Merge branch 'eprop_bio_feature' into remove-irregular-spike-arrival

JesusEV · May 15, 2024 · 643ddbf · 643ddbf
2 parents 792675d + 9c0df80
commit 643ddbf
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diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -47,11 +47,11 @@ jobs:
           disable-telemetry: true
 
       - name: Checkout repository
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@3ab4101902695724f9365a384f86c1074d94e18c # v3.24.7
+        uses: github/codeql-action/init@05963f47d870e2cb19a537396c1f668a348c7d8f # v3.24.8
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -61,7 +61,7 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild
-        uses: github/codeql-action/autobuild@3ab4101902695724f9365a384f86c1074d94e18c # v3.24.7
+        uses: github/codeql-action/autobuild@05963f47d870e2cb19a537396c1f668a348c7d8f # v3.24.8
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -74,6 +74,6 @@ jobs:
       #   ./location_of_script_within_repo/buildscript.sh
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@3ab4101902695724f9365a384f86c1074d94e18c # v3.24.7
+        uses: github/codeql-action/analyze@05963f47d870e2cb19a537396c1f668a348c7d8f # v3.24.8
         with:
           category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -23,6 +23,6 @@ jobs:
           disable-telemetry: true
 
       - name: 'Checkout Repository'
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
       - name: 'Dependency Review'
         uses: actions/dependency-review-action@9129d7d40b8c12c1ed0f60400d00c92d437adcce # v4.1.3
diff --git a/.github/workflows/nestbuildmatrix.yml b/.github/workflows/nestbuildmatrix.yml
@@ -20,7 +20,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -43,7 +43,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -66,7 +66,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -93,7 +93,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -125,7 +125,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -152,7 +152,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -175,7 +175,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -193,7 +193,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -220,7 +220,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -247,7 +247,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -313,7 +313,7 @@ jobs:
   #   needs: [build_macos]
   #   steps:
   #     - name: "Checkout repository content"
-  #       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+  #       uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
   #       with:
   #         fetch-depth: 0
 
@@ -340,7 +340,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -361,7 +361,7 @@ jobs:
     runs-on: "ubuntu-20.04"
     steps:
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -380,7 +380,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -399,7 +399,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -428,7 +428,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -474,7 +474,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -527,7 +527,7 @@ jobs:
           - "boost, optimize, warning"
           - "openmp, python, gsl, ltdl, boost, optimize, warning"
           - "mpi, python, gsl, ltdl, boost, optimize, warning"
-          - "openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning"
+          - "openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning, music"
 
     steps:
       - name: Harden Runner
@@ -537,7 +537,7 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
@@ -547,7 +547,7 @@ jobs:
           python-version: 3.9
 
       - name: "Restore apt cache"
-        uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # v4.0.1
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         env:
           cache-name: "apt-cache"
         with:
@@ -588,7 +588,7 @@ jobs:
         # source (hashed), compiler (mtime+size) and compile flags.
         env:
           cache-name: "ccache"
-        uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # v4.0.1
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: |
             $HOME/.ccache
@@ -604,7 +604,7 @@ jobs:
       - name: "Restore pip cache"
         env:
           cache-name: "pip-cache"
-        uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # v4.0.1
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: |
             /opt/hostedtoolcache/Python/**/site-packages/*
@@ -678,14 +678,23 @@ jobs:
               -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
               -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
               -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
+              -Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' || 'OFF' }} \
               ..
 
+      - name: "Add GCC problem matcher"
+        run: |
+          echo "::add-matcher::gcc_problem_matcher.json"
+
       - name: "Build NEST"
         run: |
           cd "$NEST_VPATH"
           env
           make VERBOSE=1
 
+      - name: "Remove GCC problem matcher"
+        run: |
+          echo "::remove-matcher owner=gcc-problem-matcher::"
+
       - name: "Install NEST"
         run: |
           cd "$NEST_VPATH"
@@ -742,14 +751,14 @@ jobs:
           disable-telemetry: true
 
       - name: "Checkout repository content"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
         with:
-          python-version: 3.9
+          python-version: 3.12
 
       - name: "Install MacOS system dependencies"
         run: |
@@ -758,7 +767,7 @@ jobs:
       - name: "Restore pip cache"
         env:
           cache-name: "pip-cache"
-        uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # v4.0.1
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
         with:
           path: |
             /opt/hostedtoolcache/Python/**/site-packages/*
@@ -798,14 +807,23 @@ jobs:
               -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
               -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
               -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
+              -Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' || 'OFF' }} \
               ..
 
+      - name: "Add GCC problem matcher"
+        run: |
+          echo "::add-matcher::gcc_problem_matcher.json"
+
       - name: "Build NEST"
         run: |
           cd "$NEST_VPATH"
           env
           make VERBOSE=1
 
+      - name: "Remove GCC problem matcher"
+        run: |
+          echo "::remove-matcher owner=gcc-problem-matcher::"
+
       - name: "Install NEST"
         run: |
           cd "$NEST_VPATH"

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
@@ -36,7 +36,7 @@ jobs:
           egress-policy: audit
 
       - name: "Checkout code"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           persist-credentials: false
 
@@ -71,6 +71,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@3ab4101902695724f9365a384f86c1074d94e18c # v3.24.7
+        uses: github/codeql-action/upload-sarif@05963f47d870e2cb19a537396c1f668a348c7d8f # v3.24.8
         with:
           sarif_file: results.sarif
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![Documentation](https://img.shields.io/readthedocs/nest-simulator?logo=readthedocs&logo=Read%20the%20Docs&label=Documentation)](https://nest-simulator.org/documentation)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/2218/badge)](https://bestpractices.coreinfrastructure.org/projects/2218)
 [![License](http://img.shields.io/:license-GPLv2+-green.svg)](http://www.gnu.org/licenses/gpl-2.0.html)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8069926.svg)](https://doi.org/10.5281/zenodo.8069926)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10834751.svg)](https://doi.org/10.5281/zenodo.10834751)
 
 [![Latest release](https://img.shields.io/github/release/nest/nest-simulator.svg?color=brightgreen&label=latest%20release)](https://github.com/nest/nest-simulator/releases)
 [![GitHub contributors](https://img.shields.io/github/contributors/nest/nest-simulator?logo=github)](https://github.com/nest/nest-simulator)

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-3.6.0-post0.dev0
+3.7.0-post0.dev0
diff --git a/cmake/ProcessOptions.cmake b/cmake/ProcessOptions.cmake
@@ -420,7 +420,11 @@ endfunction()
 function( NEST_PROCESS_WITH_MPI )
   # Find MPI
   set( HAVE_MPI OFF PARENT_SCOPE )
-  if ( with-mpi )
+  if ( NOT "${with-mpi}" STREQUAL "OFF" )
+    if ( NOT ${with-mpi} STREQUAL "ON" )
+      # if set, use this prefix
+      set( MPI_ROOT "${with-mpi}" )
+    endif ()
     find_package( MPI REQUIRED )
     if ( MPI_CXX_FOUND )
       set( HAVE_MPI ON PARENT_SCOPE )
@@ -649,7 +653,7 @@ function( NEST_PROCESS_WITH_MPI4PY )
 endfunction ()
 
 function( NEST_PROCESS_USERDOC )
-  if ( with-userdoc )
+  if ( ${with-userdoc} STREQUAL "ON")
     message( STATUS "Configuring user documentation" )
     find_package( Sphinx REQUIRED)
     find_package( Pandoc REQUIRED)
@@ -660,7 +664,7 @@ function( NEST_PROCESS_USERDOC )
 endfunction ()
 
 function( NEST_PROCESS_DEVDOC )
-  if ( with-devdoc )
+  if ( ${with-devdoc} STREQUAL "ON" )
     message( STATUS "Configuring developer documentation" )
     find_package( Doxygen REQUIRED dot )
     set( BUILD_DOXYGEN_DOCS ON PARENT_SCOPE )
@@ -669,7 +673,7 @@ function( NEST_PROCESS_DEVDOC )
 endfunction ()
 
 function( NEST_PROCESS_FULL_LOGGING )
-  if ( with-full-logging )
+  if ( ${with-full-logging} STREQUAL "ON" )
     message( STATUS "Configuring full logging" )
     set( ENABLE_FULL_LOGGING ON PARENT_SCOPE )
   endif ()