release/8.2 can use Python 3.13

.github/workflows/coverage.yml

@@ -20,8 +20,8 @@ on:
 #      - 'docs/**'
 
 env:
-  PY_MIN_VERSION: '3.7'
-  PY_MAX_VERSION: '3.11'
+  PY_MIN_VERSION: '3.9'
+  PY_MAX_VERSION: '3.13'
 
 jobs:
   coverage:

.readthedocs.yml

@@ -1,9 +1,30 @@
 version: 2
 
+sphinx:
+  configuration: docs/conf.py
+
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "mambaforge-22.9"
+    python: "3.12"
+  apt_packages:
+    - build-essential
+    - libx11-dev
+    - libxcomposite-dev
+    - libmpich-dev
+    - ffmpeg
+    - doxygen
+    - pandoc
+    - cmake
+    - bison
+    - flex
+    - libfl-dev
+    - libreadline-dev
+
+submodules:
+  recursive: true
 
-conda:
-  environment: docs/conda_environment.yml
+python:
+  install:
+    - requirements: nrn_requirements.txt
+    - requirements: docs/docs_requirements.txt

docs/conf.py

@@ -10,9 +10,11 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+import glob
 import os
 import sys
 import subprocess
+from pathlib import Path
 
 # Make translators & domains available for include
 sys.path.insert(0, os.path.abspath("./translators"))
@@ -40,6 +42,7 @@
     "sphinx.ext.mathjax",
     "nbsphinx",
     "sphinx_design",
+    "sphinx_inline_tabs",
 ]
 
 source_suffix = {
@@ -112,17 +115,32 @@ def setup(app):
 
     rtd_ver = PKGVER.parse(os.environ.get("READTHEDOCS_VERSION"))
 
-    # Install neuron accordingly (nightly for master, otherwise incoming version)
-    # Note that neuron wheel must be published a priori.
-    subprocess.run(
-        "pip install neuron{}".format(
-            "=={}".format(rtd_ver.base_version)
-            if isinstance(rtd_ver, PKGVER.Version)
-            else "-nightly"
-        ),
-        shell=True,
-        check=True,
-    )
+    # see:
+    # https://docs.readthedocs.com/platform/stable/reference/environment-variables.html#envvar-READTHEDOCS_VERSION_TYPE
+    if os.environ.get("READTHEDOCS_VERSION_TYPE") == "external":
+        # Build and install NEURON from source
+        subprocess.run(
+            "cd .. && python setup.py build_ext bdist_wheel",
+            shell=True,
+            check=True,
+        )
+        subprocess.run(
+            f"pip install {glob.glob('../dist/*.whl')[0]}",
+            shell=True,
+            check=True,
+        )
+    else:
+        # Install neuron accordingly (nightly for master, otherwise incoming version)
+        # Note that neuron wheel must be published a priori.
+        subprocess.run(
+            "pip install neuron{}".format(
+                f"=={rtd_ver.base_version}"
+                if isinstance(rtd_ver, PKGVER.Version)
+                else "-nightly"
+            ),
+            shell=True,
+            check=True,
+        )
 
     # Execute & convert notebooks + doxygen
     subprocess.run("cd .. && python setup.py docs", check=True, shell=True)

docs/docs_requirements.txt

@@ -1,18 +1,20 @@
 sphinx
+# do not check import of next line
 sphinx_rtd_theme
 jupyter
 nbconvert
 recommonmark
 matplotlib
-# bokeh 3 seems to break docs notebooks
-bokeh<3
+bokeh>=3
 # do not check import of next line
 ipython
 plotnine
-numpy<2
+numpy>=2
 plotly
 nbsphinx
 jinja2
 sphinx-design
+sphinx-inline-tabs
 packaging==21.3
 tenacity<8.4
+anywidget

nrn_requirements.txt

@@ -2,12 +2,11 @@ wheel
 setuptools<=70.3.0
 scikit-build
 matplotlib
-# bokeh 3 seems to break docs notebooks
-bokeh<3
+bokeh>=3
 ipython
-cython<3
+cython>=3
 packaging
 pytest
 pytest-cov
 mpi4py
-numpy<2
+numpy>=2

setup.py

@@ -410,7 +410,7 @@ def setup_package():
     NRN_COLLECT_DIRS = ["bin", "lib", "include", "share"]
 
     docs_require = []  # sphinx, themes, etc
-    maybe_rxd_reqs = ["numpy<2", "Cython<3"] if Components.RX3D else []
+    maybe_rxd_reqs = ["numpy", "Cython"] if Components.RX3D else []
     maybe_docs = docs_require if "docs" in sys.argv else []
     maybe_test_runner = ["pytest-runner"] if "test" in sys.argv else []
 

share/lib/python/neuron/__init__.py

@@ -1751,3 +1751,14 @@ def _mview_html_tree(hlist, inside_mechanisms_in_use=0):
 if _get_ipython() is not None:
     html_formatter = _get_ipython().display_formatter.formatters["text/html"]
     html_formatter.for_type(hoc.HocObject, _hocobj_html)
+
+# in case Bokeh is installed, register a serialization function for hoc.Vector
+try:
+    from bokeh.core.serialization import Serializer
+
+    Serializer.register(
+        type(h.Vector),
+        lambda obj, serializer: [serializer.encode(item) for item in obj],
+    )
+except ImportError:
+    pass

share/lib/python/neuron/gui.py

@@ -7,11 +7,11 @@
 Note that python threads are not used if nrniv is launched instead of Python
 """
 
-
 from neuron import h
-
+from contextlib import contextmanager
 import threading
 import time
+import atexit
 
 # recursive, especially in case stop/start pairs called from doNotify code.
 _lock = threading.RLock()
@@ -29,9 +29,10 @@ def process_events():
     _lock.acquire()
     try:
         h.doNotify()
-    except:
-        print("Exception in gui thread")
-    _lock.release()
+    except Exception as e:
+        print(f"Exception in gui thread: {e}")
+    finally:
+        _lock.release()
 
 
 class Timer:
@@ -67,31 +68,40 @@ def end(self):
 
 class LoopTimer(threading.Thread):
     """
-    a Timer that calls f every interval
+    A Timer that calls a function at regular intervals.
     """
 
     def __init__(self, interval, fun):
-        """
-        @param interval: time in seconds between call to fun()
-        @param fun: the function to call on timer update
-        """
         self.started = False
         self.interval = interval
         self.fun = fun
-        threading.Thread.__init__(self)
-        self.setDaemon(True)
+        self._running = threading.Event()
+        threading.Thread.__init__(self, daemon=True)
 
     def run(self):
         h.nrniv_bind_thread(threading.current_thread().ident)
         self.started = True
-        while True:
+        self._running.set()
+        while self._running.is_set():
             self.fun()
             time.sleep(self.interval)
 
+    def stop(self):
+        """Stop the timer thread and wait for it to terminate."""
+        self._running.clear()
+        self.join()
+
 
-if h.nrnversion(9) == "2":  #  launched with python (instead of nrniv)
+if h.nrnversion(9) == "2":  # Launched with Python (instead of nrniv)
     timer = LoopTimer(0.1, process_events)
     timer.start()
+
+    def cleanup():
+        if timer.started:
+            timer.stop()
+
+    atexit.register(cleanup)
+
     while not timer.started:
         time.sleep(0.001)
 

src/nrnpython/inithoc.cpp

@@ -215,18 +215,52 @@ static int have_opt(const char* arg) {
     return 0;
 }
 
+#if defined(__linux__) || defined(DARWIN)
+
+/* we do this because thread sanitizer does not allow system calls.
+   In particular
+      system("stty sane")
+   returns an error code of 139
+*/
+
+#include <iostream>
+#include <termios.h>
+#include <unistd.h>
+
+static struct termios original_termios;
+
+static void save_original_terminal_settings() {
+    if (tcgetattr(STDIN_FILENO, &original_termios) == -1 && isatty(STDIN_FILENO)) {
+        std::cerr << "Error getting original terminal attributes\n";
+    }
+}
+
+static void restore_original_terminal_settings() {
+    if (tcsetattr(STDIN_FILENO, TCSANOW, &original_termios) == -1 && isatty(STDIN_FILENO)) {
+        std::cerr << "Error restoring terminal attributes\n";
+    }
+}
+#endif  // __linux__
+
 void nrnpython_finalize() {
 #if USE_PTHREAD
     pthread_t now = pthread_self();
     if (pthread_equal(main_thread_, now)) {
 #else
     {
 #endif
+        // Call python_gui_cleanup() if defined in Python
+        PyRun_SimpleString(
+            "try:\n"
+            "    gui.cleanup()\n"
+            "except NameError:\n"
+            "    pass\n");
+
+        // Finalize Python
         Py_Finalize();
     }
-#if linux
-    if (system("stty sane > /dev/null 2>&1")) {
-    }  // 'if' to avoid ignoring return value warning
+#if defined(__linux__) || defined(DARWIN)
+    restore_original_terminal_settings();
 #endif
 }
 
@@ -239,6 +273,10 @@ extern "C" PyObject* PyInit_hoc() {
     main_thread_ = pthread_self();
 #endif
 
+#if defined(__linux__) || defined(DARWIN)
+    save_original_terminal_settings();
+#endif  // __linux__
+
     if (nrn_global_argv) {  // ivocmain was already called so already loaded
         return nrnpy_hoc();
     }

src/nrnpython/nrnpy_hoc.cpp

@@ -1596,13 +1596,16 @@ PyObject* nrnpy_forall(PyObject* self, PyObject* args) {
 static PyObject* hocobj_iter(PyObject* self) {
     //	printf("hocobj_iter %p\n", self);
     PyHocObject* po = (PyHocObject*) self;
-    if (po->type_ == PyHoc::HocObject) {
+    if (po->type_ == PyHoc::HocObject || po->type_ == PyHoc::HocSectionListIterator) {
         if (po->ho_->ctemplate == hoc_vec_template_) {
             return PySeqIter_New(self);
         } else if (po->ho_->ctemplate == hoc_list_template_) {
             return PySeqIter_New(self);
         } else if (po->ho_->ctemplate == hoc_sectionlist_template_) {
             // need a clone of self so nested loops do not share iteritem_
+            // The HocSectionListIter arm of the outer 'if' became necessary
+            // at Python-3.13.1 upon which the following body is executed
+            // twice. See https://github.com/python/cpython/issues/127682
             PyObject* po2 = nrnpy_ho2po(po->ho_);
             PyHocObject* pho2 = (PyHocObject*) po2;
             pho2->type_ = PyHoc::HocSectionListIterator;

src/nrnpython/nrnpython.cpp

@@ -210,6 +210,13 @@ extern "C" int nrnpython_start(int b) {
         // del g
         // Also, NEURONMainMenu/File/Quit did not work. The solution to both
         // seems to be to just avoid gui threads if MINGW and launched nrniv
+
+        // Beginning with Python 3.13.0 it seems that the readline
+        // module has not been loaded yet. Since PyInit_readline sets
+        // PyOS_ReadlineFunctionPointer = call_readline; without checking,
+        // we need to import here.
+        PyRun_SimpleString("import readline as nrn_readline");
+
         PyOS_ReadlineFunctionPointer = nrnpython_getline;
 
         // Is there a -c "command" or file.py arg.