Merge branch 'rxd_mcr_mult_fix' of ssh://github.com/neuronsimulator/nrn into rxd_mcr_mult_fix

Author: adam

CMakeLists.txt

@@ -19,7 +19,7 @@ project(
   NEURON
   VERSION 9.0.1
   LANGUAGES C CXX
-  HOMEPAGE_URL "https://nrn.readthedocs.io/")
+  HOMEPAGE_URL "https://www.neuronsimulator.org/")
 
 # =============================================================================
 # CMake common project settings

README.md

@@ -1,7 +1,7 @@
 [![Build Status](https://dev.azure.com/neuronsimulator/nrn/_apis/build/status/neuronsimulator.nrn?branchName=master)](https://dev.azure.com/neuronsimulator/nrn/_build/latest?definitionId=1&branchName=master) [![Actions Status](https://github.com/neuronsimulator/nrn/actions/workflows/windows.yml/badge.svg?branch=master)](https://github.com/neuronsimulator/nrn/actions) [![Actions Status](https://github.com/neuronsimulator/nrn/workflows/NEURON%20CI/badge.svg)](https://github.com/neuronsimulator/nrn/actions) [![codecov](https://codecov.io/gh/neuronsimulator/nrn/branch/master/graph/badge.svg?token=T7PIDw6LrC)](https://codecov.io/gh/neuronsimulator/nrn) [![Documentation Status](https://readthedocs.org/projects/nrn/badge/?version=latest)](http://nrn.readthedocs.io/?badge=latest)
 
 # NEURON
-NEURON is a simulator for models of neurons and networks of neuron. See [nrn.readthedocs.io](https://nrn.readthedocs.io) for documentation, tutorials, and announcements of courses and conferences. Installers are available on [GitHub Releases](https://github.com/neuronsimulator/nrn/releases) and the source code on [GitHub](https://github.com/neuronsimulator/nrn).
+NEURON is a simulator for models of neurons and networks of neuron. See [https://www.neuronsimulator.org](https://www.neuronsimulator.org) for documentation, tutorials, and announcements of courses and conferences. Installers are available on [GitHub Releases](https://github.com/neuronsimulator/nrn/releases) and the source code on [GitHub](https://github.com/neuronsimulator/nrn).
 Ask questions on our [Discussion Forum](https://github.com/neuronsimulator/nrn/discussions).
 
 ## Installing NEURON
@@ -26,7 +26,7 @@ It is possible to install the Linux Python wheels on Windows via the Windows Sub
 
 ## Documentation
 
-* See [https://nrn.readthedocs.io/en/latest/](https://nrn.readthedocs.io/en/latest/) for latest, nightly snapshot
+* See [https://www.neuronsimulator.org/en/latest/](https://www.neuronsimulator.org/en/latest/) for latest, nightly snapshot
 * See [docs/README.md](docs/README.md) for information on documentation (local build, Read the Docs setup)
 
 ## Changelog

bin/nrnivmodl.in

@@ -287,7 +287,7 @@ make -j 4 -f "${bindir}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS
      echo "Successfully created $MODSUBDIR/special"
  else
      printf "\nNOTE: If you are encountering MOD file compilation errors only with NEURON version 9.0 or later\n"
-     printf "refer to the C++ migration guide at https://nrn.readthedocs.io/en/9.0.0/guide/porting_mechanisms_to_cpp.html\n\n"
+     printf "refer to the C++ migration guide at https://www.neuronsimulator.org/en/9.0.0/guide/porting_mechanisms_to_cpp.html\n\n"
  fi
 
 exit $MAKE_STATUS

ci/win_download_deps.cmd

@@ -15,7 +15,7 @@ pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile msmpisdk.msi https
 
 :: nsis + plugin
 curl -LO --retry 4 http://prdownloads.sourceforge.net/nsis/nsis-3.05-setup.exe || goto :error
-pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile EnVar_pugin.zip https://nsis.sourceforge.io/mediawiki/images/7/7f/EnVar_plugin.zip || goto :error
+pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile EnVar_plugin.zip https://github.com/GsNSIS/EnVar/releases/download/v0.3.1/EnVar-Plugin.zip || goto :error
 
 :: if all goes well, go to end
 goto :EOF

ci/win_install_deps.cmd

@@ -30,7 +30,7 @@ C:\Python314\python.exe -m pip install "setuptools<=80.8.0" || goto :error
 
 :: install nsis
 nsis-3.05-setup.exe /S || goto :error
-pwsh -command Expand-Archive EnVar_pugin.zip -DestinationPath "${env:ProgramFiles(x86)}\NSIS" || goto :error
+pwsh -command Expand-Archive EnVar_plugin.zip -DestinationPath "${env:ProgramFiles(x86)}\NSIS" || goto :error
 
 :: install mpi
 msmpisetup.exe -unattend -installroot C:\msmpi || goto :error

codemeta.json

@@ -34,7 +34,7 @@
         "C++",
         "Python 3"
     ],
-    "relatedLink": "https://nrn.readthedocs.io/",
+    "relatedLink": "https://www.neuronsimulator.org/",
     "schema:releaseNotes": "This release fixes several bugs and adds support for Python 3.14.\n\n### What's New\n- Add Python 3.14 support (#3635)\n- Remove doxygen from search results on readthedocs (#3664)\n- Add example with compilation for C API (#3658)\n\n### Bug Fixes\n- Use `[:blank:]` character class for SWC parser (#3651)\n- Fix HOC File.dir() on Windows (#3653)\n- NET_RECEIVE INITIAL not vectorized translation needs set_globals_from_prop (#3640)\n\n### Improvements /  Other Changes\n- Make `NRN_INSTALL_PYTHON_PREFIX` configurable (#3654)\n- Improve error message when Python lib is not found (#3650)\n- Use `command -v` instead of `which` in nrnpyenv.sh (#3516)\n- Better errors for `report.conf` (#3641)\n- Bump min required CMake version to 3.19\n",
     "softwareRequirements": [
         "Bison",

contributing_to_documentation.md

@@ -56,7 +56,7 @@ If your notebook downloads external data or depends on MOD files, include all re
 
 ## Contributing Videos
 
-The [videos section of the NEURON documentation](https://nrn.readthedocs.io/en/latest/videos/) is primarily a curated list of recorded courses and lectures, many hosted externally on YouTube or similar platforms. Contributing a video is therefore a two-step process: creating the video itself, and then adding a reference to it in the documentation.
+The [videos section of the NEURON documentation](https://www.neuronsimulator.org/en/latest/videos/) is primarily a curated list of recorded courses and lectures, many hosted externally on YouTube or similar platforms. Contributing a video is therefore a two-step process: creating the video itself, and then adding a reference to it in the documentation.
 
 For the reference page, videos are documented in `.rst` files under `docs/videos/`. Each entry typically includes the video title, a brief description of what is covered, the year or course it belongs to, and an embedded link or thumbnail. Follow the existing format in those files when adding a new entry.
 

docs/README.md

@@ -4,7 +4,7 @@
 
 Latest NEURON documentation is available on:
 
-* ReadTheDocs @ [https://nrn.readthedocs.io/en/latest/](https://nrn.readthedocs.io/en/latest/).
+* ReadTheDocs @ [https://www.neuronsimulator.org](https://www.neuronsimulator.org).
 
 Contents:
 

docs/capi.rst

@@ -526,18 +526,45 @@ Segments
     :param x: Normalized position along Section (0.0 to 1.0).
     :returns: Diameter in microns at the specified position.
 
+    When the section geometry is defined by 3d points (:func:`pt3dadd`), the
+    segment diameter is derived from those points. This getter triggers that
+    recompute if it is pending, so the value is correct even before an explicit
+    geometry pass such as :func:`define_shape` or :func:`finitialize`.
+
     **C Usage:**
-    
+
     .. code-block:: c
-    
+
         double diameter = nrn_segment_diam_get(soma, 0.5);  // Get diameter at middle
 
     **Python Equivalent:**
-    
+
     .. code-block:: python
-    
+
         diameter = soma(0.5).diam  # Get diameter at middle of Section
 
+.. c:function:: int nrn_segment_node_index(Section* sec, double x)
+
+    Get the index of the node for the segment at normalized position x along
+    the Section, in NEURON's internal node array. Node indices become canonical
+    once the tree has been set up (for example after :func:`finitialize`).
+
+    :param sec: Pointer to the Section.
+    :param x: Normalized position along Section (0.0 to 1.0).
+    :returns: The node index, or -1 if sec is NULL or has been deleted.
+
+    **C Usage:**
+
+    .. code-block:: c
+
+        int idx = nrn_segment_node_index(soma, 0.5);  // node index at middle
+
+    **Python Equivalent:**
+
+    .. code-block:: python
+
+        idx = soma(0.5).node_index()  # node index at middle of Section
+
 .. c:function:: void nrn_rangevar_push(Symbol* sym, Section* sec, double x)
 
     Push a range variable for a Section at position x onto the NEURON stack.
@@ -709,10 +736,14 @@ Functions, objects, and the stack
 
 .. c:function:: double* nrn_symbol_dataptr(const Symbol* sym)
 
-    Get a pointer to the data for a symbol (for variables).
+    Get a pointer to the storage for a scalar variable, for direct reading and
+    writing. This covers built-in ``USERDOUBLE`` scalars such as ``t`` (time) as
+    well as runtime scalars created in HOC (e.g. ``x = 42``), whose value lives
+    in the top-level object-data array rather than at ``sym->u.pval``.
 
     :param sym: Pointer to the symbol.
-    :returns: Pointer to the symbol's data, or NULL if not applicable.
+    :returns: Pointer to the symbol's data, or the raw ``sym->u.pval`` for
+              symbols that are not top-level runtime scalars.
 
     **Usage Pattern:**
 

docs/cmake_doc/options.rst

@@ -308,11 +308,10 @@ NRN_ENABLE_PYTHON:BOOL=ON
 
 NRN_INSTALL_PYTHON_PREFIX:STRING="lib/python/neuron/"
 -----------------------------------------------------
-  Path where NEURON Python components will be installed, relative to CMAKE_INSTALL_PREFIX. Must end with a directory named "neuron"
-
-  Environment variable PYTHONPATH must contain the real path to NRN_INSTALL_PYTHON_PREFIX in order for python to find neuron.
-
-  This path must end with a directory named "neuron"
+  Path where NEURON Python components will be installed, relative to
+  ``CMAKE_INSTALL_PREFIX``. Must end with a directory named "neuron".
+  Environment variable ``PYTHONPATH`` must contain the real path to
+  ``NRN_INSTALL_PYTHON_PREFIX`` in order for python to find neuron.
 
   For venv's, configure cmake with: