From c81ea7db499f776ce9ff6755fb0bc942704f5a18 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Thu, 14 Nov 2024 16:25:24 -0800 Subject: [PATCH] docs: updated software list --- includes/data/software.yml | 887 +++++++++++++++++----------------- src/docs/software/updates.xml | 9 + 2 files changed, 460 insertions(+), 436 deletions(-) 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 2.0.0 The 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.