Merge branch 'master' into hines/soma-center

.github/workflows/coverage.yml

@@ -58,7 +58,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py "cython<3" 'numpy<2' setuptools
+          python3 -m pip install 'mpi4py<4' "cython<3" 'numpy<2' setuptools
           sudo mkdir -p $MUSIC_INSTALL_DIR
           sudo chown -R $USER $MUSIC_INSTALL_DIR
           curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip

.github/workflows/neuron-ci.yml

@@ -207,7 +207,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py "cython<3" 'numpy<2' setuptools
+          python3 -m pip install 'mpi4py<4' "cython<3" 'numpy<2' setuptools
           sudo mkdir -p $MUSIC_INSTALL_DIR
           sudo chown -R $USER $MUSIC_INSTALL_DIR
           curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip

bin/nrnivmodl.in

@@ -81,8 +81,19 @@ while [ "$1" ] ; do
         UserNMODLFLAGS="$UserNMODLFLAGS $2"
         shift
         shift;;
+    -h|--help)
+        echo "Usage: nrnivmodl [options] [mod files or directories with mod files]"
+        echo "Options:"
+        echo "  -coreneuron                      Compile MOD files for CoreNEURON using nrnivmodl-core."
+        echo "  -incflags    \"include flags\"     Extra include flags and paths when MOD (C++) files are compiled."
+        echo "  -loadflags   \"link flags\"        Extra link flags, paths, and libraries when MOD (C++) files are linked."
+        echo "  -nmodl /path/to/nmodl            Path to the new NMODL transpiler for MOD files (pre-alpha, development use only)."
+        echo "  -nmodlflags  \"CLI flags\"         Additional CLI flags for new NMODL transpiler"
+        echo "  -h, --help                       Show this help message and exit."
+        echo "If no MOD files or directories provided then MOD files from current directory are used."
+        exit 0;;
     -*)
-        echo "$1 unrecognized"
+        echo "$1 unrecognized, check available CLI options with --help"
         exit 1;;
     *)
         break;;

docs/changelog.md

@@ -1,5 +1,21 @@
 # NEURON 8.2
 
+## 8.2.6
+_Release Date_ : 24-07-2024
+
+This release pins numpy to <2 and includes backports for several fixes.
+
+### Bug Fixes
+- Informative error when cannot import hoc module
+- ParallelContext: hoc_ac_ encodes global id of submitted process.
+- Python 3.12 compatibility with Windows installer (#2963)
+- Windows 11 fix for nrniv -python (#2946)
+- Fix for dynamic ECS diffusion characteristics.
+- python38 is back. For testing can use rx3doptlevel=0 bash bldnrnmacpkgcmake.sh
+- Fix cvode.use_fast_imem(1) error with electrode time varying conductance.
+- Apple M1 cmake failure in cloning subrepository. See #2326.
+- Update iv
+
 ## 8.2.4
 _Release Date_ : 08-02-2024
 

docs/index.rst

@@ -98,7 +98,7 @@ Installation
 
          pip3 install neuron
 
-      Alternatively, you can use the `PKG installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.4/nrn-8.2.4-macosx-10.9-universal2-py-38-39-310-311.pkg>`_.
+      Alternatively, you can use the `PKG installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.6/nrn-8.2.6-macosx-10.9-universal2-py-38-39-310-311-312.pkg>`_.
 
       For troubleshooting, see the `detailed installation instructions <install/install_instructions.md>`_.
 
@@ -115,7 +115,7 @@ Installation
 
    .. tab-item:: Windows
 
-      `Download the Windows Installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.4/nrn-8.2.4.w64-mingw-py-37-38-39-310-311-setup.exe>`_.
+      `Download the Windows Installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.6/nrn-8.2.6.w64-mingw-py-38-39-310-311-312-setup.exe>`_.
 
       You can also install the Linux wheel via the Windows Subsystem for Linux (WSL). See `instructions <install/install_instructions.html#windows-subsystem-for-linux-wsl-python-wheel>`_.
 

docs/install/python_wheels.md

@@ -264,24 +264,39 @@ $ git checkout 8.1a -b release/8.1a-aarch64
 # manually updated `.circleci/config.yml`
 $ git diff
 
-@@ -15,6 +15,10 @@ jobs:
+@@ -14,6 +14,11 @@ jobs:
+
      machine:
        image: ubuntu-2004:202101-01
 +    environment:
-+      SETUPTOOLS_SCM_PRETEND_VERSION: 8.1a
++      SETUPTOOLS_SCM_PRETEND_VERSION: 8.2.6
 +      NEURON_NIGHTLY_TAG: ""
 +      NRN_NIGHTLY_UPLOAD: false
 +      NRN_RELEASE_UPLOAD: false
 
-@@ -89,7 +95,7 @@ workflows:
-       - manylinux2014-aarch64:
+     resource_class: arm.medium
+
+@@ -54,6 +59,7 @@ jobs:
+               39) pyenv_py_ver="3.9.1" ;;
+               310) pyenv_py_ver="3.10.1" ;;
+               311) pyenv_py_ver="3.11.0" ;;
++              312) pyenv_py_ver="3.12.2" ;;
+               *) echo "Error: pyenv python version not specified!" && exit 1;;
+             esac
+
+@@ -95,7 +101,7 @@ workflows:
+                 - /circleci\/.*/
            matrix:
              parameters:
 -              NRN_PYTHON_VERSION: ["311"]
-+              NRN_PYTHON_VERSION: ["38", "39", "310", "311"]
++              NRN_PYTHON_VERSION: ["38", "39", "310", "311", "312"]
+               NRN_NIGHTLY_UPLOAD: ["false"]
+
+   nightly:
 ```
 
 The reason we are setting `SETUPTOOLS_SCM_PRETEND_VERSION` to a desired version `8.1a` because `setup.py` uses `git describe` and it will give different version name as we are now on a new branch!
+`NEURON_WHEEL_VERSION` will also stop your wheels from getting extra numbers on the version
 
 
 ## Nightly wheels

nrn_requirements.txt

@@ -1,6 +1,6 @@
 wheel
-setuptools
 setuptools_scm
+setuptools<=70.3.0
 scikit-build
 matplotlib
 # bokeh 3 seems to break docs notebooks
@@ -10,6 +10,6 @@ cython<3
 packaging
 pytest<=8.1.1 # potential bug from 8.2.0 due to parallelism?
 pytest-cov
-mpi4py
+mpi4py<4 # MUSIC not compatible with MPI 4
 numpy<2
 find_libpython

packaging/python/build_requirements.txt

@@ -1,8 +1,8 @@
 cython<3
 packaging
 numpy==1.17.5;python_version=='3.8'
-numpy==1.19.3;python_version=='3.9' and platform_machine=='x86_64'
+numpy==1.19.3;python_version=='3.9' and platform_machine!='arm64'
 numpy==1.21.3;python_version=='3.9' and platform_machine=='arm64'
-numpy==1.21.3;python_version=='3.10'
+numpy==1.21.4;python_version=='3.10'
 numpy==1.23.5;python_version=='3.11'
 numpy==1.26.0;python_version=='3.12'

setup.py

@@ -513,7 +513,7 @@ def setup_package():
             "numpy>=1.9.3,<2",
             "packaging",
             "find_libpython",
-            "setuptools",
+            "setuptools<=70.3.0",
         ]
         + (
             [

src/mswin/bin/nrnivmodl.bat

@@ -3,10 +3,23 @@ setlocal
 set nrnhome=/cygdrive/%~dp0%/..
 set "nrnhome=%nrnhome:\=/%"
 set "nrnhome=%nrnhome::=%"
+if /I not "%~1" == "-h" (
+    if /I not "%~1" == "--help" (
+        goto :afterhelp
+    )
+)
+
+echo Usage: nrnivmodl [options] [mod files or directories with mod files]
+echo Options:
+echo   -h, --help                       Show this help message and exit.
+echo If no MOD files or directories provided then MOD files from current directory are used.
+goto :done
+:afterhelp
 if not "%~1"=="" (
     pushd %~1
     %~dp0/../mingw/usr/bin/sh %~dp0/../lib/mknrndll.sh %nrnhome% "--OUTPUTDIR=%CD%"
     popd
 ) else (
     %~dp0/../mingw/usr/bin/sh %~dp0/../lib/mknrndll.sh %nrnhome% --OUTPUTDIR=.
 )
+:done

src/nmodl/parse1.ypp

@@ -172,14 +172,26 @@ model: MODEL line
 line:	{$$ = inputline();}
 	;
 define1: DEFINE1 NAME INTEGER
-		/* all subsequent occurences of NAME will be replaced
-			by integer during parseing.  See 'integer:' */
-	{ Symbol *sp = SYM($2);
-	 if (sp->subtype)
-		diag(sp->name, " used before DEFINEed");
-	 sp->u.str = STR($3);
-	 sp->type = DEFINEDVAR;
-	 deltokens($1, $3);}
+	/* all subsequent occurences of NAME will be replaced
+	   by integer during parseing.  See 'integer:' */
+	{
+	    Symbol *sp = SYM($2);
+	    if (sp->subtype)
+	        diag(sp->name, " used before DEFINEed");
+	    sp->u.str = STR($3);
+	    sp->type = DEFINEDVAR;
+	    deltokens($1, $3);
+	}
+	| DEFINE1 NAME '-' INTEGER
+	{
+	   Symbol *sp = SYM($2);
+	   if (sp->subtype)
+	       diag(sp->name, " used before DEFINEed");
+	   Sprintf(buf, "-%s", STR($4));
+	   sp->u.str = stralloc(buf, nullptr);
+	   sp->type = DEFINEDVAR;
+	   deltokens($1, $4);
+    }
 	| DEFINE1 error {myerr("syntax: DEFINE name integer");}
 	;
 Name:	NAME

src/nrnoc/eion.cpp

@@ -392,7 +392,13 @@ double nrn_nernst_coef(int type) {
 }
 
 /*
-It is generally an error for two models to WRITE the same concentration
+It is generally an error for two models to WRITE the same concentration.
+
+This functions checks that there's no write conflict; and warns if it detects
+one. It also sets respective write flag in the style of the ion.
+
+The argument `i` specifies which concentration is being written to. It's 0 for
+exterior; and 1 for interior.
 */
 void nrn_check_conc_write(Prop* p_ok, Prop* pion, int i) {
     static long *chk_conc_, *ion_bit_, size_;
@@ -546,13 +552,13 @@ void nrn_promote(Prop* p, int conc, int rev) {
 }
 
 /*the bitmap is
-03	concentration unused, nrnocCONST, DEP, STATE
-04	initialize concentrations
-030	reversal potential unused, nrnocCONST, DEP, STATE
-040	initialize reversal potential
-0100	calc reversal during fadvance
-0200	ci being written by a model
-0400	co being written by a model
+  03  concentration unused, nrnocCONST, DEP, STATE
+  04  initialize concentrations
+ 030  reversal potential unused, nrnocCONST, DEP, STATE
+ 040  initialize reversal potential
+0100  calc reversal during fadvance
+0200  ci being written by a model
+0400  co being written by a model
 */
 
 /* Must be called prior to any channels which update the currents */