From 88b9a9e70b33b851cde6143108524ac01d025688 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 12:57:55 +0200
Subject: [PATCH 01/22] Modify CI to use 3.13

---
 .github/workflows/coverage.yml  | 23 ++---------------
 .github/workflows/neuron-ci.yml | 44 ++-------------------------------
 azure-pipelines.yml             | 20 ++++++++++-----
 nrn_requirements.txt            |  2 +-
 4 files changed, 19 insertions(+), 70 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index ce0bb21bae..65650c86fe 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -24,7 +24,7 @@ on:
 env:
   PY_MIN_VERSION: '3.8'
   PY_MID_VERSION: '3.10'
-  PY_MAX_VERSION: '3.12'
+  PY_MAX_VERSION: '3.13'
 
 jobs:
   coverage:
@@ -36,8 +36,6 @@ jobs:
 
     env:
       DISPLAY: ${{ ':0' }}
-      MUSIC_INSTALL_DIR: /opt/MUSIC
-      MUSIC_VERSION: 1.2.0
 
     steps:
 
@@ -54,21 +52,6 @@ jobs:
           cmake ..
           make && sudo make install
 
-      - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
-        run: |
-          python3 -m venv music-venv
-          source music-venv/bin/activate
-          python3 -m pip install 'mpi4py<4' cython numpy 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
-          unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC
-          ./autogen.sh
-          ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource
-          make -j install
-          deactivate
-        working-directory: ${{runner.temp}}
-
       - name: Setup Xvfb
         run: |
           sudo apt-get install xvfb
@@ -148,9 +131,7 @@ jobs:
                       -DNRN_PYTHON_DYNAMIC="${PYTHON_MIN};${PYTHON_MAX}" \
                       -DNRN_PYTHON_EXTRA_FOR_TESTS=${PYTHON_MID} \
                       -DNRN_ENABLE_TESTS=ON \
-                      -DNRN_ENABLE_MUSIC=ON \
-                      -DCMAKE_PREFIX_PATH="${MUSIC_INSTALL_DIR}" \
-                      -DMUSIC_ROOT="${MUSIC_INSTALL_DIR}")
+                      -DNRN_ENABLE_MUSIC=OFF)
           cmake .. "${cmake_args[@]}"
           # Coverage
           # The Linux runners apparently have 2 cores, but jobs were being killed when we did not specify this explicitly.
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index e3ca977eb4..21f13ec096 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -39,16 +39,14 @@ jobs:
       DESIRED_CMAKE_VERSION: 3.17
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }}
-      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.12' }}
-      MUSIC_INSTALL_DIR: /opt/MUSIC
-      MUSIC_VERSION: 1.2.1
+      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13' }}
 
     strategy:
       matrix:
         os: [ macOS-12, ubuntu-20.04]
         config:
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "setuptools"}
-          - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", music: ON}
+          - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake"}
           - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", python_dynamic: ON}
           - { matrix_eval : "CC=gcc-9 CXX=g++-9" ,  build_mode: "cmake", cmake_option: "-DNRN_ENABLE_CORENEURON=ON"}
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "cmake", cmake_option: "-DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_CORENEURON=ON"}
@@ -187,38 +185,6 @@ jobs:
           python -m pip install --upgrade -r ci_requirements.txt
           python -m pip install --upgrade pip -r nrn_requirements.txt
 
-      - name: Install a new automake
-        # A new automake is needed for python 3.12 because it generate a python script
-        # called py-compile and the original one is not supporting this version of python
-        # Once ubuntu got a newer version of automake we can remove this part.
-        if: matrix.config.music == 'ON' && startsWith(matrix.os, 'ubuntu')
-        run: |
-          curl -L -o automake.tar.xz https://ftp.gnu.org/gnu/automake/automake-1.16.5.tar.xz
-          tar -xf automake.tar.xz
-          cd automake-1.16.5/
-          ./configure --prefix=/usr/
-          make -j
-          sudo make -j install
-          automake --version
-        working-directory: ${{runner.temp}}
-
-      - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
-        if: matrix.config.music == 'ON'
-        run: |
-          python3 -m venv music-venv
-          source music-venv/bin/activate
-          python3 -m pip install 'mpi4py<4' cython numpy 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
-          unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC
-          ./autogen.sh
-          # on some systems MPI library detection fails, provide exact flags/compilers
-          ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource MPI_CXXFLAGS="-g -O3" MPI_CFLAGS="-g -O3" MPI_LDFLAGS=" " CC=mpicc CXX=mpicxx
-          make -j install
-          deactivate
-        working-directory: ${{runner.temp}}
-
       - name: Register gcc problem matcher
         if: ${{matrix.config.flag_warnings == 'ON'}}
         run: echo "::add-matcher::.github/problem-matchers/gcc.json"
@@ -329,11 +295,6 @@ jobs:
               else
                 cmake_args+=(-DPYTHON_EXECUTABLE="${PYTHON}")
               fi
-              if [[ "$NRN_ENABLE_MUSIC" == "ON" ]]; then
-                cmake_args+=(-DNRN_ENABLE_MUSIC=ON \
-                             -DCMAKE_PREFIX_PATH=${MUSIC_INSTALL_DIR} \
-                             -DMUSIC_ROOT=${MUSIC_INSTALL_DIR})
-              fi
               # Enable more warnings in the builds whose compiler warnings we
               # highlight in the GitHub UI
               if [[ "${{matrix.config.flag_warnings}}" == "ON" ]]; then
@@ -435,7 +396,6 @@ jobs:
           CCACHE_BASEDIR: ${{runner.workspace}}/nrn
           CCACHE_DIR: ${{runner.workspace}}/ccache
           NRN_ENABLE_PYTHON_DYNAMIC : ${{ matrix.config.python_dynamic }}
-          NRN_ENABLE_MUSIC: ${{ matrix.config.music }}
           PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
           PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
           INSTALL_DIR : ${{ runner.workspace }}/install
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 238988a536..2715be4010 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -44,6 +44,9 @@ stages:
             python.version: '3.11'
           Python312:
             python.version: '3.12'
+          Python313:
+            python.version: '3.13'
+
       steps:
 
       # Secure files documentation:
@@ -91,28 +94,33 @@ stages:
           Python38:
             python.version: '3.8'
             python.org.version: '3.8.9'
-            python.installer.name: 'macosx10.9.pkg'
+            python.installer.name: '3.8.9-macosx10.9.pkg'
           Python39:
             python.version: '3.9'
             python.org.version: '3.9.13'
-            python.installer.name: 'macos11.pkg'
+            python.installer.name: '3.9.13-macos11.pkg'
           Python310:
             python.version: '3.10'
             python.org.version: '3.10.11'
-            python.installer.name: 'macos11.pkg'
+            python.installer.name: '3.10.11-macos11.pkg'
           Python311:
             python.version: '3.11'
             python.org.version: '3.11.7'
-            python.installer.name: 'macos11.pkg'
+            python.installer.name: '3.11.7-macos11.pkg'
           Python312:
             python.version: '3.12'
             python.org.version: '3.12.0'
-            python.installer.name: 'macos11.pkg'
+            python.installer.name: '3.12.0-macos11.pkg'
+
+          Python312:
+            python.version: '3.13'
+            python.org.version: '3.13.0'
+            python.installer.name: '3.13.0rc2-macos11.pkg'
 
       steps:
 
       - script: |
-          installer=python-$(python.org.version)-$(python.installer.name)
+          installer=python-$(python.installer.name)
           url=https://www.python.org/ftp/python/$(python.org.version)/$installer
           curl $url -o $installer
           sudo installer -pkg $installer -target /
diff --git a/nrn_requirements.txt b/nrn_requirements.txt
index f049602b4e..eabc83e78d 100644
--- a/nrn_requirements.txt
+++ b/nrn_requirements.txt
@@ -10,6 +10,6 @@ cython
 packaging
 pytest<=8.1.1 # potential bug from 8.2.0 due to parallelism?
 pytest-cov
-mpi4py<4 # MUSIC not compatible with MPI 4
+mpi4py
 numpy
 find_libpython

From 6cfd1f98b4e80fb0a3a9b0e49531f686323630a4 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 11:15:44 +0200
Subject: [PATCH 02/22] Bump MacOS versions in CI

---
 .github/workflows/neuron-ci.yml | 2 +-
 azure-pipelines.yml             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index 21f13ec096..d13324d1cb 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -43,7 +43,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [ macOS-12, ubuntu-20.04]
+        os: [macOS-13, ubuntu-20.04]
         config:
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "setuptools"}
           - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake"}
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 2715be4010..25bba532be 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -88,7 +88,7 @@ stages:
     - job: 'MacOSWheels'
       timeoutInMinutes: 60
       pool:
-        vmImage: 'macOS-12'
+        vmImage: 'macOS-13'
       strategy:
         matrix:
           Python38:

From 349d03bb6ee6f86499de59d69181fa2ab2ead1a5 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 13:02:27 +0200
Subject: [PATCH 03/22] Add right version in action setup

---
 .github/workflows/neuron-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index d13324d1cb..646da9428a 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -39,7 +39,7 @@ jobs:
       DESIRED_CMAKE_VERSION: 3.17
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }}
-      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13' }}
+      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13.0-rc.2' }}
 
     strategy:
       matrix:

From 713f197dcaacfa406655ee480432d1cfcdd09162 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 13:22:46 +0200
Subject: [PATCH 04/22] Wrong Python interpreter

---
 .github/workflows/neuron-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index 646da9428a..6e80a5d979 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -397,7 +397,7 @@ jobs:
           CCACHE_DIR: ${{runner.workspace}}/ccache
           NRN_ENABLE_PYTHON_DYNAMIC : ${{ matrix.config.python_dynamic }}
           PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
-          PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
+          PYTHON_MAX_NAME: "python3.13"
           INSTALL_DIR : ${{ runner.workspace }}/install
           MATRIX_EVAL: ${{ matrix.config.matrix_eval }}
 

From 3bff32bcfefc4fa58c38bb99f6690b1cd86e88ed Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 13:23:41 +0200
Subject: [PATCH 05/22] Yeah the coverage one too

---
 .github/workflows/coverage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 65650c86fe..cfc5b4e5f6 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -156,7 +156,7 @@ jobs:
           MATRIX_EVAL: "CC=gcc CXX=g++"
           PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
           PYTHON_MID_NAME: "python${{ env.PY_MID_VERSION }}"
-          PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
+          PYTHON_MAX_NAME: "python3.13"
 
       # This step will set up an SSH connection on tmate.io for live debugging.
       # To enable it, you have to:

From 907725477b2893a639f26626ceef9a5bf1bde084 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 13:29:45 +0200
Subject: [PATCH 06/22] Okay for real this time

---
 .github/workflows/coverage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index cfc5b4e5f6..052f85f585 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -24,7 +24,7 @@ on:
 env:
   PY_MIN_VERSION: '3.8'
   PY_MID_VERSION: '3.10'
-  PY_MAX_VERSION: '3.13'
+  PY_MAX_VERSION: '3.13.0-rc.2'
 
 jobs:
   coverage:

From 7378300dcbb3cf99bb8368e3e9b5b10d7f9d4aaf Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 15:34:10 +0200
Subject: [PATCH 07/22] Fix: remove deprecated test methods

---
 share/lib/python/neuron/tests/test_neuron.py | 3 +--
 share/lib/python/neuron/tests/test_rxd.py    | 3 +--
 share/lib/python/neuron/tests/test_vector.py | 3 +--
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/share/lib/python/neuron/tests/test_neuron.py b/share/lib/python/neuron/tests/test_neuron.py
index 6c49934f30..d300aa3c26 100644
--- a/share/lib/python/neuron/tests/test_neuron.py
+++ b/share/lib/python/neuron/tests/test_neuron.py
@@ -294,8 +294,7 @@ def suite():
         ]
     except:
         pass
-    suite = unittest.makeSuite(NeuronTestCase, "test")
-    return suite
+    return unittest.defaultTestLoader.loadTestsFromTestCase(NeuronTestCase)
 
 
 if __name__ == "__main__":
diff --git a/share/lib/python/neuron/tests/test_rxd.py b/share/lib/python/neuron/tests/test_rxd.py
index 964bd53738..db85696c90 100644
--- a/share/lib/python/neuron/tests/test_rxd.py
+++ b/share/lib/python/neuron/tests/test_rxd.py
@@ -798,8 +798,7 @@ def test_ecs_diffusion_variable_step_fine(self):
 
 
 def suite():
-    suite = unittest.makeSuite(RxDTestCase, "test")
-    return suite
+    return unittest.defaultTestLoader.loadTestsFromTestCase(RxDTestCase)
 
 
 def test():
diff --git a/share/lib/python/neuron/tests/test_vector.py b/share/lib/python/neuron/tests/test_vector.py
index ee92f0bb27..17ed26bd42 100644
--- a/share/lib/python/neuron/tests/test_vector.py
+++ b/share/lib/python/neuron/tests/test_vector.py
@@ -156,8 +156,7 @@ def testErrorHandling(self):
 
 
 def suite():
-    suite = unittest.makeSuite(VectorTestCase, "test")
-    return suite
+    return unittest.defaultTestLoader.loadTestsFromTestCase(VectorTestCase)
 
 
 if __name__ == "__main__":

From 30fb89a16e9c4692af51196e9d03ee9aa776e13d Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 15:38:26 +0200
Subject: [PATCH 08/22] Fix: pytest warning

---
 test/pytest_coreneuron/test_nlayer.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/test/pytest_coreneuron/test_nlayer.py b/test/pytest_coreneuron/test_nlayer.py
index 5a7670da58..7e45c4a444 100644
--- a/test/pytest_coreneuron/test_nlayer.py
+++ b/test/pytest_coreneuron/test_nlayer.py
@@ -36,7 +36,7 @@ def run(self):
         return res
 
 
-def test_nlayer():
+def _test_nlayer():
     res = []
     for nlayer in [1, 2, 3]:
         h.nlayer_extracellular(nlayer)
@@ -52,10 +52,14 @@ def test_nlayer():
     return res
 
 
-if __name__ == "__main__":
-    res = test_nlayer()
+def test_main():
+    res = _test_nlayer()
     for i in range(len(res[0][0])):
         for j in range(2):
             for k in range(3):
                 print("%g" % res[k][j].x[i], end=" ")
         print()
+
+
+if __name__ == "__main__":
+    test_main()

From 71d1cfa7758f2ccaa9a065517dc1207e28c020c0 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 1 Oct 2024 16:02:30 +0200
Subject: [PATCH 09/22] Whoops I broke azure

---
 azure-pipelines.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 25bba532be..08ce6d11c3 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -111,8 +111,7 @@ stages:
             python.version: '3.12'
             python.org.version: '3.12.0'
             python.installer.name: '3.12.0-macos11.pkg'
-
-          Python312:
+          Python313:
             python.version: '3.13'
             python.org.version: '3.13.0'
             python.installer.name: '3.13.0rc2-macos11.pkg'

From 2bac6ff0c7d3f6773b0d3110451babc414517b5c Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Wed, 2 Oct 2024 09:38:08 +0200
Subject: [PATCH 10/22] Bring back the music

---
 .github/workflows/coverage.yml  | 21 ++++++++++++++++-
 .github/workflows/neuron-ci.yml | 42 ++++++++++++++++++++++++++++++++-
 setup.py                        |  2 +-
 3 files changed, 62 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 052f85f585..9087cb42bb 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -36,6 +36,8 @@ jobs:
 
     env:
       DISPLAY: ${{ ':0' }}
+      MUSIC_INSTALL_DIR: /opt/MUSIC
+      MUSIC_VERSION: 1.2.0
 
     steps:
 
@@ -52,6 +54,21 @@ jobs:
           cmake ..
           make && sudo make install
 
+      - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
+        run: |
+          python3 -m venv music-venv
+          source music-venv/bin/activate
+          python3 -m pip install mpi4py cython numpy 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
+          unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC
+          ./autogen.sh
+          ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource
+          make -j install
+          deactivate
+        working-directory: ${{runner.temp}}
+
       - name: Setup Xvfb
         run: |
           sudo apt-get install xvfb
@@ -131,7 +148,9 @@ jobs:
                       -DNRN_PYTHON_DYNAMIC="${PYTHON_MIN};${PYTHON_MAX}" \
                       -DNRN_PYTHON_EXTRA_FOR_TESTS=${PYTHON_MID} \
                       -DNRN_ENABLE_TESTS=ON \
-                      -DNRN_ENABLE_MUSIC=OFF)
+                      -DNRN_ENABLE_MUSIC=ON \
+                      -DCMAKE_PREFIX_PATH="${MUSIC_INSTALL_DIR}" \
+                      -DMUSIC_ROOT="${MUSIC_INSTALL_DIR}")
           cmake .. "${cmake_args[@]}"
           # Coverage
           # The Linux runners apparently have 2 cores, but jobs were being killed when we did not specify this explicitly.
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index 6e80a5d979..beda7f9729 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -40,13 +40,15 @@ jobs:
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }}
       PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13.0-rc.2' }}
+      MUSIC_INSTALL_DIR: /opt/MUSIC
+      MUSIC_VERSION: 1.2.1
 
     strategy:
       matrix:
         os: [macOS-13, ubuntu-20.04]
         config:
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "setuptools"}
-          - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake"}
+          - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", music: ON}
           - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", python_dynamic: ON}
           - { matrix_eval : "CC=gcc-9 CXX=g++-9" ,  build_mode: "cmake", cmake_option: "-DNRN_ENABLE_CORENEURON=ON"}
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "cmake", cmake_option: "-DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_CORENEURON=ON"}
@@ -185,6 +187,38 @@ jobs:
           python -m pip install --upgrade -r ci_requirements.txt
           python -m pip install --upgrade pip -r nrn_requirements.txt
 
+      - name: Install a new automake
+        # A new automake is needed for python 3.12 because it generate a python script
+        # called py-compile and the original one is not supporting this version of python
+        # Once ubuntu got a newer version of automake we can remove this part.
+        if: matrix.config.music == 'ON' && startsWith(matrix.os, 'ubuntu')
+        run: |
+          curl -L -o automake.tar.xz https://ftp.gnu.org/gnu/automake/automake-1.16.5.tar.xz
+          tar -xf automake.tar.xz
+          cd automake-1.16.5/
+          ./configure --prefix=/usr/
+          make -j
+          sudo make -j install
+          automake --version
+        working-directory: ${{runner.temp}}
+
+      - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
+        if: matrix.config.music == 'ON'
+        run: |
+          python3 -m venv music-venv
+          source music-venv/bin/activate
+          python3 -m pip install mpi4py cython numpy 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
+          unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC
+          ./autogen.sh
+          # on some systems MPI library detection fails, provide exact flags/compilers
+          ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource MPI_CXXFLAGS="-g -O3" MPI_CFLAGS="-g -O3" MPI_LDFLAGS=" " CC=mpicc CXX=mpicxx
+          make -j install
+          deactivate
+        working-directory: ${{runner.temp}}
+
       - name: Register gcc problem matcher
         if: ${{matrix.config.flag_warnings == 'ON'}}
         run: echo "::add-matcher::.github/problem-matchers/gcc.json"
@@ -295,6 +329,11 @@ jobs:
               else
                 cmake_args+=(-DPYTHON_EXECUTABLE="${PYTHON}")
               fi
+              if [[ "$NRN_ENABLE_MUSIC" == "ON" ]]; then
+                cmake_args+=(-DNRN_ENABLE_MUSIC=ON \
+                             -DCMAKE_PREFIX_PATH=${MUSIC_INSTALL_DIR} \
+                             -DMUSIC_ROOT=${MUSIC_INSTALL_DIR})
+              fi
               # Enable more warnings in the builds whose compiler warnings we
               # highlight in the GitHub UI
               if [[ "${{matrix.config.flag_warnings}}" == "ON" ]]; then
@@ -396,6 +435,7 @@ jobs:
           CCACHE_BASEDIR: ${{runner.workspace}}/nrn
           CCACHE_DIR: ${{runner.workspace}}/ccache
           NRN_ENABLE_PYTHON_DYNAMIC : ${{ matrix.config.python_dynamic }}
+          NRN_ENABLE_MUSIC: ${{ matrix.config.music }}
           PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
           PYTHON_MAX_NAME: "python3.13"
           INSTALL_DIR : ${{ runner.workspace }}/install
diff --git a/setup.py b/setup.py
index e15b6e5ac0..fffb2bfec8 100644
--- a/setup.py
+++ b/setup.py
@@ -96,7 +96,7 @@ class Components:
     Components.MUSIC = True
     sys.argv.remove("--enable-music")
 
-if Components.RX3D:
+if Components.RX3D or Components.MUSIC:
     try:
         from Cython.Distutils import Extension as CyExtension
         from Cython.Distutils import build_ext

From 04c90bd3097b64fac92d381c01f38dcc8b24fb2a Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Wed, 2 Oct 2024 10:34:39 +0200
Subject: [PATCH 11/22] Pin mpi4py

---
 .github/workflows/coverage.yml  | 2 +-
 .github/workflows/neuron-ci.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 9087cb42bb..f86ff2da8a 100644
--- a/.github/workflows/coverage.yml
+++ b/.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 numpy setuptools
+          python3 -m pip install 'mpi4py<4' cython numpy 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
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index beda7f9729..6943d10c0c 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.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 numpy setuptools
+          python3 -m pip install 'mpi4py<4' cython numpy 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

From 8dbeb9eaf823a1ba3934d1003bf6ba5257acec8e Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Thu, 3 Oct 2024 13:33:08 +0200
Subject: [PATCH 12/22] Revert "Pin mpi4py"

This reverts commit 04c90bd3097b64fac92d381c01f38dcc8b24fb2a.

Also adds Python 3.13 rc3
---
 .github/workflows/coverage.yml  | 4 ++--
 .github/workflows/neuron-ci.yml | 4 ++--
 azure-pipelines.yml             | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index f86ff2da8a..185a1061eb 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -24,7 +24,7 @@ on:
 env:
   PY_MIN_VERSION: '3.8'
   PY_MID_VERSION: '3.10'
-  PY_MAX_VERSION: '3.13.0-rc.2'
+  PY_MAX_VERSION: '3.13.0-rc.3'
 
 jobs:
   coverage:
@@ -58,7 +58,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install 'mpi4py<4' cython numpy setuptools
+          python3 -m pip install mpi4py cython numpy 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
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index 6943d10c0c..fa8863c2b1 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -39,7 +39,7 @@ jobs:
       DESIRED_CMAKE_VERSION: 3.17
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }}
-      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13.0-rc.2' }}
+ 3    PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13.0-rc.3' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
       MUSIC_VERSION: 1.2.1
 
@@ -207,7 +207,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install 'mpi4py<4' cython numpy setuptools
+          python3 -m pip install mpi4py cython numpy 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
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 08ce6d11c3..2c55a1c083 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -114,7 +114,7 @@ stages:
           Python313:
             python.version: '3.13'
             python.org.version: '3.13.0'
-            python.installer.name: '3.13.0rc2-macos11.pkg'
+            python.installer.name: '3.13.0rc3-macos11.pkg'
 
       steps:
 

From 31ac6d70f96fa3cdd2571a895a9681ca2763350c Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Thu, 3 Oct 2024 13:34:53 +0200
Subject: [PATCH 13/22] Fix typo

---
 .github/workflows/neuron-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index fa8863c2b1..a730b63e24 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -39,7 +39,7 @@ jobs:
       DESIRED_CMAKE_VERSION: 3.17
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }}
- 3    PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13.0-rc.3' }}
+      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13.0-rc.3' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
       MUSIC_VERSION: 1.2.1
 

From 1c7aa9d5baf3092942febe6326c58dbbdb751ecf Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Thu, 3 Oct 2024 13:41:07 +0200
Subject: [PATCH 14/22] Try workaround for mpi4py

---
 .github/workflows/coverage.yml  | 7 +++++--
 .github/workflows/neuron-ci.yml | 5 ++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 185a1061eb..b59df4a6d1 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -37,7 +37,7 @@ jobs:
     env:
       DISPLAY: ${{ ':0' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
-      MUSIC_VERSION: 1.2.0
+      MUSIC_VERSION: 1.2.1
 
     steps:
 
@@ -58,7 +58,10 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py cython numpy setuptools
+          python3 -m pip install cython numpy setuptools
+          # workaround for Python 3.13 incompat
+          git clone --branch maint-3.1 https://github.com/mpi4py/mpi4py
+          cd mpi4py && bash conf/cython.sh && python3 -m pip install . && cd - && rm -fr mpi4py
           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
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index a730b63e24..f47309acd6 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -207,7 +207,10 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py cython numpy setuptools
+          python3 -m pip install cython numpy setuptools
+          # workaround for Python 3.13 incompat
+          git clone --branch maint-3.1 https://github.com/mpi4py/mpi4py
+          cd mpi4py && bash conf/cython.sh && python3 -m pip install . && cd - && rm -fr mpi4py
           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

From 868264cb41e88e7d11da21cee7fc74dd434097fc Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Thu, 3 Oct 2024 13:46:26 +0200
Subject: [PATCH 15/22] Fix typo

---
 .github/workflows/coverage.yml  | 2 +-
 .github/workflows/neuron-ci.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index b59df4a6d1..ed521441b4 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -61,7 +61,7 @@ jobs:
           python3 -m pip install cython numpy setuptools
           # workaround for Python 3.13 incompat
           git clone --branch maint-3.1 https://github.com/mpi4py/mpi4py
-          cd mpi4py && bash conf/cython.sh && python3 -m pip install . && cd - && rm -fr mpi4py
+          cd mpi4py && bash conf/cythonize.sh && python3 -m pip install . && cd - && rm -fr mpi4py
           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
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index f47309acd6..2c3964297f 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -210,7 +210,7 @@ jobs:
           python3 -m pip install cython numpy setuptools
           # workaround for Python 3.13 incompat
           git clone --branch maint-3.1 https://github.com/mpi4py/mpi4py
-          cd mpi4py && bash conf/cython.sh && python3 -m pip install . && cd - && rm -fr mpi4py
+          cd mpi4py && bash conf/cythonize.sh && python3 -m pip install . && cd - && rm -fr mpi4py
           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

From f9c77ad178cbf3cfe79946fad6398eca76829c56 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Fri, 4 Oct 2024 10:47:44 +0200
Subject: [PATCH 16/22] Remove OpenMPI

---
 .github/workflows/coverage.yml  | 7 ++-----
 .github/workflows/neuron-ci.yml | 9 +++------
 2 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index ed521441b4..42f1b28a8e 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -43,7 +43,7 @@ jobs:
 
       - name: Install apt packages
         run: |
-          sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin gpg ninja-build flex bison libfl-dev
+          sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libmpich-dev libx11-dev libxcomposite-dev mpich gpg ninja-build flex bison libfl-dev
         shell: bash
 
       - name: Setup Caliper profiler
@@ -58,10 +58,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install cython numpy setuptools
-          # workaround for Python 3.13 incompat
-          git clone --branch maint-3.1 https://github.com/mpi4py/mpi4py
-          cd mpi4py && bash conf/cythonize.sh && python3 -m pip install . && cd - && rm -fr mpi4py
+          python3 -m pip install mpi4py cython numpy 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
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index 2c3964297f..78673701c5 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -139,9 +139,9 @@ jobs:
       - name: Install apt packages
         if: startsWith(matrix.os, 'ubuntu')
         run: |
-          sudo apt-get install build-essential ccache libopenmpi-dev \
+          sudo apt-get install build-essential ccache \
             libmpich-dev libx11-dev libxcomposite-dev mpich ninja-build \
-            openmpi-bin flex libfl-dev bison libreadline-dev
+            flex libfl-dev bison libreadline-dev
           # The sanitizer builds use ubuntu 22.04
           if [[ "${{matrix.os}}" == "ubuntu-20.04" ]]; then
             sudo apt-get install g++-7 g++-8
@@ -207,10 +207,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install cython numpy setuptools
-          # workaround for Python 3.13 incompat
-          git clone --branch maint-3.1 https://github.com/mpi4py/mpi4py
-          cd mpi4py && bash conf/cythonize.sh && python3 -m pip install . && cd - && rm -fr mpi4py
+          python3 -m pip install mpi4py cython numpy 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

From 58b9b6fe18b0ece1cae23a1e585addab9038e150 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Fri, 4 Oct 2024 11:52:02 +0200
Subject: [PATCH 17/22] Explicitly nuke OpenMPI

---
 .github/workflows/coverage.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 42f1b28a8e..88ad1be976 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -44,6 +44,7 @@ jobs:
       - name: Install apt packages
         run: |
           sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libmpich-dev libx11-dev libxcomposite-dev mpich gpg ninja-build flex bison libfl-dev
+          sudo apt-get purge -y libopenmpi-dev openmpi-bin
         shell: bash
 
       - name: Setup Caliper profiler

From e6266320880c93e8951fae2d6c6b1d0d115190e4 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Fri, 4 Oct 2024 12:04:51 +0200
Subject: [PATCH 18/22] Fix MUSIC in CI as well

---
 .github/workflows/neuron-ci.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index e624fd2ea7..c1873ec35f 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -205,6 +205,8 @@ jobs:
       - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
         if: matrix.config.music == 'ON'
         run: |
+          # the version of OpenMPI on Ubuntu does not support MPI 4, so we remove it
+          apt-get purge -y libopenmpi-dev openmpi-bin
           python3 -m venv music-venv
           source music-venv/bin/activate
           python3 -m pip install mpi4py cython numpy setuptools
@@ -217,6 +219,8 @@ jobs:
           ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource MPI_CXXFLAGS="-g -O3" MPI_CFLAGS="-g -O3" MPI_LDFLAGS=" " CC=mpicc CXX=mpicxx
           make -j install
           deactivate
+          # install back OpenMPI so NEURON can use it
+          apt-get install -y libopenmpi-dev openmpi-bin
         working-directory: ${{runner.temp}}
 
       - name: Register gcc problem matcher

From 06f06d832fb297da4f2f52b1b9a5051f48aedbad Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Fri, 4 Oct 2024 12:22:03 +0200
Subject: [PATCH 19/22] Install custom OpenMPI that supports MPI 4

---
 .github/workflows/neuron-ci.yml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index c1873ec35f..8e0b547b77 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -200,13 +200,19 @@ jobs:
           make -j
           sudo make -j install
           automake --version
+          cd -
+          sudo apt-get purge -y libopenmpi-dev openmpi-bin
+          curl -L -o openmpi.tar.gz https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
+          tar -xf openmpi.tar.gz
+          cd openmpi-5.0.5/
+          ./configure --prefix=/usr/
+          make -j
+          sudo make -j install
         working-directory: ${{runner.temp}}
 
       - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
         if: matrix.config.music == 'ON'
         run: |
-          # the version of OpenMPI on Ubuntu does not support MPI 4, so we remove it
-          apt-get purge -y libopenmpi-dev openmpi-bin
           python3 -m venv music-venv
           source music-venv/bin/activate
           python3 -m pip install mpi4py cython numpy setuptools
@@ -219,8 +225,6 @@ jobs:
           ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource MPI_CXXFLAGS="-g -O3" MPI_CFLAGS="-g -O3" MPI_LDFLAGS=" " CC=mpicc CXX=mpicxx
           make -j install
           deactivate
-          # install back OpenMPI so NEURON can use it
-          apt-get install -y libopenmpi-dev openmpi-bin
         working-directory: ${{runner.temp}}
 
       - name: Register gcc problem matcher

From 68799cb0a307bd0077a29e068cfc0093390b2db6 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Fri, 4 Oct 2024 13:18:49 +0200
Subject: [PATCH 20/22] OpenMPI stuff

---
 .github/workflows/neuron-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index 8e0b547b77..d2d9cc3397 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -139,9 +139,9 @@ jobs:
       - name: Install apt packages
         if: startsWith(matrix.os, 'ubuntu')
         run: |
-          sudo apt-get install build-essential ccache \
+          sudo apt-get install build-essential ccache libopenmpi-dev \
             libmpich-dev libx11-dev libxcomposite-dev mpich ninja-build \
-            flex libfl-dev bison libreadline-dev
+            openmpi-bin flex libfl-dev bison libreadline-dev
           # The sanitizer builds use ubuntu 22.04
           if [[ "${{matrix.os}}" == "ubuntu-20.04" ]]; then
             sudo apt-get install g++-7 g++-8

From 127bd125956f4a4a3bc96943b7645c818b797ae5 Mon Sep 17 00:00:00 2001
From: JCGoran <goran.jelic-cizmek@epfl.ch>
Date: Tue, 8 Oct 2024 16:15:19 +0200
Subject: [PATCH 21/22] Fix MPI issues with MUSIC

---
 .github/workflows/coverage.yml  | 13 ++++++++++++-
 .github/workflows/neuron-ci.yml | 20 ++++++++++++--------
 2 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 88ad1be976..119a718957 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -44,9 +44,20 @@ jobs:
       - name: Install apt packages
         run: |
           sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libmpich-dev libx11-dev libxcomposite-dev mpich gpg ninja-build flex bison libfl-dev
-          sudo apt-get purge -y libopenmpi-dev openmpi-bin
         shell: bash
 
+      - name: Install a new version of OpenMPI
+        # The version of OpenMPI on Ubuntu 22.04 does not support MPI 4 features, so we install it manually
+        run: |
+          sudo apt-get purge -y libopenmpi-dev openmpi-bin
+          curl -L -o openmpi.tar.gz https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
+          tar -xf openmpi.tar.gz
+          cd openmpi-5.0.5/
+          ./configure --prefix=/usr/
+          make -j
+          sudo make -j install
+        working-directory: ${{runner.temp}}
+
       - name: Setup Caliper profiler
         run: |
           git clone https://github.com/LLNL/Caliper.git
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index d2d9cc3397..819d883237 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -187,6 +187,18 @@ jobs:
           python -m pip install --upgrade -r ci_requirements.txt
           python -m pip install --upgrade pip -r nrn_requirements.txt
 
+      - name: Install a new version of OpenMPI
+        # The version of OpenMPI on Ubuntu 22.04 does not support MPI 4 features, so we install it manually
+        run: |
+          sudo apt-get purge -y libopenmpi-dev openmpi-bin
+          curl -L -o openmpi.tar.gz https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
+          tar -xf openmpi.tar.gz
+          cd openmpi-5.0.5/
+          ./configure --prefix=/usr/
+          make -j
+          sudo make -j install
+        working-directory: ${{runner.temp}}
+
       - name: Install a new automake
         # A automake >= 1.16.5 is needed for python 3.12 because it generates a python script
         # called py-compile and the original one is not supporting this version of python
@@ -200,14 +212,6 @@ jobs:
           make -j
           sudo make -j install
           automake --version
-          cd -
-          sudo apt-get purge -y libopenmpi-dev openmpi-bin
-          curl -L -o openmpi.tar.gz https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
-          tar -xf openmpi.tar.gz
-          cd openmpi-5.0.5/
-          ./configure --prefix=/usr/
-          make -j
-          sudo make -j install
         working-directory: ${{runner.temp}}
 
       - name: Setup MUSIC@${{ env.MUSIC_VERSION }}

From ed6f7ccf68909b92209cd2c1dfaee6e23970bab0 Mon Sep 17 00:00:00 2001
From: JCGoran <goran.jelic-cizmek@epfl.ch>
Date: Tue, 8 Oct 2024 16:16:31 +0200
Subject: [PATCH 22/22] Remove Python 3.13 stuff

---
 .github/workflows/coverage.yml  |  4 ++--
 .github/workflows/neuron-ci.yml |  6 +++---
 azure-pipelines.yml             | 21 +++++++--------------
 3 files changed, 12 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 119a718957..c37bbec630 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -24,7 +24,7 @@ on:
 env:
   PY_MIN_VERSION: '3.8'
   PY_MID_VERSION: '3.10'
-  PY_MAX_VERSION: '3.13.0-rc.3'
+  PY_MAX_VERSION: '3.12'
 
 jobs:
   coverage:
@@ -187,7 +187,7 @@ jobs:
           MATRIX_EVAL: "CC=gcc CXX=g++"
           PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
           PYTHON_MID_NAME: "python${{ env.PY_MID_VERSION }}"
-          PYTHON_MAX_NAME: "python3.13"
+          PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
 
       # This step will set up an SSH connection on tmate.io for live debugging.
       # To enable it, you have to:
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index 819d883237..0c731d70b6 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.github/workflows/neuron-ci.yml
@@ -39,13 +39,13 @@ jobs:
       DESIRED_CMAKE_VERSION: 3.17
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }}
-      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13.0-rc.3' }}
+      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.12' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
       MUSIC_VERSION: 1.2.1
 
     strategy:
       matrix:
-        os: [macOS-13, ubuntu-20.04]
+        os: [ macOS-12, ubuntu-20.04]
         config:
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "setuptools"}
           - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", music: ON}
@@ -449,7 +449,7 @@ jobs:
           NRN_ENABLE_PYTHON_DYNAMIC : ${{ matrix.config.python_dynamic }}
           NRN_ENABLE_MUSIC: ${{ matrix.config.music }}
           PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
-          PYTHON_MAX_NAME: "python3.13"
+          PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
           INSTALL_DIR : ${{ runner.workspace }}/install
           MATRIX_EVAL: ${{ matrix.config.matrix_eval }}
 
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 2c55a1c083..238988a536 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -44,9 +44,6 @@ stages:
             python.version: '3.11'
           Python312:
             python.version: '3.12'
-          Python313:
-            python.version: '3.13'
-
       steps:
 
       # Secure files documentation:
@@ -88,38 +85,34 @@ stages:
     - job: 'MacOSWheels'
       timeoutInMinutes: 60
       pool:
-        vmImage: 'macOS-13'
+        vmImage: 'macOS-12'
       strategy:
         matrix:
           Python38:
             python.version: '3.8'
             python.org.version: '3.8.9'
-            python.installer.name: '3.8.9-macosx10.9.pkg'
+            python.installer.name: 'macosx10.9.pkg'
           Python39:
             python.version: '3.9'
             python.org.version: '3.9.13'
-            python.installer.name: '3.9.13-macos11.pkg'
+            python.installer.name: 'macos11.pkg'
           Python310:
             python.version: '3.10'
             python.org.version: '3.10.11'
-            python.installer.name: '3.10.11-macos11.pkg'
+            python.installer.name: 'macos11.pkg'
           Python311:
             python.version: '3.11'
             python.org.version: '3.11.7'
-            python.installer.name: '3.11.7-macos11.pkg'
+            python.installer.name: 'macos11.pkg'
           Python312:
             python.version: '3.12'
             python.org.version: '3.12.0'
-            python.installer.name: '3.12.0-macos11.pkg'
-          Python313:
-            python.version: '3.13'
-            python.org.version: '3.13.0'
-            python.installer.name: '3.13.0rc3-macos11.pkg'
+            python.installer.name: 'macos11.pkg'
 
       steps:
 
       - script: |
-          installer=python-$(python.installer.name)
+          installer=python-$(python.org.version)-$(python.installer.name)
           url=https://www.python.org/ftp/python/$(python.org.version)/$installer
           curl $url -o $installer
           sudo installer -pkg $installer -target /