Merge remote-tracking branch 'origin/master' into clopath-histentry-doc

nest · Dec 9, 2024 · 234ed64 · 234ed64
2 parents c8db4ea + 94c755d
commit 234ed64
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diff --git a/.github/workflows/build_dispatch.yml b/.github/workflows/build_dispatch.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -41,7 +41,7 @@ jobs:
 
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true

diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true

diff --git a/.github/workflows/ebrains-push.yml b/.github/workflows/ebrains-push.yml
@@ -10,7 +10,7 @@ jobs:
     if: ${{ github.repository_owner == 'nest' }}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true

diff --git a/.github/workflows/hifis-push.yml b/.github/workflows/hifis-push.yml
@@ -10,7 +10,7 @@ jobs:
     if: ${{ github.repository_owner == 'nest' }}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true

diff --git a/.github/workflows/jsc-push.yml b/.github/workflows/jsc-push.yml
@@ -10,7 +10,7 @@ jobs:
     if: ${{ github.repository_owner == 'nest' }}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true

diff --git a/.github/workflows/nestbuildmatrix.yml b/.github/workflows/nestbuildmatrix.yml
@@ -14,7 +14,7 @@ jobs:
       CLANG_FORMAT_FILE: ".clang-format"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -37,7 +37,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -60,7 +60,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -71,7 +71,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -87,7 +87,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -98,7 +98,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -119,7 +119,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -130,7 +130,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -146,7 +146,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -157,7 +157,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -169,7 +169,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -187,7 +187,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -214,7 +214,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -225,7 +225,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -241,7 +241,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -252,7 +252,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -291,7 +291,7 @@ jobs:
   #         name: "build-${{ matrix.os }}-${{ matrix.cpp_compiler }}-${{ matrix.use }}"
 
   #     - name: "Set up Python 3.x"
-  #       uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+  #       uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
   #       with:
   #         python-version: "3.10"
 
@@ -318,7 +318,7 @@ jobs:
   #         fetch-depth: 0
 
   #     - name: "Set up Python 3.x"
-  #       uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+  #       uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
   #       with:
   #         python-version: "3.10"
 
@@ -334,7 +334,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -345,7 +345,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -374,7 +374,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -393,7 +393,7 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -404,7 +404,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -422,7 +422,7 @@ jobs:
     needs: [pydocstyle, rstcheck, vale]
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -433,7 +433,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           # Using 3.8 because Read the docs does not work with higher versions.
           # See also: https://github.com/nest/nest-simulator/pull/2744
@@ -468,7 +468,7 @@ jobs:
     needs: [pydocstyle, rstcheck, vale]
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -531,7 +531,7 @@ jobs:
 
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -542,7 +542,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.10"
 
@@ -746,7 +746,7 @@ jobs:
 
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
           disable-telemetry: true
@@ -757,7 +757,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python 3.x"
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: 3.12
 

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
@@ -31,7 +31,7 @@ jobs:
 
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
         with:
           egress-policy: audit
 

diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
@@ -17,7 +17,7 @@ jobs:
 
     steps:
     - name: Harden Runner
-      uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
+      uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
       with:
         egress-policy: audit
         disable-telemetry: true

diff --git a/.pylintrc b/.pylintrc
@@ -12,3 +12,4 @@ const-naming-style = snake_case
 method-naming-style = PascalCase
 
 max-line-length = 120
+fail-under = 9.98
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
 
 [![Ubuntu version](https://img.shields.io/badge/ubuntu-(PPA)-blue?logo=debian)](https://nest-simulator.readthedocs.io/en/latest/installation/)
 [![Fedora package](https://img.shields.io/fedora/v/nest?logo=fedora)](https://src.fedoraproject.org/rpms/nest)
-[![Conda version](https://img.shields.io/conda/vn/conda-forge/nest-simulator.svg?logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/nest-simulator)
+[![conda-forge version](https://img.shields.io/conda/vn/conda-forge/nest-simulator.svg?logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/nest-simulator)
 [![Homebrew version](https://img.shields.io/homebrew/v/nest.svg?logo=apple)](https://formulae.brew.sh/formula/nest)
 [![Docker Image Version](https://img.shields.io/docker/v/nest/nest-simulator?color=blue&label=docker&logo=docker&logoColor=white&sort=semver)](https://hub.docker.com/r/nest/nest-simulator)
 [![Virtual applicance](https://img.shields.io/badge/VM-v3.7-blue?logo=CodeSandbox)](https://nest-simulator.readthedocs.io/en/latest/installation/livemedia.html#live-media)
@@ -127,5 +127,3 @@ to find out how to install NEST.
 Please cite NEST if you use it in your work.
 
 - You can find all the information for [citing NEST here](https://nest-simulator.readthedocs.io/en/latest/citing-nest.html)
-
-
diff --git a/bin/nest-server-mpi b/bin/nest-server-mpi
@@ -73,4 +73,4 @@ else:
                 continue
 
         log(call_name, f"sending reponse gather, data={response}")
-        comm.gather(nest.serializable(response), root=0)
+        comm.gather(nest.serialize_data(response), root=0)
diff --git a/doc/htmldoc/conf.py b/doc/htmldoc/conf.py
@@ -93,7 +93,7 @@
 copybutton_only_copy_prompt_lines = True
 
 mermaid_output_format = "raw"
-mermaid_version = "10.2.0"
+mermaid_version = "10.3.0"
 
 # disable require js - mermaid doesn't work if require.js is loaded before it
 nbsphinx_requirejs_path = ""

diff --git a/doc/htmldoc/connect_nest/nest_server.rst b/doc/htmldoc/connect_nest/nest_server.rst
@@ -59,11 +59,11 @@ For native installations, the requirements can be simply installed via ``pip``::
 
   pip3 install Flask Flask-Cors gunicorn RestrictedPython
 
-or by installing the full NEST development environment in case you prefer using ``conda``::
+or by installing the full NEST development environment in case you prefer using ``mamba``::
 
   cd <nest-source-dir>
-  conda env create -p conda/
-  conda activate conda/
+  mamba env create -p mamba/
+  mamba activate mamba/
 
 As an alternative to a native installation, NEST Server is available from the NEST Docker image. Please check out the
 corresponding :ref:`installation instructions <docker>` for more details.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -12,3 +12,4 @@ const-naming-style = snake_case
		method-naming-style = PascalCase

		max-line-length = 120
		fail-under = 9.98