From 2a4ad63961a60049a6cbf186a97d86b076c2b53e Mon Sep 17 00:00:00 2001 From: Erik Heeren Date: Mon, 8 Apr 2024 11:24:40 +0200 Subject: [PATCH] Cherry-pick changelog and installer links for 8.2.4 (#2735) --- docs/changelog.md | 52 ++++++++++++++++++++++++++++++++++++----------- docs/index.rst | 21 +++++++++---------- 2 files changed, 50 insertions(+), 23 deletions(-) diff --git a/docs/changelog.md b/docs/changelog.md index ab3b1002c5..0185999a9d 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -1,5 +1,33 @@ # NEURON 8.2 +## 8.2.4 +_Release Date_ : 08-02-2024 + + +### 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 + +### Improvements / Other Changes +- Disabled RXD code in notebook to avoid breaking docs build (see [GitHub Issue #2710](https://github.com/neuronsimulator/nrn/issues/2710)) +- Disabled RXD tests on Windows (see [GitHub Issue #2585](https://github.com/neuronsimulator/nrn/issues/2585)) + + +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 @@ -64,7 +92,7 @@ _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) @@ -76,7 +104,7 @@ _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). @@ -87,7 +115,7 @@ _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++. @@ -102,7 +130,7 @@ _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 @@ -213,7 +241,7 @@ _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 @@ -246,7 +274,7 @@ 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 @@ -270,7 +298,7 @@ _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` @@ -279,7 +307,7 @@ _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 @@ -287,18 +315,18 @@ For the complete list of bug fixes, see the list on the [GitHub here](https://gi - 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. diff --git a/docs/index.rst b/docs/index.rst index 00d8791a9e..06b1a34a9e 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -5,10 +5,10 @@ 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 `, +Build and simulate models using Python, HOC, and/or NEURON's graphical interface. From this page you can watch :ref:`recorded NEURON classes `, read the :ref:`Python ` or :ref:`HOC ` programmer's references, `browse the NEURON forum `_, -explore the `source code for over 800 NEURON models on ModelDB `_, +explore the `source code for over 800 NEURON models on ModelDB `_, and more (use the links on the side or search). .. toctree:: @@ -31,7 +31,7 @@ and more (use the links on the side or search). The NEURON forum publications publications-using-neuron - + .. toctree:: @@ -97,8 +97,8 @@ Installation .. code:: pip3 install neuron - - Alternatively, you can use the `PKG installer `_. + + Alternatively, you can use the `PKG installer `_. For troubleshooting, see the `detailed installation instructions `_. @@ -110,19 +110,18 @@ Installation .. code:: pip3 install neuron - For troubleshooting, see the `detailed installation instructions `_. .. tab-item:: Windows - `Download the Windows Installer `_. + `Download the Windows Installer `_. You can also install the Linux wheel via the Windows Subsystem for Linux (WSL). See `instructions `_. For troubleshooting, see the `detailed installation instructions `_. - + .. tab-item:: Cloud On `Google Colab `_ and many other cloud Jupyter providers, you can install @@ -131,10 +130,10 @@ Installation .. code:: !pip install neuron - + NEURON is already installed on `The Neuroscience Gateway `_ and on `EBRAINS `_. - + .. tab-item:: Source code View and suggest changes to the source code at: @@ -168,7 +167,7 @@ Installation nav("userAgent", "Windows"); nav("platform", "Win", "Windows"); nav("oscpu", "Windows"); - + if (osName == "MacOS") { $("#installation input")[0].checked = true; } else if (osName == "Linux") {