diff --git a/includes/data/software.yml b/includes/data/software.yml
index 7ec216959..921af9b02 100644
--- a/includes/data/software.yml
+++ b/includes/data/software.yml
@@ -2534,6 +2534,21 @@ software_modules:
versions:
- {description: tinygrad is a deep learning framework that aims to provide a
balance between simplicity and functionality., markedDefault: false, versionName: 0.8.0_py312}
+ - categories: math, numerical library
+ defaultVersionName: 6.0.4
+ description: Software package and libraries for sequential and parallel graph
+ partitioning, static mapping and clustering, sequential mesh and hypergraph
+ partitioning, and sequential and parallel sparse matrix block ordering.
+ package: scotch
+ url: http://www.labri.fr/perso/pelegrin/scotch
+ versions:
+ - description: Software package and libraries for sequential and parallel graph
+ partitioning, static mapping and clustering, sequential mesh and hypergraph
+ partitioning, and sequential and parallel sparse matrix block ordering.
+ markedDefault: false
+ properties:
+ parallel: {mpi: 1}
+ versionName: 6.0.4
- categories: math, statistics
defaultVersionName: 3.1.4_py39
description: The Python ensemble sampling toolkit for affine-invariant MCMC
@@ -2603,18 +2618,17 @@ software_modules:
arch: {gpu: 1}
parallel: {mpi: 1}
versionName: 0.12.1_py27
- - categories: math, deep learning
- defaultVersionName: 1.8_py27
- description: TensorboardX is TensorBoard™ for PyTorch (and Chainer, MXNet, NumPy...)
- package: py-tensorboardx
- url: https://tensorboardx.readthedocs.io
+ - categories: math, linear algebra
+ defaultVersionName: 8.200.1
+ description: Armadillo is a high quality linear algebra library (matrix maths)
+ for the C++ language, aiming towards a good balance between speed and ease
+ of use.
+ package: armadillo
+ url: http://arma.sourceforge.net/
versions:
- - description: TensorboardX is TensorBoard™ for PyTorch (and Chainer, MXNet,
- NumPy...)
- markedDefault: false
- properties:
- arch: {gpu: 1}
- versionName: 1.8_py27
+ - {description: 'Armadillo is a high quality linear algebra library (matrix
+ maths) for the C++ language, aiming towards a good balance between speed
+ and ease of use.', markedDefault: false, versionName: 8.200.1}
- categories: math, machine learning
defaultVersionName: 0.19.1_py27
description: Scikit-learn is a free software machine learning library for the
@@ -2658,6 +2672,45 @@ software_modules:
properties:
arch: {gpu: 1}
versionName: 2.6.3_py312
+ - categories: math, deep learning
+ defaultVersionName: 1.8_py27
+ description: TensorboardX is TensorBoard™ for PyTorch (and Chainer, MXNet, NumPy...)
+ package: py-tensorboardx
+ url: https://tensorboardx.readthedocs.io
+ versions:
+ - description: TensorboardX is TensorBoard™ for PyTorch (and Chainer, MXNet,
+ NumPy...)
+ markedDefault: false
+ properties:
+ arch: {gpu: 1}
+ versionName: 1.8_py27
+ - categories: math, deep learning
+ defaultVersionName: 10.0.1_py312
+ description: Python bindings for the TensorRT library.
+ package: py-tensorrt
+ url: https://developer.nvidia.com/tensorrt
+ versions:
+ - description: Python bindings for the TensorRT library.
+ markedDefault: false
+ properties:
+ arch: {gpu: 1}
+ versionName: 8.5.1.7_py39
+ - description: Python bindings for the TensorRT library.
+ markedDefault: false
+ properties:
+ arch: {gpu: 1}
+ versionName: 10.0.1_py312
+ - categories: math, numerical library
+ defaultVersionName: 1.4.1
+ description: 'harminv is a program designed to solve the problem of harmonic
+ inversion: given a time series consisting of a sum of sinusoids (modes), extract
+ their frequencies and amplitudes.'
+ package: harminv
+ url: https://github.com/stevengj/harminv
+ versions:
+ - {description: 'harminv is a program designed to solve the problem of harmonic
+ inversion: given a time series consisting of a sum of sinusoids (modes),
+ extract their frequencies and amplitudes.', markedDefault: false, versionName: 1.4.1}
- categories: math, numerical library
defaultVersionName: 1.14.3_py27
description: NumPy is the fundamental package for scientific computing with
@@ -2681,38 +2734,6 @@ software_modules:
Python., markedDefault: false, versionName: 1.26.3_py312}
- {description: NumPy is the fundamental package for scientific computing with
Python., markedDefault: true, versionName: 1.14.3_py27}
- - categories: math, optimization
- defaultVersionName: 2.10.0_py39
- description: Optuna is an automatic hyperparameter optimization software framework,
- particularly designed for machine learning.
- package: py-optuna
- url: https://optuna.readthedocs.io/
- versions:
- - {description: 'Optuna is an automatic hyperparameter optimization software
- framework, particularly designed for machine learning.', markedDefault: false,
- versionName: 2.10.0_py39}
- - categories: math, numerical library
- defaultVersionName: 1.4.1
- description: 'harminv is a program designed to solve the problem of harmonic
- inversion: given a time series consisting of a sum of sinusoids (modes), extract
- their frequencies and amplitudes.'
- package: harminv
- url: https://github.com/stevengj/harminv
- versions:
- - {description: 'harminv is a program designed to solve the problem of harmonic
- inversion: given a time series consisting of a sum of sinusoids (modes),
- extract their frequencies and amplitudes.', markedDefault: false, versionName: 1.4.1}
- - categories: math, linear algebra
- defaultVersionName: 8.200.1
- description: Armadillo is a high quality linear algebra library (matrix maths)
- for the C++ language, aiming towards a good balance between speed and ease
- of use.
- package: armadillo
- url: http://arma.sourceforge.net/
- versions:
- - {description: 'Armadillo is a high quality linear algebra library (matrix
- maths) for the C++ language, aiming towards a good balance between speed
- and ease of use.', markedDefault: false, versionName: 8.200.1}
- categories: math, numerical library
defaultVersionName: 5.1.0
description: METIS is a set of serial programs for partitioning graphs, partitioning
@@ -2790,13 +2811,19 @@ software_modules:
properties:
arch: {gpu: 1}
versionName: 2.1.0_py36
- - categories: math, numerical library
- defaultVersionName: 3.18.2_py39
- description: Python bindings for SLEPc.
- package: py-slepc4py
- url: https://slepc.upv.es/
+ - categories: math, deep learning
+ defaultVersionName: '20180202'
+ description: Torch is a scientific computing framework with wide support for
+ machine learning algorithms that puts GPUs first.
+ package: torch
+ url: http://torch.ch
versions:
- - {description: Python bindings for SLEPc., markedDefault: false, versionName: 3.18.2_py39}
+ - description: Torch is a scientific computing framework with wide support for
+ machine learning algorithms that puts GPUs first.
+ markedDefault: false
+ properties:
+ arch: {gpu: 1}
+ versionName: '20180202'
- categories: math, machine learning
defaultVersionName: 0.29.3_py312
description: Huggingface Accelerate is a library that enables the same PyTorch
@@ -2820,19 +2847,19 @@ software_modules:
- {description: LIBXSMM is a library for small dense and small sparse matrix-matrix
multiplications as well as for deep learning primitives such as small convolutions,
markedDefault: false, versionName: '1.17'}
- - categories: math, deep learning
- defaultVersionName: '20180202'
- description: Torch is a scientific computing framework with wide support for
- machine learning algorithms that puts GPUs first.
- package: torch
- url: http://torch.ch
+ - categories: math, statistics
+ defaultVersionName: 2022.02.2-485
+ description: RStudio is an integrated development environment (IDE) for R. It
+ includes a console, syntax-highlighting editor that supports direct code execution,
+ as well as tools for plotting, history, debugging and workspace management.
+ This is the X11/GUI version.
+ package: rstudio-desktop
+ url: http://www.rstudio.com
versions:
- - description: Torch is a scientific computing framework with wide support for
- machine learning algorithms that puts GPUs first.
- markedDefault: false
- properties:
- arch: {gpu: 1}
- versionName: '20180202'
+ - {description: 'RStudio is an integrated development environment (IDE) for
+ R. It includes a console, syntax-highlighting editor that supports direct
+ code execution, as well as tools for plotting, history, debugging and workspace
+ management. This is the X11/GUI version.', markedDefault: false, versionName: 2022.02.2-485}
- categories: math, statistics
defaultVersionName: 2.9.2_py36
description: rpy2 is an interface to R running embedded in a Python process.
@@ -2851,49 +2878,6 @@ software_modules:
versions:
- {description: Efficient matrix representations for working with tabular data.,
markedDefault: false, versionName: 3.1.2_py39}
- - categories: math, computational geometry
- defaultVersionName: '4.10'
- description: polymake is open source software for research in polyhedral geometry.
- package: polymake
- url: https://polymake.org
- versions:
- - {description: polymake is open source software for research in polyhedral
- geometry., markedDefault: false, versionName: '4.10'}
- - categories: math, optimization
- defaultVersionName: 2.6.2
- description: NLopt is a free/open-source library for nonlinear optimization.
- package: nlopt
- url: https://nlopt.readthedocs.io/
- versions:
- - {description: NLopt is a free/open-source library for nonlinear optimization.,
- markedDefault: false, versionName: 2.6.2}
- - categories: math, deep learning
- defaultVersionName: 0.21.0_py39
- description: Gym is a toolkit for developing and comparing reinforcement learning
- algorithms.
- package: py-gym
- url: https://gym.openai.com/
- versions:
- - {description: Gym is a toolkit for developing and comparing reinforcement
- learning algorithms., markedDefault: false, versionName: 0.21.0_py39}
- - categories: math, machine learning
- defaultVersionName: 0.4.3_py312
- description: Hugging Face Evaluate is a library for easily evaluating machine
- learning models and datasets.
- package: py-evaluate
- url: https://huggingface.co/docs/evaluate
- versions:
- - {description: Hugging Face Evaluate is a library for easily evaluating machine
- learning models and datasets., markedDefault: false, versionName: 0.4.3_py312}
- - categories: math, symbolic
- defaultVersionName: 5.47.0
- description: Maxima is a system for the manipulation of symbolic and numerical
- expressions.
- package: maxima
- url: https://maxima.sourceforge.io/
- versions:
- - {description: Maxima is a system for the manipulation of symbolic and numerical
- expressions., markedDefault: false, versionName: 5.47.0}
- categories: math, numerical library
defaultVersionName: 1.1.0_py27
description: The SciPy library provides many user-friendly and efficient numerical
@@ -2919,89 +2903,116 @@ software_modules:
- {description: The SciPy library provides many user-friendly and efficient
numerical routines such as routines for numerical integration and optimization.,
family: scipy, markedDefault: true, versionName: 1.1.0_py27}
- - categories: math, linear algebra
- defaultVersionName: 0.6.3.2
- description: NVIDIA cuSPARSELt is a high-performance CUDA library for sparse
- matrix-matrix multiplication.
- package: cusparselt
- url: https://docs.nvidia.com/cuda/cusparselt/index.html
+ - categories: math, optimization
+ defaultVersionName: 2.6.2
+ description: NLopt is a free/open-source library for nonlinear optimization.
+ package: nlopt
+ url: https://nlopt.readthedocs.io/
versions:
- - description: NVIDIA cuSPARSELt is a high-performance CUDA library for sparse
- matrix-matrix multiplication.
- markedDefault: false
- properties:
- arch: {gpu: 1}
- versionName: 0.2.0.1
- - description: NVIDIA cuSPARSELt is a high-performance CUDA library for sparse
- matrix-matrix multiplication.
- markedDefault: false
- properties:
- arch: {gpu: 1}
- versionName: 0.6.3.2
+ - {description: NLopt is a free/open-source library for nonlinear optimization.,
+ markedDefault: false, versionName: 2.6.2}
+ - categories: math, machine learning
+ defaultVersionName: 0.4.2_py312
+ description: Simple, safe way to store and distribute tensors.
+ package: py-safetensors
+ url: https://huggingface.co/docs/safetensors
+ versions:
+ - {description: 'Simple, safe way to store and distribute tensors.', markedDefault: false,
+ versionName: 0.4.2_py312}
- categories: math, numerical library
- defaultVersionName: 4.1.0
- description: The MPFR library is a C library for multiple-precision floating-point
- computations with correct rounding.
- package: mpfr
- url: https://www.mpfr.org
+ defaultVersionName: 2017.1_py27
+ description: PyUblas provides a seamless glue layer between Numpy and Boost.Ublas
+ for use with Boost.Python.
+ package: py-pyublas
+ url: https://mathema.tician.de/software/pyublas/
versions:
- - {description: The MPFR library is a C library for multiple-precision floating-point
- computations with correct rounding., markedDefault: false, versionName: 3.1.5}
- - {description: The MPFR library is a C library for multiple-precision floating-point
- computations with correct rounding., markedDefault: false, versionName: 4.1.0}
- - categories: math, statistics
- defaultVersionName: 2.1.2_py39
- description: glum is a fast, modern, Python-first GLM estimation library.
- package: py-glum
- url: https://github.com/Quantco/glum
+ - {description: PyUblas provides a seamless glue layer between Numpy and Boost.Ublas
+ for use with Boost.Python., markedDefault: false, versionName: 2017.1_py27}
+ - categories: math, symbolic
+ defaultVersionName: 5.47.0
+ description: Maxima is a system for the manipulation of symbolic and numerical
+ expressions.
+ package: maxima
+ url: https://maxima.sourceforge.io/
versions:
- - {description: 'glum is a fast, modern, Python-first GLM estimation library.',
- markedDefault: false, versionName: 2.1.2_py39}
+ - {description: Maxima is a system for the manipulation of symbolic and numerical
+ expressions., markedDefault: false, versionName: 5.47.0}
- categories: math, numerical library
- defaultVersionName: 3.1.0
- description: libflame is a portable library for dense matrix computations, providing
- much of the functionality present in LAPACK
- package: libflame
- url: https://github.com/amd/libflame
+ defaultVersionName: 2.9.0
+ description: FLINT is a C library for doing number theory.
+ package: flint
+ url: https://flintlib.org/
versions:
- - {description: 'libflame is a portable library for dense matrix computations,
- providing much of the functionality present in LAPACK', markedDefault: false,
- versionName: '2.1'}
- - {description: 'libflame is a portable library for dense matrix computations,
- providing much of the functionality present in LAPACK', markedDefault: false,
- versionName: 2.2.4}
- - {description: 'libflame is a portable library for dense matrix computations,
- providing much of the functionality present in LAPACK', markedDefault: false,
- versionName: 3.1.0}
+ - {description: FLINT is a C library for doing number theory., markedDefault: false,
+ versionName: 2.9.0}
+ - categories: math, numerical library
+ defaultVersionName: 6.2.1
+ description: GMP is a free library for arbitrary precision arithmetic, operating
+ on signed integers, rational numbers, and floating-point numbers.
+ package: gmp
+ url: https://gmplib.org
+ versions:
+ - {description: 'GMP is a free library for arbitrary precision arithmetic, operating
+ on signed integers, rational numbers, and floating-point numbers.', markedDefault: false,
+ versionName: 6.1.2}
+ - {description: 'GMP is a free library for arbitrary precision arithmetic, operating
+ on signed integers, rational numbers, and floating-point numbers.', markedDefault: false,
+ versionName: 6.2.1}
+ - categories: math, numerical library
+ defaultVersionName: 4.1.0
+ description: The MPFR library is a C library for multiple-precision floating-point
+ computations with correct rounding.
+ package: mpfr
+ url: https://www.mpfr.org
+ versions:
+ - {description: The MPFR library is a C library for multiple-precision floating-point
+ computations with correct rounding., markedDefault: false, versionName: 3.1.5}
+ - {description: The MPFR library is a C library for multiple-precision floating-point
+ computations with correct rounding., markedDefault: false, versionName: 4.1.0}
- categories: math, statistics
- defaultVersionName: 2022.02.2-485
- description: RStudio is an integrated development environment (IDE) for R. It
- includes a console, syntax-highlighting editor that supports direct code execution,
- as well as tools for plotting, history, debugging and workspace management.
- This is the X11/GUI version.
- package: rstudio-desktop
- url: http://www.rstudio.com
+ defaultVersionName: 2.1.2_py39
+ description: glum is a fast, modern, Python-first GLM estimation library.
+ package: py-glum
+ url: https://github.com/Quantco/glum
versions:
- - {description: 'RStudio is an integrated development environment (IDE) for
- R. It includes a console, syntax-highlighting editor that supports direct
- code execution, as well as tools for plotting, history, debugging and workspace
- management. This is the X11/GUI version.', markedDefault: false, versionName: 2022.02.2-485}
+ - {description: 'glum is a fast, modern, Python-first GLM estimation library.',
+ markedDefault: false, versionName: 2.1.2_py39}
+ - categories: math, numerical library
+ defaultVersionName: 0.3.10
+ description: OpenBLAS is an optimized BLAS library
+ package: openblas
+ url: http://www.openblas.net/
+ versions:
+ - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
+ versionName: 0.2.19}
+ - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
+ versionName: 0.3.4}
+ - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
+ versionName: 0.3.9}
+ - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
+ versionName: 0.3.20}
+ - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
+ versionName: 0.3.26}
+ - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
+ versionName: 0.3.28}
+ - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: true,
+ versionName: 0.3.10}
+ - categories: math, numerical library
+ defaultVersionName: 5.1.2
+ description: A parallel sparse direct solver.
+ package: mumps
+ url: https://mumps-solver.org/
+ versions:
+ - {description: A parallel sparse direct solver., markedDefault: false, versionName: 5.1.2}
- categories: math, deep learning
- defaultVersionName: 10.0.1_py312
- description: Python bindings for the TensorRT library.
- package: py-tensorrt
- url: https://developer.nvidia.com/tensorrt
+ defaultVersionName: 0.21.0_py39
+ description: Gym is a toolkit for developing and comparing reinforcement learning
+ algorithms.
+ package: py-gym
+ url: https://gym.openai.com/
versions:
- - description: Python bindings for the TensorRT library.
- markedDefault: false
- properties:
- arch: {gpu: 1}
- versionName: 8.5.1.7_py39
- - description: Python bindings for the TensorRT library.
- markedDefault: false
- properties:
- arch: {gpu: 1}
- versionName: 10.0.1_py312
+ - {description: Gym is a toolkit for developing and comparing reinforcement
+ learning algorithms., markedDefault: false, versionName: 0.21.0_py39}
- categories: math, deep learning
defaultVersionName: 1.0.1_py27
description: Theano is a Python library that allows you to define, optimize,
@@ -3026,19 +3037,25 @@ software_modules:
- {description: 'GNU datamash is a command-line program which performs basic
numeric, textual and statistical operations on input textual data files.',
markedDefault: false, versionName: '1.3'}
- - categories: math, numerical library
- defaultVersionName: 6.2.1
- description: GMP is a free library for arbitrary precision arithmetic, operating
- on signed integers, rational numbers, and floating-point numbers.
- package: gmp
- url: https://gmplib.org
+ - categories: math, linear algebra
+ defaultVersionName: 0.6.3.2
+ description: NVIDIA cuSPARSELt is a high-performance CUDA library for sparse
+ matrix-matrix multiplication.
+ package: cusparselt
+ url: https://docs.nvidia.com/cuda/cusparselt/index.html
versions:
- - {description: 'GMP is a free library for arbitrary precision arithmetic, operating
- on signed integers, rational numbers, and floating-point numbers.', markedDefault: false,
- versionName: 6.1.2}
- - {description: 'GMP is a free library for arbitrary precision arithmetic, operating
- on signed integers, rational numbers, and floating-point numbers.', markedDefault: false,
- versionName: 6.2.1}
+ - description: NVIDIA cuSPARSELt is a high-performance CUDA library for sparse
+ matrix-matrix multiplication.
+ markedDefault: false
+ properties:
+ arch: {gpu: 1}
+ versionName: 0.2.0.1
+ - description: NVIDIA cuSPARSELt is a high-performance CUDA library for sparse
+ matrix-matrix multiplication.
+ markedDefault: false
+ properties:
+ arch: {gpu: 1}
+ versionName: 0.6.3.2
- categories: math, symbolic
defaultVersionName: 1.1.11
description: GNU libmatheval is a library (callable from C and Fortran) to parse
@@ -3062,55 +3079,53 @@ software_modules:
properties:
arch: {gpu: 1}
versionName: 1.6.3_py27
- - categories: math, numerical analysis
- defaultVersionName: 4.2.1
- description: GNU Octave is a high-level language primarily intended for numerical
- computations.
- package: octave
- url: https://www.gnu.org/software/octave/
+ - categories: math, optimization
+ defaultVersionName: 11.0.2
+ description: The Gurobi Optimizer is a commercial optimization solver for mathematical
+ programming.
+ package: gurobi
+ url: http://www.gurobi.com
versions:
- - {description: GNU Octave is a high-level language primarily intended for numerical
- computations., markedDefault: false, versionName: 4.2.1}
- - categories: math, numerical library
- defaultVersionName: 2017.1_py27
- description: PyUblas provides a seamless glue layer between Numpy and Boost.Ublas
- for use with Boost.Python.
- package: py-pyublas
- url: https://mathema.tician.de/software/pyublas/
+ - {description: The Gurobi Optimizer is a commercial optimization solver for
+ mathematical programming., markedDefault: false, versionName: 7.5.1}
+ - {description: The Gurobi Optimizer is a commercial optimization solver for
+ mathematical programming., markedDefault: false, versionName: 8.0.1_py27}
+ - {description: The Gurobi Optimizer is a commercial optimization solver for
+ mathematical programming., markedDefault: false, versionName: 8.0.1_py36}
+ - {description: The Gurobi Optimizer is a commercial optimization solver for
+ mathematical programming., markedDefault: false, versionName: 9.0.3_py36}
+ - {description: The Gurobi Optimizer is a commercial optimization solver for
+ mathematical programming., markedDefault: false, versionName: 10.0.1_py39}
+ - {description: The Gurobi Optimizer is a commercial optimization solver for
+ mathematical programming., markedDefault: false, versionName: 11.0.2}
+ - categories: math, technical computing
+ defaultVersionName: 13.1.0
+ description: A symbolic language and platform for modern technical computing.
+ package: mathematica
+ url: http://www.wolfram.com/mathematica
versions:
- - {description: PyUblas provides a seamless glue layer between Numpy and Boost.Ublas
- for use with Boost.Python., markedDefault: false, versionName: 2017.1_py27}
- - categories: math, numerical library
- defaultVersionName: 0.3.10
- description: OpenBLAS is an optimized BLAS library
- package: openblas
- url: http://www.openblas.net/
+ - description: A symbolic language and platform for modern technical computing.
+ markedDefault: false
+ properties:
+ license: {restricted: 1}
+ versionName: 13.1.0
+ - categories: math, machine learning
+ defaultVersionName: 0.4.3_py312
+ description: Hugging Face Evaluate is a library for easily evaluating machine
+ learning models and datasets.
+ package: py-evaluate
+ url: https://huggingface.co/docs/evaluate
versions:
- - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
- versionName: 0.2.19}
- - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
- versionName: 0.3.4}
- - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
- versionName: 0.3.9}
- - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
- versionName: 0.3.20}
- - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
- versionName: 0.3.26}
- - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: false,
- versionName: 0.3.28}
- - {description: OpenBLAS is an optimized BLAS library, family: blas, markedDefault: true,
- versionName: 0.3.10}
- - categories: math, numerical library
- defaultVersionName: 1.6.0
- description: TetGen provides various features to generate good quality and adaptive
- tetrahedral meshes suitable for numerical methods, such as finite element
- or finite volume methods.
- package: tetgen
- url: http://wias-berlin.de/software/index.jsp?id=TetGen
+ - {description: Hugging Face Evaluate is a library for easily evaluating machine
+ learning models and datasets., markedDefault: false, versionName: 0.4.3_py312}
+ - categories: math, computational geometry
+ defaultVersionName: '4.10'
+ description: polymake is open source software for research in polyhedral geometry.
+ package: polymake
+ url: https://polymake.org
versions:
- - {description: 'TetGen provides various features to generate good quality and
- adaptive tetrahedral meshes suitable for numerical methods, such as finite
- element or finite volume methods.', markedDefault: false, versionName: 1.6.0}
+ - {description: polymake is open source software for research in polyhedral
+ geometry., markedDefault: false, versionName: '4.10'}
- categories: math, numerical library
defaultVersionName: '2.7'
description: The GNU Scientific Library (GSL) is a numerical library for C and
@@ -3132,20 +3147,20 @@ software_modules:
routines such as random number generators, special functions and least-squares
fitting.', markedDefault: false, versionName: '2.7'}
- categories: math, numerical library
- defaultVersionName: 5.1.2
- description: A parallel sparse direct solver.
- package: mumps
- url: https://mumps-solver.org/
- versions:
- - {description: A parallel sparse direct solver., markedDefault: false, versionName: 5.1.2}
- - categories: math, machine learning
- defaultVersionName: 0.4.2_py312
- description: Simple, safe way to store and distribute tensors.
- package: py-safetensors
- url: https://huggingface.co/docs/safetensors
+ defaultVersionName: 4.0.3
+ description: ParMETIS is an MPI-based parallel library that implements a variety
+ of algorithms for partitioning unstructured graphs, meshes, and for computing
+ fill-reducing orderings of sparse matrices.
+ package: parmetis
+ url: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
versions:
- - {description: 'Simple, safe way to store and distribute tensors.', markedDefault: false,
- versionName: 0.4.2_py312}
+ - description: ParMETIS is an MPI-based parallel library that implements a variety
+ of algorithms for partitioning unstructured graphs, meshes, and for computing
+ fill-reducing orderings of sparse matrices.
+ markedDefault: false
+ properties:
+ parallel: {mpi: 1}
+ versionName: 4.0.3
- categories: math, numerical library
defaultVersionName: 3.1.0
description: BLIS is a portable software framework for instantiating high-performance
@@ -3162,6 +3177,16 @@ software_modules:
- {description: BLIS is a portable software framework for instantiating high-performance
BLAS-like dense linear algebra libraries., family: blas, markedDefault: false,
versionName: 3.1.0}
+ - categories: math, optimization
+ defaultVersionName: 2.10.0_py39
+ description: Optuna is an automatic hyperparameter optimization software framework,
+ particularly designed for machine learning.
+ package: py-optuna
+ url: https://optuna.readthedocs.io/
+ versions:
+ - {description: 'Optuna is an automatic hyperparameter optimization software
+ framework, particularly designed for machine learning.', markedDefault: false,
+ versionName: 2.10.0_py39}
- categories: math, deep learning
defaultVersionName: 2.0.2.5
description: GPU-accelerated tensor linear algebra library.
@@ -3193,24 +3218,16 @@ software_modules:
- {description: qrupdate is a Fortran library for fast updates of QR and Cholesky
decompositions., markedDefault: false, versionName: 1.1.2}
- categories: math, optimization
- defaultVersionName: 11.0.2
- description: The Gurobi Optimizer is a commercial optimization solver for mathematical
- programming.
- package: gurobi
- url: http://www.gurobi.com
+ defaultVersionName: 10.3.0
+ description: Artelys Knitro is an optimization solver for difficult large-scale
+ nonlinear problems.
+ package: knitro
+ url: https://www.artelys.com/en/optimization-tools/knitro
versions:
- - {description: The Gurobi Optimizer is a commercial optimization solver for
- mathematical programming., markedDefault: false, versionName: 7.5.1}
- - {description: The Gurobi Optimizer is a commercial optimization solver for
- mathematical programming., markedDefault: false, versionName: 8.0.1_py27}
- - {description: The Gurobi Optimizer is a commercial optimization solver for
- mathematical programming., markedDefault: false, versionName: 8.0.1_py36}
- - {description: The Gurobi Optimizer is a commercial optimization solver for
- mathematical programming., markedDefault: false, versionName: 9.0.3_py36}
- - {description: The Gurobi Optimizer is a commercial optimization solver for
- mathematical programming., markedDefault: false, versionName: 10.0.1_py39}
- - {description: The Gurobi Optimizer is a commercial optimization solver for
- mathematical programming., markedDefault: false, versionName: 11.0.2}
+ - {description: Artelys Knitro is an optimization solver for difficult large-scale
+ nonlinear problems., markedDefault: false, versionName: 12.4.0}
+ - {description: Artelys Knitro is an optimization solver for difficult large-scale
+ nonlinear problems., markedDefault: true, versionName: 10.3.0}
- categories: math, computational geometry
defaultVersionName: '4.11'
description: A mesh and field I/O library and scientific database.
@@ -3228,15 +3245,28 @@ software_modules:
versions:
- {description: The MPI-IS Mesh Processing Library contains core functions for
manipulating meshes and visualizing them., markedDefault: false, versionName: 0.4_py39}
- - categories: math, graph computing
- defaultVersionName: '0.73'
- description: A tool for computing automorphism groups and canonical forms of
- graphs.
- package: bliss
- url: http://www.tcs.hut.fi/Software/bliss/
+ - categories: math, numerical library
+ defaultVersionName: 3.18.5
+ description: PETSc, the Portable, Extensible Toolkit for Scientific Computation,
+ is a suite of data structures and routines for the scalable (parallel) solution
+ of scientific applications modeled by partial differential equations.
+ package: petsc
+ url: http://petsc.org
versions:
- - {description: A tool for computing automorphism groups and canonical forms
- of graphs., markedDefault: false, versionName: '0.73'}
+ - description: PETSc is a suite of data structures and routines for the scalable
+ (parallel) solution of scientific applications modeled by partial differential
+ equations.
+ markedDefault: false
+ properties:
+ parallel: {mpi: 1}
+ versionName: 3.10.3
+ - description: PETSc, the Portable, Extensible Toolkit for Scientific Computation,
+ is a suite of data structures and routines for the scalable (parallel) solution
+ of scientific applications modeled by partial differential equations.
+ markedDefault: false
+ properties:
+ parallel: {mpi: 1}
+ versionName: 3.18.5
- categories: math, topic modelling
defaultVersionName: 4.2.0_py39
description: Gensim is a Python library for topic modelling, document indexing
@@ -3246,21 +3276,14 @@ software_modules:
versions:
- {description: 'Gensim is a Python library for topic modelling, document indexing
and similarity retrieval with large corpora.', markedDefault: false, versionName: 4.2.0_py39}
- - categories: math, numerical library
- defaultVersionName: 4.0.3
- description: ParMETIS is an MPI-based parallel library that implements a variety
- of algorithms for partitioning unstructured graphs, meshes, and for computing
- fill-reducing orderings of sparse matrices.
- package: parmetis
- url: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
+ - categories: math, symbolic
+ defaultVersionName: 0.12.3_py39
+ description: High-Performance Symbolic Regression in Python and Julia.
+ package: py-pysr
+ url: https://github.com/MilesCranmer/PySR
versions:
- - description: ParMETIS is an MPI-based parallel library that implements a variety
- of algorithms for partitioning unstructured graphs, meshes, and for computing
- fill-reducing orderings of sparse matrices.
- markedDefault: false
- properties:
- parallel: {mpi: 1}
- versionName: 4.0.3
+ - {description: High-Performance Symbolic Regression in Python and Julia., markedDefault: false,
+ versionName: 0.12.3_py39}
- categories: math, machine learning
defaultVersionName: 2.18.0_py312
description: Hugging Face Datasets is a library for easily accessing and sharing
@@ -3279,46 +3302,24 @@ software_modules:
package: scalapack
url: http://www.netlib.org/scalapack/
versions:
- - description: ScaLAPACK is a library of high-performance linear algebra routines
- for parallel distributed memory machines.
- markedDefault: false
- properties:
- parallel: {mpi: 1}
- versionName: 2.0.2
- - description: ScaLAPACK is a library of high-performance linear algebra routines
- for parallel distributed memory machines.
- markedDefault: false
- properties:
- parallel: {mpi: 1}
- versionName: '2.1'
- - description: ScaLAPACK is a library of high-performance linear algebra routines
- for parallel distributed memory machines.
- markedDefault: false
- properties:
- parallel: {mpi: 1}
- versionName: 2.2.0
- - categories: math, numerical library
- defaultVersionName: 3.18.5
- description: PETSc, the Portable, Extensible Toolkit for Scientific Computation,
- is a suite of data structures and routines for the scalable (parallel) solution
- of scientific applications modeled by partial differential equations.
- package: petsc
- url: http://petsc.org
- versions:
- - description: PETSc is a suite of data structures and routines for the scalable
- (parallel) solution of scientific applications modeled by partial differential
- equations.
+ - description: ScaLAPACK is a library of high-performance linear algebra routines
+ for parallel distributed memory machines.
markedDefault: false
properties:
parallel: {mpi: 1}
- versionName: 3.10.3
- - description: PETSc, the Portable, Extensible Toolkit for Scientific Computation,
- is a suite of data structures and routines for the scalable (parallel) solution
- of scientific applications modeled by partial differential equations.
+ versionName: 2.0.2
+ - description: ScaLAPACK is a library of high-performance linear algebra routines
+ for parallel distributed memory machines.
markedDefault: false
properties:
parallel: {mpi: 1}
- versionName: 3.18.5
+ versionName: '2.1'
+ - description: ScaLAPACK is a library of high-performance linear algebra routines
+ for parallel distributed memory machines.
+ markedDefault: false
+ properties:
+ parallel: {mpi: 1}
+ versionName: 2.2.0
- categories: math, deep learning
defaultVersionName: 9.4.0
description: NVIDIA cuDNN is a GPU-accelerated library of primitives for deep
@@ -3410,6 +3411,49 @@ software_modules:
properties:
arch: {gpu: 1}
versionName: 9.4.0
+ - categories: math, statistics
+ defaultVersionName: '9.4'
+ description: SAS is a software suite developed by SAS Institute for advanced
+ analytics, multivariate analyses, business intelligence, data management,
+ and predictive analytics.
+ package: sas
+ url: http://www.sas.com/
+ versions:
+ - description: SAS is a software suite developed by SAS Institute for advanced
+ analytics, multivariate analyses, business intelligence, data management,
+ and predictive analytics.
+ markedDefault: false
+ properties:
+ license: {restricted: 1}
+ versionName: '9.4'
+ - categories: math, computational geometry
+ defaultVersionName: '2015.2'
+ description: Qhull computes the convex hull, Delaunay triangulation, Voronoi
+ diagram, halfspace intersection about a point, furthest-site Delaunay triangulation,
+ and furthest-site Voronoi diagram.
+ package: qhull
+ url: http://www.qhull.org/
+ versions:
+ - {description: 'Qhull computes the convex hull, Delaunay triangulation, Voronoi
+ diagram, halfspace intersection about a point, furthest-site Delaunay triangulation,
+ and furthest-site Voronoi diagram.', markedDefault: false, versionName: '2015.2'}
+ - categories: math, numerical library
+ defaultVersionName: 3.18.2_py39
+ description: Python bindings for SLEPc.
+ package: py-slepc4py
+ url: https://slepc.upv.es/
+ versions:
+ - {description: Python bindings for SLEPc., markedDefault: false, versionName: 3.18.2_py39}
+ - categories: math, numerical library
+ defaultVersionName: 1.2.1
+ description: GNU MPC is a C library for the arithmetic of complex numbers with
+ arbitrarily high precision and correct rounding of the result.
+ package: mpc
+ url: http://www.multiprecision.org/mpc
+ versions:
+ - {description: GNU MPC is a C library for the arithmetic of complex numbers
+ with arbitrarily high precision and correct rounding of the result., markedDefault: false,
+ versionName: 1.2.1}
- categories: math, numerical library
defaultVersionName: 3.9.0
description: Collection of Fortran77 subroutines designed to solve large scale
@@ -3431,41 +3475,6 @@ software_modules:
properties:
parallel: {mpi: 1}
versionName: 3.9.0
- - categories: math, numerical library
- defaultVersionName: 6.0.4
- description: Software package and libraries for sequential and parallel graph
- partitioning, static mapping and clustering, sequential mesh and hypergraph
- partitioning, and sequential and parallel sparse matrix block ordering.
- package: scotch
- url: http://www.labri.fr/perso/pelegrin/scotch
- versions:
- - description: Software package and libraries for sequential and parallel graph
- partitioning, static mapping and clustering, sequential mesh and hypergraph
- partitioning, and sequential and parallel sparse matrix block ordering.
- markedDefault: false
- properties:
- parallel: {mpi: 1}
- versionName: 6.0.4
- - categories: math, machine learning
- defaultVersionName: 0.22.1_py312
- description: The huggingface_hub library allows you to interact with the Hugging
- Face Hub, a machine learning platform for creators and collaborators.
- package: py-huggingface-hub
- url: https://huggingface.co/docs/huggingface_hub
- versions:
- - {description: 'The huggingface_hub library allows you to interact with the
- Hugging Face Hub, a machine learning platform for creators and collaborators.',
- markedDefault: false, versionName: 0.22.1_py312}
- - categories: math, numerical library
- defaultVersionName: 1.2.1
- description: GNU MPC is a C library for the arithmetic of complex numbers with
- arbitrarily high precision and correct rounding of the result.
- package: mpc
- url: http://www.multiprecision.org/mpc
- versions:
- - {description: GNU MPC is a C library for the arithmetic of complex numbers
- with arbitrarily high precision and correct rounding of the result., markedDefault: false,
- versionName: 1.2.1}
- categories: math, numerical library
defaultVersionName: 3.18.2
description: SLEPc is a Scalable Library for Eigenvalue Problem Computations.
@@ -3508,17 +3517,16 @@ software_modules:
properties:
parallel: {mpi: 1}
versionName: 3.3.10
- - categories: math, computational geometry
- defaultVersionName: '2015.2'
- description: Qhull computes the convex hull, Delaunay triangulation, Voronoi
- diagram, halfspace intersection about a point, furthest-site Delaunay triangulation,
- and furthest-site Voronoi diagram.
- package: qhull
- url: http://www.qhull.org/
+ - categories: math, machine learning
+ defaultVersionName: 0.22.1_py312
+ description: The huggingface_hub library allows you to interact with the Hugging
+ Face Hub, a machine learning platform for creators and collaborators.
+ package: py-huggingface-hub
+ url: https://huggingface.co/docs/huggingface_hub
versions:
- - {description: 'Qhull computes the convex hull, Delaunay triangulation, Voronoi
- diagram, halfspace intersection about a point, furthest-site Delaunay triangulation,
- and furthest-site Voronoi diagram.', markedDefault: false, versionName: '2015.2'}
+ - {description: 'The huggingface_hub library allows you to interact with the
+ Hugging Face Hub, a machine learning platform for creators and collaborators.',
+ markedDefault: false, versionName: 0.22.1_py312}
- categories: math, numerical library
defaultVersionName: 1.0_py39
description: Autograd can automatically differentiate native Python and Numpy
@@ -3543,21 +3551,6 @@ software_modules:
- {description: 'The GLPK (GNU Linear Programming Kit) package is intended for
solving large-scale linear programming (LP), mixed integer programming (MIP),
and other related problems.', markedDefault: false, versionName: '4.63'}
- - categories: math, statistics
- defaultVersionName: '9.4'
- description: SAS is a software suite developed by SAS Institute for advanced
- analytics, multivariate analyses, business intelligence, data management,
- and predictive analytics.
- package: sas
- url: http://www.sas.com/
- versions:
- - description: SAS is a software suite developed by SAS Institute for advanced
- analytics, multivariate analyses, business intelligence, data management,
- and predictive analytics.
- markedDefault: false
- properties:
- license: {restricted: 1}
- versionName: '9.4'
- categories: math, numerical analysis
defaultVersionName: R2022b
description: MATLAB is a multi-paradigm numerical computing environment and
@@ -3614,6 +3607,21 @@ software_modules:
properties:
license: {restricted: 1}
versionName: R2022b
+ - categories: math, deep learning
+ defaultVersionName: 0.18.7_py312
+ description: WandB (Weights & Biases) is a machine learning development platform
+ that enables data scientists and machine learning engineers to track, visualize,
+ and reproduce their experiments in real-time.
+ package: py-wandb
+ url: https://wandb.ai
+ versions:
+ - description: WandB (Weights & Biases) is a machine learning development platform
+ that enables data scientists and machine learning engineers to track, visualize,
+ and reproduce their experiments in real-time.
+ markedDefault: false
+ properties:
+ arch: {gpu: 1}
+ versionName: 0.18.7_py312
- categories: math, optimization
defaultVersionName: 6.4.1
description: SUNDIALS is a family of software packages providing robust and
@@ -3636,6 +3644,34 @@ software_modules:
in Python., markedDefault: false, versionName: 1.6.0_py39}
- {description: PyWavelets is a free Open Source library for wavelet transforms
in Python., markedDefault: false, versionName: 1.6.0_py312}
+ - categories: math, numerical library
+ defaultVersionName: 3.1.0
+ description: libflame is a portable library for dense matrix computations, providing
+ much of the functionality present in LAPACK
+ package: libflame
+ url: https://github.com/amd/libflame
+ versions:
+ - {description: 'libflame is a portable library for dense matrix computations,
+ providing much of the functionality present in LAPACK', markedDefault: false,
+ versionName: '2.1'}
+ - {description: 'libflame is a portable library for dense matrix computations,
+ providing much of the functionality present in LAPACK', markedDefault: false,
+ versionName: 2.2.4}
+ - {description: 'libflame is a portable library for dense matrix computations,
+ providing much of the functionality present in LAPACK', markedDefault: false,
+ versionName: 3.1.0}
+ - categories: math, deep learning
+ defaultVersionName: 1.12.0_py39
+ description: ONNX is a open format to represent deep learning models.
+ package: py-onnx
+ url: https://onnx.ai
+ versions:
+ - {description: ONNX is a open format to represent deep learning models., markedDefault: false,
+ versionName: 1.0.1_py27}
+ - {description: ONNX is a open format to represent deep learning models., markedDefault: false,
+ versionName: 1.8.1_py36}
+ - {description: ONNX is a open format to represent deep learning models., markedDefault: false,
+ versionName: 1.12.0_py39}
- categories: math, deep learning
defaultVersionName: 2.1.5_py27
description: Keras is a high-level neural networks API, written in Python and
@@ -3679,38 +3715,17 @@ software_modules:
properties:
arch: {gpu: 1}
versionName: 2.1.5_py27
- - categories: math, deep learning
- defaultVersionName: 1.12.0_py39
- description: ONNX is a open format to represent deep learning models.
- package: py-onnx
- url: https://onnx.ai
- versions:
- - {description: ONNX is a open format to represent deep learning models., markedDefault: false,
- versionName: 1.0.1_py27}
- - {description: ONNX is a open format to represent deep learning models., markedDefault: false,
- versionName: 1.8.1_py36}
- - {description: ONNX is a open format to represent deep learning models., markedDefault: false,
- versionName: 1.12.0_py39}
- categories: math, numerical library
- defaultVersionName: 3.1.3
- description: FlexiBLAS is a BLAS and LAPACK wrapper library with runtime exchangeable
- backends.
- package: flexiblas
- url: https://github.com/mpimd-csc/flexiblas
- versions:
- - {description: FlexiBLAS is a BLAS and LAPACK wrapper library with runtime
- exchangeable backends., family: blas, markedDefault: false, versionName: 3.1.3}
- - categories: math, technical computing
- defaultVersionName: 13.1.0
- description: A symbolic language and platform for modern technical computing.
- package: mathematica
- url: http://www.wolfram.com/mathematica
+ defaultVersionName: 1.6.0
+ description: TetGen provides various features to generate good quality and adaptive
+ tetrahedral meshes suitable for numerical methods, such as finite element
+ or finite volume methods.
+ package: tetgen
+ url: http://wias-berlin.de/software/index.jsp?id=TetGen
versions:
- - description: A symbolic language and platform for modern technical computing.
- markedDefault: false
- properties:
- license: {restricted: 1}
- versionName: 13.1.0
+ - {description: 'TetGen provides various features to generate good quality and
+ adaptive tetrahedral meshes suitable for numerical methods, such as finite
+ element or finite volume methods.', markedDefault: false, versionName: 1.6.0}
- categories: math, deep learning
defaultVersionName: 8.3.14_py312
description: Ultra YOLO11 is a cutting-edge, state-of-the-art (SOTA) model that
@@ -3795,25 +3810,6 @@ software_modules:
properties:
arch: {gpu: 1}
versionName: 13.3.0_py312
- - categories: math, numerical library
- defaultVersionName: 2.9.0
- description: FLINT is a C library for doing number theory.
- package: flint
- url: https://flintlib.org/
- versions:
- - {description: FLINT is a C library for doing number theory., markedDefault: false,
- versionName: 2.9.0}
- - categories: math, optimization
- defaultVersionName: 10.3.0
- description: Artelys Knitro is an optimization solver for difficult large-scale
- nonlinear problems.
- package: knitro
- url: https://www.artelys.com/en/optimization-tools/knitro
- versions:
- - {description: Artelys Knitro is an optimization solver for difficult large-scale
- nonlinear problems., markedDefault: false, versionName: 12.4.0}
- - {description: Artelys Knitro is an optimization solver for difficult large-scale
- nonlinear problems., markedDefault: true, versionName: 10.3.0}
- categories: math, numerical library
defaultVersionName: 3.18.5_py39
description: Python bindings for PETSc, the Portable, Extensible Toolkit for
@@ -3823,14 +3819,33 @@ software_modules:
versions:
- {description: 'Python bindings for PETSc, the Portable, Extensible Toolkit
for Scientific Computation.', markedDefault: false, versionName: 3.18.5_py39}
- - categories: math, symbolic
- defaultVersionName: 0.12.3_py39
- description: High-Performance Symbolic Regression in Python and Julia.
- package: py-pysr
- url: https://github.com/MilesCranmer/PySR
+ - categories: math, graph computing
+ defaultVersionName: '0.73'
+ description: A tool for computing automorphism groups and canonical forms of
+ graphs.
+ package: bliss
+ url: http://www.tcs.hut.fi/Software/bliss/
versions:
- - {description: High-Performance Symbolic Regression in Python and Julia., markedDefault: false,
- versionName: 0.12.3_py39}
+ - {description: A tool for computing automorphism groups and canonical forms
+ of graphs., markedDefault: false, versionName: '0.73'}
+ - categories: math, numerical analysis
+ defaultVersionName: 4.2.1
+ description: GNU Octave is a high-level language primarily intended for numerical
+ computations.
+ package: octave
+ url: https://www.gnu.org/software/octave/
+ versions:
+ - {description: GNU Octave is a high-level language primarily intended for numerical
+ computations., markedDefault: false, versionName: 4.2.1}
+ - categories: math, numerical library
+ defaultVersionName: 3.1.3
+ description: FlexiBLAS is a BLAS and LAPACK wrapper library with runtime exchangeable
+ backends.
+ package: flexiblas
+ url: https://github.com/mpimd-csc/flexiblas
+ versions:
+ - {description: FlexiBLAS is a BLAS and LAPACK wrapper library with runtime
+ exchangeable backends., family: blas, markedDefault: false, versionName: 3.1.3}
- categories: math, numerical library
defaultVersionName: 2.0.8_py36
description: gmpy2 is a C-coded Python extension module that supports multiple-precision
diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml
index 08c8479ef..59964b9fb 100644
--- a/src/docs/software/updates.xml
+++ b/src/docs/software/updates.xml
@@ -5,6 +5,15 @@
Sherlock software update feed
https://www.sherlock.stanford.edu/docs/software/list
+
+ New module: math/py-wandb version 0.18.7_py312
+ WandB (Weights & Biases) is a machine learning development platform that enables data scientists and machine learning engineers to track, visualize, and reproduce their experiments in real-time.
+ https://wandb.ai
+ https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.18.7_py312#py-wandb
+ math, deep learning
+ kilian@stanford.edu (Kilian Cavalotti)
+ Thu, 14 Nov 2024 11:36:19 -0800
+ New module: biology/bases2fastq version 2.0.0The Bases2Fastq Software demultiplexess sequencing data from Element instruments and converts base calls into FASTQ files for secondary analysis with the FASTQ-compatible software of your choice.