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Modifications for automatic packaging on github (#494)
* Modifications for automatic packaging on github * Added changelog * Fixes for NeuroML2 reader - Exponential operator '^' in neurml2 expressions replaced by '**' - Corrected voltage and ca dependency checks - Added scalar check for result of expression evaluation - in some cases it can be actually a constant expression evaluating to a scalar * Fixed an error with SBML reading. * github hosted runner for MacOS - fix for pkgconfig Looks like github fixed the issue with pkg-config, so earlier workaround now causing error * Updated AUTHORS
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‎.github/workflows/package.yml

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name: Python package
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on: [push]
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jobs:
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build_wheel:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-14, windows-latest]
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build_type: [Release]
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c_compiler: [clang]
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python-version: ['3.11']
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# python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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- name: Install cibuildwheel
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run: python -m pip install cibuildwheel==2.21.3
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- name: MacOS dpendencies
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if: ${{ runner.os == 'macOS' }}
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run: |
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brew install gsl
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brew install hdf5
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- name: Windows dependencies
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if: ${{ runner.os == 'Windows' }}
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uses: mamba-org/setup-micromamba@v1
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with:
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environment-name: moose
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cache-environment: true
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cache-downloads: true
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create-args: >-
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python=${{ matrix.python-version }}
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pkg-config
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clang
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hdf5
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pybind11[global]
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graphviz
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pytables
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numpy
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matplotlib
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vpython
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lxml
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doxygen
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setuptools
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wheel
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meson
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ninja
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meson-python
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gsl
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cibuildwheel
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post-cleanup: all
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generate-run-shell: false
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- name: Linux package
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if: runner.os == 'Linux'
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env:
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CIBW_BUILD_VERBOSITY: 1
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CIBW_BEFORE_ALL: 'uname -a'
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CIBW_BEFORE_ALL_LINUX: >
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yum install -y epel-release &&
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yum install -y pkgconfig &&
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yum install -y gsl-devel &&
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yum install -y hdf5-devel
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CIBW_BUILD: '*-manylinux_x86_64'
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CIBW_SKIP: 'pp*'
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CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
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CIBW_MANYLINUX_PYPY_X86_64_IMAGE: manylinux_2_28
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run: |
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python -m cibuildwheel --output-dir wheelhouse
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ls wheelhouse
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- name: MacOS package
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if: runner.os == 'macOS'
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env:
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CIBW_BUILD_VERBOSITY: 1
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CIBW_BEFORE_ALL: 'uname -a'
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CIBW_BEFORE_ALL_MACOS: >
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brew uninstall pkg-config || :
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brew uninstall pkg-config@0.29.2 || :
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brew install gsl hdf5 meson ninja cmake &&
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export PKG_CONFIG=`which pkg-config` &&
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echo "<<<<<<<<<#########################################>>>>>>>>>>" &&
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echo "$$$$$ `pkg-config --libs gsl`" &&
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echo "@@@@@ `pkg-config --cflags gsl`"
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CIBW_ARCHS: 'arm64'
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CIBW_BUILD: '*-macosx_arm64'
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CIBW_SKIP: 'pp* cp38*'
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run: |
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export "MACOSX_DEPLOYMENT_TARGET=$(echo ${{ matrix.os }} | cut -c 7-8).0" # required because gsl2.8 has minimum target of 14.0
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python -m cibuildwheel --output-dir wheelhouse
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ls wheelhouse
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- name: Windows package
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if: runner.os == 'Windows'
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env:
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CIBW_BEFORE_ALL: 'uname -a'
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CIBW_BUILD: '*-win_*'
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CIBW_SKIP: '*-win32 pp*'
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run: |
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micromamba shell hook -s powershell | Out-String | Invoke-Expression
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micromamba activate moose
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python -m cibuildwheel --output-dir wheelhouse
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dir wheelhouse
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- name: Upload packages
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uses: xresloader/upload-to-github-release@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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file: "wheelhouse/pymoose*.whl"

‎.github/workflows/pymoose.yml

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name: Python package
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name: Build install test
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on: [push]
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-14, windows-latest]
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os: [ubuntu-22.04, macos-14, windows-latest]
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build_type: [Release]
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c_compiler: [clang]
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python-version: ["3.12"]
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include:
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- os: ubuntu-latest
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- os: ubuntu-22.04
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apt: 10
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- os: macos-14
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brew: 20
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python -c "import sys; print(sys.version)"
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- if: ${{ matrix.apt }}
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run: |
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sudo apt-get -y install libhdf5-dev libgsl0-dev graphviz-dev python3-lxml doxygen libgsl-dev
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sudo apt-get update
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sudo apt-get -y install libgsl0-dev libgsl-dev libhdf5-dev
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- if: ${{ matrix.brew }}
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run: |
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brew install gsl
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brew install hdf5
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brew install graphviz
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brew install doxygen
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- name: checkout
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uses: actions/checkout@v4
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- name: build and install (non-windows)
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- name: Build and install (non-windows)
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if: runner.os != 'Windows'
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run: |
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eval "$(micromamba shell hook --shell bash)"
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pip install python-libsbml
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pip install .
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python -c "import moose; moose.le()"
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- name: build and install (windows)
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- name: Build and install (windows)
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if: runner.os == 'Windows'
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run: |
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micromamba shell hook -s powershell | Out-String | Invoke-Expression

‎AUTHORS

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Upinder S. Bhalla Primary Architect, rdesigneur
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HarshaRani. G.V MOOSE Website, SBML support, GUI
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Dilawar Singh Multithreading, GSoC, Packaging, Maintenance, BOOST solvers
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Subhasis Ray Lead Developer, Python interface, Packaging, Maintenance
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# Past developers
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Subhasis Ray Python interface, GUI
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Dilawar Singh Multithreading, GSoC, Packaging, Maintenance, BOOST solvers
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Niraj Dudani Neuronal solver
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Aditya Gilra NeuroML support
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Aviral Goel Moogli

‎AppleM1_Guide.md renamed to ‎AppleM1Build.md

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# Building MOOSE on MacOS with Apple M1 CPU
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- Install homebrew: https://brew.sh/
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- Set up required development environment
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- Install command line tools for XCode
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- Install build dependencies by running these commands in a terminal
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```
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brew install gsl
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brew install hdf5
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brew install graphviz
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brew install cmake
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brew install doxygen
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```
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- Install anaconda/miniconda/micromamba/miniforge. For example, for micromamba, run
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- Restart terminal and create an environment with necessary packages:
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```
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micromamba create -n moose hdf5 graphviz pytables numpy matplotlib vpython lxml doxygen setuptools wheel pybind11[global]
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micromamba create -n moose numpy matplotlib vpython lxml meson ninja meson-python gsl setuptools pybind11[global] pkg-config -c conda-forge
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```
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- Activate the moose environment: `micromamba activate moose`
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- Install libsbml: `pip install python-libsbml`
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- Install moose from github: `pip install git+https://github.com/BhallaLab/moose-core.git`

‎CHANGELOG.md

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# Changelog
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*See https://keepachangelog.com/en/1.0.0/ for how to maintain changelog*
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## Unreleased
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*Unreleased changes go here*
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## [4.1.0] - 2024-11-28
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Jhangri
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### Added
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- Support for 2D HHGate/HHChannel in NeuroML reader
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- Native binaries for Windows
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### Fixed
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- Updated to conform to c/c++-17 standard
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### Changed
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- `HHGate2D`: separate `xminA`, `xminB`, etc. for `A` and `B` tables
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replaced by single `xmin`, `xmax`, `xdivs`, `ymin`, `ymax`, and
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`ydivs` fields for both tables.
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- Build system switched from `cmake` to `meson`
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### Removed
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- Temporarily removed NSDF support due to issues with finding HDF5 in
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a platform independent manner.
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## [4.0.0] - 2022-04-15
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Jalebi
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### Added
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- Addition of a thread-safe and faster parser based on ExprTK
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### Changed
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- A major under-the-hood change to numerics for chemical calculations,
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eliminating the use of 'zombie' objects for the solvers. This
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simplifies and cleans up the code and object access, but doesn't
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alter runtimes.
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- Another major under-the-hood change to use pybind11 as a much
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cleaner way to interface the parser with the C++ numerical code.
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- Resurrected objects for handling simulation output saving using HDF5
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format. There is an HDFWriter class, an NSDFWriter, and a new
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NSDFWriter2. The latter two implement storage in NSDF, Neuronal
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Simulation Data Format, Ray et al Neuroinformatics 2016. NSDF is
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built on HDF5 and builds up a specification designed to ensure ready
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replicability as well as self- description of model output.
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- Multiple enhancements to rdesigneur, including vastly improved 3-D
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graphics output using VPython.
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### Fixed
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- Various bugfixes
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