diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 50d42052a4..eedfcc154c 100644
--- a/.github/workflows/coverage.yml
+++ b/.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:
diff --git a/.readthedocs.yml b/.readthedocs.yml
index dc4223186f..3b4186235a 100644
--- a/.readthedocs.yml
+++ b/.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
diff --git a/docs/conf.py b/docs/conf.py
index c9e1f5c8ae..9c5713aaeb 100644
--- a/docs/conf.py
+++ b/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)
diff --git a/docs/docs_requirements.txt b/docs/docs_requirements.txt
index a8a10b7fdd..d4a57b1711 100644
--- a/docs/docs_requirements.txt
+++ b/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
diff --git a/nrn_requirements.txt b/nrn_requirements.txt
index c4ce7d3ae0..661904304c 100644
--- a/nrn_requirements.txt
+++ b/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
diff --git a/setup.py b/setup.py
index 0ca138e607..45b0c4473d 100644
--- a/setup.py
+++ b/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 []
diff --git a/share/lib/python/neuron/__init__.py b/share/lib/python/neuron/__init__.py
index 823fbec2d2..5f69b03816 100644
--- a/share/lib/python/neuron/__init__.py
+++ b/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
diff --git a/share/lib/python/neuron/gui.py b/share/lib/python/neuron/gui.py
index 3314aa0d52..c049d6d638 100644
--- a/share/lib/python/neuron/gui.py
+++ b/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)
diff --git a/src/nrnpython/inithoc.cpp b/src/nrnpython/inithoc.cpp
index 5744c7c88e..27f96329a9 100644
--- a/src/nrnpython/inithoc.cpp
+++ b/src/nrnpython/inithoc.cpp
@@ -215,6 +215,33 @@ 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();
@@ -222,11 +249,18 @@ void nrnpython_finalize() {
#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();
}
diff --git a/src/nrnpython/nrnpy_hoc.cpp b/src/nrnpython/nrnpy_hoc.cpp
index 2d225e7df6..c8988ce1ec 100644
--- a/src/nrnpython/nrnpy_hoc.cpp
+++ b/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;
diff --git a/src/nrnpython/nrnpython.cpp b/src/nrnpython/nrnpython.cpp
index b774623aa5..b09a77c07d 100644
--- a/src/nrnpython/nrnpython.cpp
+++ b/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.