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C.A.P. Linssen
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Merge remote-tracking branch 'origin/master' into clopath-histentry-doc
2 parents c8db4ea + 94c755d commit 234ed64

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.github/workflows/build_dispatch.yml

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runs-on: ubuntu-latest
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- name: Harden Runner
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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.github/workflows/codeql.yml

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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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.github/workflows/dependency-review.yml

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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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.github/workflows/ebrains-push.yml

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if: ${{ github.repository_owner == 'nest' }}
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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.github/workflows/hifis-push.yml

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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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.github/workflows/jsc-push.yml

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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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.github/workflows/nestbuildmatrix.yml

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CLANG_FORMAT_FILE: ".clang-format"
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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runs-on: "ubuntu-22.04"
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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runs-on: "ubuntu-22.04"
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- name: Harden Runner
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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- name: "Set up Python 3.x"
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uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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- name: "Set up Python 3.x"
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uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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# uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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# uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
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uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
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.github/workflows/scorecards.yml

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.github/workflows/stale.yml

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.pylintrc

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README.md

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[![Ubuntu version](https://img.shields.io/badge/ubuntu-(PPA)-blue?logo=debian)](https://nest-simulator.readthedocs.io/en/latest/installation/)
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[![Fedora package](https://img.shields.io/fedora/v/nest?logo=fedora)](https://src.fedoraproject.org/rpms/nest)
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[![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)
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[![Homebrew version](https://img.shields.io/homebrew/v/nest.svg?logo=apple)](https://formulae.brew.sh/formula/nest)
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[![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)
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@@ -127,5 +127,3 @@ to find out how to install NEST.
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doc/htmldoc/conf.py

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doc/htmldoc/connect_nest/nest_server.rst

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or by installing the full NEST development environment in case you prefer using ``conda``::
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or by installing the full NEST development environment in case you prefer using ``mamba``::
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conda env create -p conda/
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conda activate conda/
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mamba env create -p mamba/
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mamba activate mamba/
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As an alternative to a native installation, NEST Server is available from the NEST Docker image. Please check out the
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corresponding :ref:`installation instructions <docker>` for more details.

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