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* Changelog: 8.2.4
* Update installer links in index.rst
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heerener committed Feb 6, 2024
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48 changes: 36 additions & 12 deletions docs/changelog.md
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# NEURON 8.2

## 8.2.4
_Release Date_ : 06-02-2024


### What's New

This release brings no new features, just bugfixes and minor improvements.


### Bug Fixes
- Python 3.12 compatibility fixes
- replace distutils with setuptools
- fix segfault on exit
- updates to CI
- move from MacOS 11 to MacOS 12
- add MUSIC
- bugfix for coverage CI
- small bugfix for edge case in RX3D
- unified setup.py
- misc cmake improvements


For the complete list of commits check [GitHub Issue #2700](https://github.com/neuronsimulator/nrn/issues/2700)

## 8.2.3
_Release Date_ : 15-09-2023

Expand Down Expand Up @@ -64,7 +88,7 @@ _Release Date_ : 12-08-2022
- Documentation
- added new INCF/CNS 2022 online material (#1932)
- updates (dealing with sims, generating movie, modelview, more #1925 )
- transfer from Yale website (#1867)
- transfer from Yale website (#1867)
- nrnmpi_load: drop printf for already loaded lib (#1938)

For the complete list of commits, see the list in [GitHub Issue #1944](https://github.com/neuronsimulator/nrn/issues/1944)
Expand All @@ -76,7 +100,7 @@ _Release Date_ : 01-07-2022
* Allow multiple BEFORE/AFTER blocks of same type in a MOD file. #1722
* Several documentation updates, including randomness in NEURON models #1727,
NEURON course exercise sets from 2018 #1735 and publications using NEURON #1819.
* CMake: improved documentation targets. (#1725)
* CMake: improved documentation targets. (#1725)

### Breaking Changes
* Support for Python 3.6 was dropped, as it has reached end-of-life (#1733).
Expand All @@ -87,7 +111,7 @@ _Release Date_ : 01-07-2022
* Declaring STATE variables as GLOBAL is now disallowed. (#1723)

### Deprecations & future changes
* NEURON is in the process of being fully migrated to a `C++` codebase.
* NEURON is in the process of being fully migrated to a `C++` codebase.
Starting with next major release `9.0.0`, `MOD` files will be converted to `C++` instead of `C`.
This will break compatibility with some legacy MOD files containing VERBATIM blocks and code may have to be updated
given that some valid C code is not valid C++.
Expand All @@ -102,7 +126,7 @@ _Release Date_ : 01-07-2022

### Improvements / Other Changes
* Support for using `mallinfo2()` (#1805)
* HOC domain for Sphinx `5.0.1`
* HOC domain for Sphinx `5.0.1`

### Upgrade Steps
* If your MOD files contain VERBATIM blocks you may need to refer to the aforementioned
Expand Down Expand Up @@ -213,7 +237,7 @@ _Release Date_ : 25-03-2022
* Internal API for saving/restoring 3D voxelization (#1476)
* Prevent RxD keeping objects alive (#1270, #1103, #1072)
* Improved assignment of 3D voxels to segments (#1149)

### Upgrade Steps
* Linux wheels are now `manylinux2014`: upgrade your `pip`
* Legacy internal `readline` source code is removed: install `readline` on your system
Expand Down Expand Up @@ -246,7 +270,7 @@ For the complete list of bug fixes, see the list in [GitHub PR #1603](https://gi

### Improvements / Other Changes

- Introduce a Sphinx HOC domain for NEURON documentation
- Introduce a Sphinx HOC domain for NEURON documentation


## 8.0.0
Expand All @@ -270,7 +294,7 @@ _Release Date_ : 30-04-2021
- For 3d reaction-diffusion simulations, the voxelization and segment mapping algorithms have been adjusted, especially around the soma. Voxel indices and sometimes counts will change from previous versions.

### Deprecations
- Five functions in the `neuron` module: `neuron.init`, `neuron.run`, `neuron.psection`, `neuron.xopen`, and `neuron.quit`.
- Five functions in the `neuron` module: `neuron.init`, `neuron.run`, `neuron.psection`, `neuron.xopen`, and `neuron.quit`.
- Autotools build is deprecated and will be removed in the next release. Use CMake instead.
- Python 2 and Python 3.5 support is deprecated and will be removed in the next release. Use `Python >= 3.6`

Expand All @@ -279,26 +303,26 @@ _Release Date_ : 30-04-2021
For the complete list of bug fixes, see the list on the [GitHub here](https://github.com/neuronsimulator/nrn/issues/1211#issuecomment-826919173).

### Improvements / Other Changes
- Allow for two point (single section) SWC somas
- Allow for two point (single section) SWC somas
- GitHub Actions and Azure as primary CI systems. Travis CI removed.
- GitHub [Releases](https://github.com/neuronsimulator/nrn/releases) provides full source tarballs, binary installers and python wheels.
- Improved testing and CI infrastructure including GPUs
- [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci) repository test nightly builds for Ubuntu 18.04, Ubuntu 20.04, Fedora 32, Fedora 33, CentOS7, CentOS8, Debian Buster (10) and macOS 10.15 platforms.
- Improved integration of CoreNEURON
- Support for recent numpy version
- Various build improvements on Linux, MacOS and HPC platforms
- Documentation from various repositories is consolidated under `nrn` repository
- New releases via Spack and Easybuild package managers
- Documentation from various repositories is consolidated under `nrn` repository
- New releases via Spack and Easybuild package managers
- Fix deadlock when compiling NEURON with AVX-512
- Add backward-cpp for better backtraces
- NEURON_MODULE_OPTIONS environment variable to pass in nrniv options before `neuron import`
- NEURON_MODULE_OPTIONS environment variable to pass in nrniv options before `neuron import`

### Upgrade Steps

Existing models should work without any changes. In order to upgrade NEURON version you can:
- Use python wheels provided for Linux or Mac OS platform
- Use binary installer provided for windows
- Install from source, preferably using CMake build system
- Install from source, preferably using CMake build system
- For new version, it's always a good idea to start over from scratch with nrnivmodl (deleting existing directory like `x86_64`)

See `Installation` section under [nrn.readthedocs.io/](nrn.readthedocs.io/). In the very rare case that numerical differences exist, check selection of legacy vs modern units.
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20 changes: 10 additions & 10 deletions docs/index.rst
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Expand Up @@ -5,7 +5,7 @@ The NEURON Simulator
====================

NEURON is a simulator for neurons and networks of neurons that runs efficiently on your local machine, in the cloud, or on an HPC.
Build and simulate models using Python, HOC, and/or NEURON's graphical interface. From this page you can watch :ref:`recorded NEURON classes <training_videos>`,
Build and simulate models using Python, HOC, and/or NEURON's graphical interface. From this page you can watch :ref:`recorded NEURON classes <training_videos>`,
read the :ref:`Python <python_prog_ref>` or :ref:`HOC <hoc_prog_ref>` programmer's references,
`browse the NEURON forum <https://www.neuron.yale.edu/phpBB/>`_,
explore the `source code for over 750 NEURON models on ModelDB <https://senselab.med.yale.edu/ModelDB/ModelList?id=1882&allsimu=true>`_, and more (use the links on the side or search).
Expand All @@ -30,7 +30,7 @@ explore the `source code for over 750 NEURON models on ModelDB <https://senselab
The NEURON forum <https://neuron.yale.edu/phpBB>
publications
publications-using-neuron



.. toctree::
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.. code::
pip3 install neuron
Alternatively, you can use the `PKG installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.3/nrn-8.2.3-macosx-10.9-universal2-py-38-39-310-311.pkg>`_.
Alternatively, you can use the `PKG installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.4/nrn-8.2.4-macosx-10.9-universal2-py-38-39-310-311.pkg>`_.

For troubleshooting, see the `detailed installation instructions <install/install_instructions.html>`_.

Expand All @@ -100,19 +100,19 @@ Installation
.. code::
pip3 install neuron
For troubleshooting, see the `detailed installation instructions <install/install_instructions.html>`_.


.. tab-item:: Windows

`Download the Windows Installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.3/nrn-8.2.3.w64-mingw-py-37-38-39-310-311-setup.exe>`_.
`Download the Windows Installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.4/nrn-8.2.4.w64-mingw-py-37-38-39-310-311-setup.exe>`_.

You can also install the Linux wheel via the Windows Subsystem for Linux (WSL). See `instructions <install/install_instructions.html#windows-subsystem-for-linux-wsl-python-wheel>`_.

For troubleshooting, see the `detailed installation instructions <install/install_instructions.html>`_.


.. tab-item:: Cloud

On `Google Colab <https://colab.research.google.com>`_ and many other cloud Jupyter providers, you can install
Expand All @@ -121,10 +121,10 @@ Installation
.. code::
!pip install neuron
NEURON is already installed on `The Neuroscience Gateway <https://www.nsgportal.org>`_
and on `EBRAINS <https://ebrains.eu>`_.

.. tab-item:: Source code

View and suggest changes to the source code at:
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nav("userAgent", "Windows");
nav("platform", "Win", "Windows");
nav("oscpu", "Windows");
if (osName == "MacOS") {
$("#installation input")[0].checked = true;
} else if (osName == "Linux") {
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