This package provides a Pytest plugin that facilitates the comparison of images produced by PyVista, generating cached images from tests and comparing subsequent results against that cache.

This is a package meant primarily for documenting histogram indexing and the PlottableHistogram Protocol and any future cross-library standards. It also contains the code for the PlottableHistogram Protocol, to be used in type checking libraries wanting to conform to the protocol. It is not usually a runtime dependency, but only a type checking, testing, and/or docs dependency in support of other libraries.

This package provides a Python library for working with NeuroML descriptions of neuronal models

python-pydicom is a Python library for reading and writing DICOM medical imaging data. It can read, modify and write DICOM data.

meshzoo is a mesh generator for finite element or finite volume computations for simple domains like regular polygons, disks, spheres, cubes, etc.

This package provides a Python interface for the SCS (Splitting conic solver) library.

Bottleneck is a collection of fast, NaN-aware NumPy array functions written in C.

PyMCubes is an implementation of the marching cubes algorithm to extract iso-surfaces from volumetric data. The volumetric data can be given as a three-dimensional NumPy array or as a Python function f(x, y, z).

Anndata is a package for simple (functional) high-level APIs for data analysis pipelines. In this context, it provides an efficient, scalable way of keeping track of data together with learned annotations and reduces the code overhead typically encountered when using a mostly object-oriented library such as scikit-learn.

This package provides fast computations for principal component analysis (PCA), SVD, and eigendecompositions via randomized methods

scikit-fem is a library for performing finite element assembly. Its main purpose is the transformation of bilinear forms into sparse matrices and linear forms into vectors.

This package provides a stable interface for interactions between Snakemake and its software deployment plugins.

geosketch is a Python package that implements the geometric sketching algorithm described by Brian Hie, Hyunghoon Cho, Benjamin DeMeo, Bryan Bryson, and Bonnie Berger in "Geometric sketching compactly summarizes the single-cell transcriptomic landscape", Cell Systems (2019). This package provides an example implementation of the algorithm as well as scripts necessary for reproducing the experiments in the paper.

iminuit is a Jupyter-friendly Python interface for the Minuit2 C++ library maintained by CERN's ROOT team.

Minuit was designed to optimize statistical cost functions, for maximum-likelihood and least-squares fits. It provides the best-fit parameters and error estimates from likelihood profile analysis.

Optionally, Iminuit supports SciPy minimizers as alternatives to Minuit's MIGRAD algorithm and Numba accelerated functions.

Optimized einsum can significantly reduce the overall execution time of einsum-like expressions by optimizing the expression's contraction order and dispatching many operations to canonical BLAS, cuBLAS, or other specialized routines. Optimized einsum is agnostic to the backend and can handle NumPy, Dask, PyTorch, Tensorflow, CuPy, Sparse, Theano, JAX, and Autograd arrays as well as potentially any library which conforms to a standard API. See the documentation for more information.

fgivenx is a Python package for plotting posteriors of functions. It is currently used in astronomy, but will be of use to any scientists performing Bayesian analyses which have predictive posteriors that are functions.

This package allows one to plot a predictive posterior of a function, dependent on sampled parameters. It assumes one has a Bayesian posterior Post(theta|D,M) described by a set of posterior samples theta_i~Post. If there is a function parameterised by theta y=f(x;theta), then this script will produce a contour plot of the conditional posterior P(y|x,D,M) in the (x,y) plane.

The TDDA Python module provides command-line and Python API support for the overall process of data analysis, through tools that perform reference testing, constraint discovery for data, automatic inference of regular expressions from text data and automatic test generation.

This package provides common functions and classes for Snakemake and its plugins.

This package provides a Python library for calculating Evapotranspiration using various standard methods.

hepunits collects the most commonly used units and constants in the HEP System of Units, as derived from the basic units originally defined by the CLHEP project.

spin is a simple interface for common development tasks. It comes with a few common build commands out the box, but can easily be customized per project.

The impetus behind developing the tool was the mass migration of scientific Python libraries (SciPy, scikit-image, and NumPy, etc.) to Meson, after distutils was deprecated. When many of the build and installation commands changed, it made sense to abstract away the nuisance of having to re-learn them.

This is a Python implementation of UpSet plots by Lex et al. UpSet plots are used to visualize set overlaps; like Venn diagrams but more readable.

pyts is a Python package for time series classification. It aims to make time series classification easily accessible by providing preprocessing and utility tools, and implementations of state-of-the-art algorithms. Most of these algorithms transform time series, thus pyts provides several tools to perform these transformations.

PyVista is...

• Pythonic VTK: a high-level API to the Visualization Toolkit (VTK);

• mesh data structures and filtering methods for spatial datasets;

• 3D plotting made simple and built for large/complex data geometries.

This package provides a Pythonic, well-documented interface exposing VTK's powerful visualization backend to facilitate rapid prototyping, analysis, and visual integration of spatially referenced datasets.