Merge branch 'master' into arith_object_flux

.circleci/config.yml

@@ -54,10 +54,9 @@ jobs:
               310) pyenv_py_ver="3.10" ;;
               311) pyenv_py_ver="3.11" ;;
               312) pyenv_py_ver="3.12" ;;
-              *) echo "Error: pyenv python version not specified!" && exit 1;;
+              *) echo "Error: pyenv python version not specified or not supported." && exit 1;;
             esac
 
-            cd /opt/circleci/.pyenv/plugins/python-build/../.. && git fetch --all && git checkout -B master origin/master && cd -
             env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install $pyenv_py_ver --force
             pyenv global $pyenv_py_ver
             export PYTHON_EXE=$(which python)

.github/ISSUE_TEMPLATE/release-patch.md

@@ -18,6 +18,8 @@ Pre-release
   - [ ] Update semantic version in `CMakeLists.txt`
   - [ ] Update changelog below and agree on it with everyone; then commit it to `docs/changelog` in the cherrypicks PR (copy structure as-is)
   - [ ] Update `docs/index.rst` accordingly with the new `.pkg` and `.exe` links for `PKG installer` and `Windows Installer`
+- [ ] Activate ReadtheDocs for the cherry-pick branch and ensure the documentation builds (when logged in, go to [the versions page](https://readthedocs.org/projects/nrn/versions/) and set the version for your branch to Active and Hidden)
+- [ ] Run a test wheel build WITHOUT upload on the cherry-pick branch to ensure all the wheels build ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 
 Sanity checks
 ---
@@ -33,7 +35,7 @@ Releasing
 - [ ] 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)
+  - [ ] arm64 wheels (manual task, check with Erik, Goran 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

.github/ISSUE_TEMPLATE/release.md

@@ -19,6 +19,7 @@ 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)
 - [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
+- [ ] Run a test wheel build WITHOUT upload for `release/x.y` to ensure all the wheels build ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 - [ ] Run BBP Simulation Stack & other relevant tests
 
 
@@ -32,7 +33,7 @@ Releasing
 - [ ] 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)
+  - [ ] arm64 wheels (manual task, check with Erik, Goran or Pramod)
   - [ ] aarch64 wheels (create a `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

.github/workflows/coverage.yml

@@ -1,7 +1,8 @@
 name: NEURON Code Coverage
 
 concurrency:
-  group: ${{ github.workflow }}#${{ github.ref }}
+  # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow
+  group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }}
   cancel-in-progress: true
 
 on:
@@ -110,7 +111,7 @@ jobs:
           python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
           python -m pip install --upgrade -r ci_requirements.txt
-          
+
 
       - name: Build & Test
         id: build-test

.github/workflows/docs.yml

@@ -1,7 +1,8 @@
 name: NEURON Documentation
 
 concurrency:
-  group: ${{ github.workflow }}#${{ github.ref }}
+  # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow
+  group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }}
   cancel-in-progress: true
 
 on:

.github/workflows/external.yml

@@ -1,7 +1,8 @@
 name: External CIs
 
 concurrency:
-  group: ${{ github.workflow }}#${{ github.ref }}
+  # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow
+  group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }}
   cancel-in-progress: true
 
 on:

.github/workflows/formatting.yml

@@ -1,7 +1,8 @@
 name: Check formatting
 
 concurrency:
-  group: ${{ github.workflow }}#${{ github.ref }}
+  # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow
+  group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }}
   cancel-in-progress: true
 
 on:
@@ -27,3 +28,24 @@ jobs:
       - name: Check formatting
         working-directory: ${{runner.workspace}}/nrn
         run: external/coding-conventions/bin/format -v --dry-run
+
+      # If formatting fails, apply formatting and push changes.
+      # This will trigger another workflow run, which will cancel the current one.
+      - name: Apply formatting
+        working-directory: ${{runner.workspace}}/nrn
+        if: failure() && github.event_name == 'pull_request'
+        run: |
+          # Checkout PR
+          gh pr checkout ${{ github.event.pull_request.number }}
+
+          # Apply formatting
+          external/coding-conventions/bin/format -v
+
+          # Commit & push changes
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add -u :/
+          git commit -a -m "Fix formatting"
+          git push
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/neuron-ci.yml

@@ -1,7 +1,8 @@
 name: NEURON CI
 
 concurrency:
-  group: ${{ github.workflow }}#${{ github.ref }}
+  # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow
+  group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }}
   cancel-in-progress: true
 
 on:
@@ -89,7 +90,7 @@ jobs:
 
     steps:
       - name: Setup cmake
-        uses: jwlawson/actions-setup-cmake@v1
+        uses: jwlawson/actions-setup-cmake@v2
         with:
           cmake-version : ${{(matrix.config.python_dynamic || matrix.config.build_mode == 'setuptools') && env.DYNAMIC_PYTHON_CMAKE_VERSION || env.DESIRED_CMAKE_VERSION}}
 
@@ -196,23 +197,11 @@ jobs:
           cat matrix.json
           echo -----
 
-      # Workaround for https://github.com/actions/cache/issues/92
-      - name: Checkout cache action
-        uses: actions/checkout@v4
-        with:
-          repository: actions/cache
-          ref: v3
-          path: tmp/actions/cache
-
-      - name: Make actions/cache@v3 run even on failure
-        run: |
-          sed -i'.bak' -e '/ post-if: /d' tmp/actions/cache/action.yml
-
       - name: Restore compiler cache
-        uses: ./tmp/actions/cache
+        uses: actions/cache@v4
         with:
-          path: |
-            ${{runner.workspace}}/ccache
+          path: ${{runner.workspace}}/ccache
+          save-always: true
           key: ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-${{github.sha}}
           restore-keys: |
             ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-

.github/workflows/windows.yml

@@ -1,7 +1,8 @@
 name: Windows Installer
 
 concurrency:
-  group: ${{ github.workflow }}#${{ github.ref }}
+  # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow
+  group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }}
   cancel-in-progress: true
 
 on:

CMakeLists.txt

@@ -521,6 +521,7 @@ if(NRN_ENABLE_CORENEURON)
   get_property(CORENRN_LIB_LINK_FLAGS GLOBAL PROPERTY CORENRN_LIB_LINK_FLAGS)
   get_property(CORENRN_NEURON_LINK_FLAGS GLOBAL PROPERTY CORENRN_NEURON_LINK_FLAGS)
   get_property(CORENRN_ENABLE_SHARED GLOBAL PROPERTY CORENRN_ENABLE_SHARED)
+  get_property(CORENRN_NMODL_BINARY GLOBAL PROPERTY CORENRN_NMODL_BINARY)
   # NEURON tests that link against CoreNEURON need to depend on it.
   set(CORENEURON_TARGET_TO_DEPEND coreneuron-for-tests)
 

bin/nrnivmodl.in

@@ -157,6 +157,10 @@ mdir="$PWD"
 
 # construct file to be included by makefile to specify mod to c rule when
 # executed in $MODSUBDIR (child folder of launch location folder)
+# Since $(PWD) may contain spaces in the path name, use the relative path.
+# Otherwise, it is very difficult to pass around paths with spaces in
+# makefiles. However, to help the user know where things are, when
+# compiling use the full path to *.cpp
 MODMAKE=makemod2c_inc
 > "$MODMAKE"
 for i in "${files[@]}" ; do
@@ -170,13 +174,13 @@ for i in "${files[@]}" ; do
   f=${f// /\\ }
   f=${f//:/\\:}
   echo "\
-./${base_name// /\\ }.cpp: ${f}.mod
+${base_name// /\\ }.cpp: ${f}.mod \$(NOCMODL)
 	@printf \" -> \$(C_GREEN)NMODL\$(C_RESET) \$<\\\n\"
 	(cd \"$dir_name\"; @NRN_NOCMODL_SANITIZER_ENVIRONMENT_STRING@ MODLUNIT=\$(NRNUNITS) \$(NOCMODL) \"$base_name.mod\" -o \"$mdir\" $UserNMODLFLAGS)
 
-./${base_name// /\\ }.o: ./${base_name// /\\ }.cpp
-	@printf \" -> \$(C_GREEN)Compiling\$(C_RESET) \$<\\\n\"
-	\$(CXXCOMPILE) -I\"$dir_name\" \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c \$< -o \$@
+./${base_name// /\\ }.o: ${base_name// /\\ }.cpp
+	@printf \" -> \$(C_GREEN)Compiling\$(C_RESET) ${PWD}/\$<\\\n\"
+	\$(CXXCOMPILE) -I\"$dir_name\" \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c \"${PWD}/\$<\" -o \$@
 " >> "$MODMAKE"
 done
 

bin/nrnivmodl_makefile_cmake.in

@@ -122,20 +122,20 @@ C_GREEN := \033[32m
 # Take the main and link with nrnmech.
 # RPATH is set for DESTDIR_RPATH and coreneuron lib
 special: $(mech_lib)
-	@printf " => $(C_GREEN)LINKING$(C_RESET) executable $(special) LDFLAGS are: $(LDFLAGS)\n"
+	@printf " => $(C_GREEN)LINKING$(C_RESET) executable \"${PWD}/$(special)\" LDFLAGS are: $(LDFLAGS)\n"
 	$(CXX_LINK_EXE) -I $(incdir) -I $(incdir)/nrncvode -DAUTO_DLOPEN_NRNMECH=0 $(datadir)/nrnmain.cpp -o $(special) \
 	  -L$(OBJS_DIR) -l$(mech_libname) $(NRNLIB_FLAGS) -l$(mech_libname) $(extra_lib_link) -Wl,-rpath,'$(DESTDIR_RPATH)' -Wl,-rpath,$(libdir) $(LDFLAGS) $(EXTRA_LDFLAGS)
 
 $(mech_lib): $(mech_lib_type)
 
 mech_lib_shared: mod_func.o $(mod_objs) build_always
-	@printf " => $(C_GREEN)LINKING$(C_RESET) shared library $(mech_lib)\n"
+	@printf " => $(C_GREEN)LINKING$(C_RESET) shared library \"${PWD}/$(mech_lib)\"\n"
 	$(CXX_LINK_SHARED) -I $(incdir) -o ${mech_lib} ${_SONAME} \
 	  $(mod_func_o) $(mod_objs) $(NRNLIB_FLAGS) $(NRNLIB_RPATH_FLAGS) $(LDFLAGS)
 	rm -f $(OBJS_DIR)/.libs/libnrnmech.so ; mkdir -p $(OBJS_DIR)/.libs ; cp $(mech_lib) $(OBJS_DIR)/.libs/libnrnmech.so
 
 mech_lib_static: mod_func.o $(mod_objs) build_always
-	@printf " => $(C_GREEN)LINKING$(C_RESET) static library $(mech_lib)\n"
+	@printf " => $(C_GREEN)LINKING$(C_RESET) static library \"${PWD}/$(mech_lib)\"\n"
 	ar cq ${mech_lib} $(mod_func_o) $(mod_objs) $(cobjs);
 
 mod_func.o: mod_func.cpp

bin/nrnpyenv.sh.in

@@ -426,7 +426,7 @@ def nrnpylib_mswin():
   f = os.popen(cmd)
   nrn_pylib = None
   for line in f:
-    if re.search('ython[a-zA-Z0-9_.]*\.dll', line):
+    if re.search(r'ython[a-zA-Z0-9_.]*\.dll', line):
       nrn_pylib = '/'.join(line.split(os.path.sep)).strip()
       nrnpylib_provenance="cygcheck"
   return nrn_pylib
@@ -474,7 +474,7 @@ def nrnpylib_linux():
       if re.search(r'libpython.*\.so', line):
         print ("# from lsof: %s" % line)
         nrn_pylib = line.strip()
-        nrnpylib_provenance = 'lsof search for libpython.*\.so'
+        nrnpylib_provenance = r'lsof search for libpython.*\.so'
         return nrn_pylib
   else: # figure it out from the os path
     p = os.path.sep.join(os.__file__.split(os.path.sep)[:-1])

docs/python/modelspec/programmatic/hocmech.rst

@@ -22,11 +22,11 @@ HOC-based Mechanisms
     Syntax:
         ``h.make_mechanism("suffix", "Template", "parm1 parm2 parm3 ...")``
 
-        ``h.make_pointprocess("Name", "Template", "parm1 parm2 parm3 ...")``
+        ``h.make_pointprocess("Template", "parm1 parm2 parm3 ...")``
 
     Description:
         Installs the HOC (in particular, *not* Python) class called "Template" as a density membrane mechanism 
-        called "suffix" or a POINT_PROCESS called Name. If the third argument exists it must be a space 
+        called "suffix" or a POINT_PROCESS called "Template". If the last argument exists it must be a space 
         separated list of public variables in the Template which are to be 
         treated as PARAMETERs. Public variables not in this list are treated as 
         ASSIGNED variables. The new mechanism is used in exactly the same 

docs/python/programming/mechstan.rst

@@ -410,6 +410,23 @@ MechanismStandard (Parameter Control)
 ----
 
 
+.. method:: MechanismStandard.is_array
+
+
+    Syntax:
+        .. code-block::
+            python
+            
+            bool = ms.is_array(index)
+
+
+    Description:
+        Returns True if the variable associated with the index is an array.
+
+
+----
+
+
 
 .. method:: MechanismStandard.name
 

docs/python/visualization/rvarplt.rst

@@ -128,7 +128,37 @@ RangeVarPlot
             rvp... #specify range begin and end 
             imp... #specify impedance computation 
             g = h.Graph() 
-            g.addobject(rvp) 
+            g.addobject(rvp)
+
+    Example (plotting a rxd species):
+        .. code-block::
+            python
+
+            from neuron import h
+            from neuron import rxd
+            import matplotlib.pyplot as plt
+
+            dend1 = h.Section("dend1")
+            dend1.nseg =4
+
+            cyt1 = rxd.Region(dend1.wholetree(), nrn_region="i")
+            ca1 = rxd.Species(cyt1, name="ca1", charge=2, initial=1e-12)
+
+            ca1.nodes(dend1(0.1))[0].include_flux(40)
+            ca1.nodes(dend1(0.4))[0].include_flux(-25)
+            ca1.nodes(dend1(0.7))[0].include_flux(70)
+
+            h.finitialize(-65)
+            h.dt /= 512
+            h.load_file("stdrun.hoc")
+            h.continuerun(0.025)
+
+            a_1 = h.RangeVarPlot(ca1, dend1(0), dend1(1))
+            a_1.plot(plt)
+            plt.show()
+
+        .. image:: ../images/rangevarplotrxd.png
+            :align: center
 
 ----
 

setup.py

@@ -509,7 +509,7 @@ def setup_package():
             else "node-and-date"
         },
         cmdclass=dict(build_ext=CMakeAugmentedBuilder, docs=Docs),
-        install_requires=["numpy>=1.9.3", "packaging", "find_libpython"],
+        install_requires=["numpy>=1.9.3", "packaging", "find_libpython", "setuptools"],
         tests_require=["flake8", "pytest"],
         setup_requires=["wheel", "setuptools_scm"]
         + maybe_docs

share/lib/python/neuron/rxd/node.py

@@ -482,6 +482,9 @@ def volume(self):
     def segment(self):
         return self._sec._sec(self.x)
 
+    def _in_seg(self, segment):
+        return segment == self.segment
+
     @property
     def surface_area(self):
         """The surface area of the compartment in square microns.

share/lib/python/neuron/tests/utils/coreneuron_available.py

@@ -0,0 +1,27 @@
+# Check if coreneuron is enabled in the current installation
+# and loadable at runtime. This may not be the case if we
+# build static library of the coreneuron.
+
+from neuron import config, h
+
+
+def coreneuron_available():
+    if not config.arguments["NRN_ENABLE_CORENEURON"]:
+        return False
+    # But can it be loaded?
+    cvode = h.CVode()
+    pc = h.ParallelContext()
+    h.finitialize()
+    result = 0
+    import sys
+    from io import StringIO
+
+    original_stderr = sys.stderr
+    sys.stderr = StringIO()
+    try:
+        pc.nrncore_run("--tstop 1 --verbose 0")
+        result = 1
+    except Exception as e:
+        pass
+    sys.stderr = original_stderr
+    return result

src/coreneuron/CMakeLists.txt

@@ -283,8 +283,8 @@ else()
     FILES ${NMODL_PROJECT_BINARY_DIR}/share/nmodl/nrnunits.lib
     DESTINATION share/nmodl
     COMPONENT nrnunits)
-
 endif()
+set_property(GLOBAL PROPERTY CORENRN_NMODL_BINARY "${CORENRN_NMODL_BINARY}")
 
 # set correct arguments for nmodl for cpu/gpu target
 set(CORENRN_NMODL_FLAGS