ -n $1 ]
+then
+    # example: 9.0a
+    export SETUPTOOLS_SCM_PRETEND_VERSION=$1
+fi
+
+set -e
+
+packaging/python/build_wheels.bash osx 3.9 coreneuron &>3.9-output
+packaging/python/build_wheels.bash osx 3.10 coreneuron &>3.10-output
+packaging/python/build_wheels.bash osx 3.11 coreneuron &>3.11-output
+
+if [ -n $INTERACTIVE_OK ]
+then
+    for py in 9 10 11
+    do
+        python3.${py} -m venv venv3.${py}
+        venv3.${py}/bin/pip install wheelhouse/NEURON-${1}-cp3${py}-cp3${py}-macosx_11_0_arm64.whl
+        venv3.${py}/bin/nrniv
+    done
+fi
+
+bash packaging/python/test_wheels.sh python3.9 wheelhouse/NEURON-*-cp39*.whl true &>3.9-test-output
+bash packaging/python/test_wheels.sh python3.10 wheelhouse/NEURON-*-cp310*.whl true &>3.10-test-output
+bash packaging/python/test_wheels.sh python3.11 wheelhouse/NEURON-*-cp311*.whl true &>3.11-test-output

ci/win_install_deps.cmd

@@ -48,6 +48,14 @@ if "%MSYS2_ROOT%"=="" set MSYS2_ROOT=C:\msys64
 if not exist "%MSYS2_ROOT%\usr\bin\bash.exe" (
     choco install -y --no-progress msys2 --params="/InstallDir:%MSYS2_ROOT% /NoUpdate /NoPath" || goto :error
 )
+
+:: With upgrade of Azure CI runner image on 21st of Sept 2023,
+:: choco brings mingw 12.2.0 and it's somehow incompatible with
+:: msys+neuron installation. So for now, just use previously working
+:: version of mingw
+choco uninstall -y mingw
+choco install --allow-downgrade -y mingw --version=11.2.0
+
 set PATH=%MSYS2_ROOT%\usr\bin;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%PATH%
 
 :: update pacman cache (sometimes required when new GH/Azure runner images are deployed)

cmake/ConfigFileSetting.cmake

@@ -18,18 +18,14 @@ nrn_set_string(PACKAGE_VERSION "${PROJECT_VERSION}")
 nrn_set_string(VERSION "${PROJECT_VERSION}")
 nrn_set_string(NRN_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib")
 nrn_set_string(NEURON_DATA_DIR "${CMAKE_INSTALL_PREFIX}/share/nrn")
-nrn_set_string(LT_OBJDIR ".libs/")
 nrn_set_string(DLL_DEFAULT_FNAME "${CMAKE_SYSTEM_PROCESSOR}/.libs/libnrnmech.so")
 
 # indicate nmodl config is used
 add_definitions(-DHAVE_CONFIG_H)
 
 set(YYTEXT_POINTER 1)
 set(TIME_WITH_SYS_TIME 1)
-set(HAVE_NAMESPACES "/**/")
-set(HAVE_STTY 0)
 # below two are universal nowadays
-set(IVOS_FABS "::fabs")
 set(prefix ${CMAKE_INSTALL_PREFIX})
 set(host_cpu ${CMAKE_SYSTEM_PROCESSOR})
 set(exec_prefix ${prefix})
@@ -145,83 +141,44 @@ set(SUNDIALS_USE_GENERIC_MATH 1)
 # =============================================================================
 # Similar to check_include_files but also construct NRN_HEADERS_INCLUDE_LIST
 # =============================================================================
-nrn_check_include_files(alloca.h HAVE_ALLOCA_H)
 nrn_check_include_files(dlfcn.h HAVE_DLFCN_H)
 nrn_check_include_files(execinfo.h HAVE_EXECINFO_H)
-nrn_check_include_files(fcntl.h HAVE_FCNTL_H)
 nrn_check_include_files(fenv.h HAVE_FENV_H)
-nrn_check_include_files(float.h HAVE_FLOAT_H)
-nrn_check_include_files(inttypes.h HAVE_INTTYPES_H)
-nrn_check_include_files(limits.h HAVE_LIMITS_H)
-nrn_check_include_files(locale.h HAVE_LOCALE_H)
 nrn_check_include_files(malloc.h HAVE_MALLOC_H)
-nrn_check_include_files(math.h HAVE_MATH_H)
-nrn_check_include_files(memory.h HAVE_MEMORY_H)
-nrn_check_include_files(sgtty.h HAVE_SGTTY_H)
-nrn_check_include_files(stdarg.h HAVE_STDARG_H)
-nrn_check_include_files(stdint.h HAVE_STDINT_H)
-nrn_check_include_files(stdlib.h HAVE_STDLIB_H)
-nrn_check_include_files(stream.h HAVE_STREAM_H)
 nrn_check_include_files(strings.h HAVE_STRINGS_H)
-nrn_check_include_files(string.h HAVE_STRING_H)
-nrn_check_include_files(stropts.h HAVE_STROPTS_H)
-nrn_check_include_files(sys/conf.h HAVE_SYS_CONF_H)
-nrn_check_include_files(sys/file.h HAVE_SYS_FILE_H)
-nrn_check_include_files(sys/ioctl.h HAVE_SYS_IOCTL_H)
-nrn_check_include_files(sys/stat.h HAVE_SYS_STAT_H)
-nrn_check_include_files(sys/time.h HAVE_SYS_TIME_H)
 nrn_check_include_files(sys/types.h HAVE_SYS_TYPES_H)
-nrn_check_include_files(sys/wait.h HAVE_SYS_WAIT_H)
-nrn_check_include_files(termio.h HAVE_TERMIO_H)
 nrn_check_include_files(unistd.h HAVE_UNISTD_H)
-nrn_check_include_files(varargs.h HAVE_VARARGS_H)
-nrn_check_include_files(sys/timeb.h HAVE_SYS_TIMEB_H)
 
 # =============================================================================
 # Check for standard headers
 # =============================================================================
 check_include_files("dlfcn.h;stdint.h;stddef.h;inttypes.h;stdlib.h;strings.h;string.h;float.h"
                     STDC_HEADERS)
-check_include_file_cxx("_G_config.h" HAVE__G_CONFIG_H)
 
 # =============================================================================
 # Check symbol using check_cxx_symbol_exists but use ${NRN_HEADERS_INCLUDE_LIST}
 # =============================================================================
 # note that this must be called after all *check_include_files because we use
 # NRN_HEADERS_INCLUDE_LIST is second argument (headers) is empty.
-nrn_check_symbol_exists("alloca" "" HAVE_ALLOCA)
-nrn_check_symbol_exists("bcopy" "" HAVE_BCOPY)
-nrn_check_symbol_exists("bzero" "" HAVE_BZERO)
-nrn_check_symbol_exists("doprnt" "" HAVE_DOPRNT)
-nrn_check_symbol_exists("ftime" "" HAVE_FTIME)
-nrn_check_symbol_exists("getcwd" "" HAVE_GETCWD)
-nrn_check_symbol_exists("gethostname" "" HAVE_GETHOSTNAME)
-nrn_check_symbol_exists("gettimeofday" "" HAVE_GETTIMEOFDAY)
-nrn_check_symbol_exists("index" "" HAVE_INDEX)
-nrn_check_symbol_exists("isatty" "" HAVE_ISATTY)
+nrn_check_symbol_exists("bcopy" "strings.h" HAVE_BCOPY)
+nrn_check_symbol_exists("bzero" "strings.h" HAVE_BZERO)
+nrn_check_symbol_exists("gettimeofday" "sys/time.h" HAVE_GETTIMEOFDAY)
+nrn_check_symbol_exists("index" "strings.h" HAVE_INDEX)
+nrn_check_symbol_exists("isatty" "unistd.h" HAVE_ISATTY)
 nrn_check_symbol_exists("iv" "" HAVE_IV)
-nrn_check_symbol_exists("lockf" "" HAVE_LOCKF)
-nrn_check_symbol_exists("mallinfo" "" HAVE_MALLINFO)
-nrn_check_symbol_exists("mallinfo2" "" HAVE_MALLINFO2)
-nrn_check_symbol_exists("mkdir" "" HAVE_MKDIR)
-nrn_check_symbol_exists("mkstemp" "" HAVE_MKSTEMP)
-nrn_check_symbol_exists("namespaces" "" HAVE_NAMESPACES)
-nrn_check_symbol_exists("posix_memalign" "" HAVE_POSIX_MEMALIGN)
-nrn_check_symbol_exists("realpath" "" HAVE_REALPATH)
-nrn_check_symbol_exists("select" "" HAVE_SELECT)
-nrn_check_symbol_exists("setenv" "" HAVE_SETENV)
-nrn_check_symbol_exists("setitimer" "" HAVE_SETITIMER)
+nrn_check_symbol_exists("mallinfo" "malloc.h" HAVE_MALLINFO)
+nrn_check_symbol_exists("mallinfo2" "malloc.h" HAVE_MALLINFO2)
+nrn_check_symbol_exists("mkstemp" "stdlib.h" HAVE_MKSTEMP)
+nrn_check_symbol_exists("posix_memalign" "stdlib.h" HAVE_POSIX_MEMALIGN)
+nrn_check_symbol_exists("realpath" "stdlib.h" HAVE_REALPATH)
+nrn_check_symbol_exists("setenv" "stdlib.h" HAVE_SETENV)
+nrn_check_symbol_exists("setitimer" "sys/time.h" HAVE_SETITIMER)
 nrn_check_symbol_exists("sigaction" "signal.h" HAVE_SIGACTION)
 nrn_check_symbol_exists("sigprocmask" "signal.h" HAVE_SIGPROCMASK)
 nrn_check_symbol_exists("SIGBUS" "signal.h" HAVE_SIGBUS)
-nrn_check_symbol_exists("SIGSEGV" "signal.h" HAVE_SIGSEGV)
-nrn_check_symbol_exists("strdup" "" HAVE_STRDUP)
-nrn_check_symbol_exists("strstr" "" HAVE_STRSTR)
 nrn_check_symbol_exists("stty" "" HAVE_STTY)
-nrn_check_symbol_exists("vprintf" "" HAVE_VPRINTF)
-nrn_check_cxx_symbol_exists("getpw" "sys/types.h;pwd.h" HAVE_GETPW)
-nrn_check_cxx_symbol_exists("fesetround" "" HAVE_FESETROUND)
-nrn_check_cxx_symbol_exists("feenableexcept" "" HAVE_FEENABLEEXCEPT)
+nrn_check_cxx_symbol_exists("fesetround" "fenv.h" HAVE_FESETROUND)
+nrn_check_cxx_symbol_exists("feenableexcept" "fenv.h" HAVE_FEENABLEEXCEPT)
 
 # =============================================================================
 # Check data types
@@ -240,13 +197,7 @@ nrn_check_signal_return_type(RETSIGTYPE)
 # =============================================================================
 # Check direcotry manipulation header
 # =============================================================================
-nrn_check_dir_exists(dirent.h HAVE_DIRENT_H)
-nrn_check_dir_exists(ndir.h HAVE_NDIR_H)
-nrn_check_dir_exists(sys/dir.h HAVE_SYS_DIR_H)
 nrn_check_dir_exists(sys/ndir.h HAVE_SYS_NDIR_H)
-if(HAVE_DIRENT_H)
-  set(HAVE_SYS_DIR_H 0)
-endif()
 
 # =============================================================================
 # Copy cmake specific template files
@@ -266,7 +217,6 @@ nrn_configure_dest_src(nrnconf.h . cmake_nrnconf.h .)
 nrn_configure_dest_src(nmodlconf.h . cmake_nrnconf.h .)
 nrn_configure_file(nrnmpiuse.h src/oc)
 nrn_configure_file(nrnconfigargs.h src/nrnoc)
-nrn_configure_file(bbsconf.h src/parallel)
 nrn_configure_file(nrnneosm.h src/nrncvode)
 nrn_configure_file(sundials_config.h src/sundials)
 nrn_configure_dest_src(nrnunits.lib share/nrn/lib nrnunits.lib share/lib)