Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.

This module provides a nearly complete wrapping of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects, and each of these is exposed as a Python type in the bsddb3.db module. The database objects can use various access methods: btree, hash, recno, and queue. Complete support of Berkeley DB distributed transactions. Complete support for Berkeley DB Replication Manager. Complete support for Berkeley DB Base Replication. Support for RPC.

BlackSheep is a lightweight, asynchronous, event driven Web framework.

The framework offers

• A rich code API, based on dependency injection and inspired by Flask and ASP.NET Core.

• A typing-friendly codebase, which enables a comfortable development experience thanks to hints when coding with IDEs.

• Built-in generation of OpenAPI Documentation, supporting version 3, YAML, and JSON.

• A cross-platform framework, using the most modern versions of Python.

• Good performance.

JSON (JavaScript Object Notation) is a subset of JavaScript syntax (ECMA-262 3rd edition) used as a lightweight data interchange format.

Simplejson exposes an API familiar to users of the standard library marshal and pickle modules. It is the externally maintained version of the json library contained in Python 2.6, but maintains compatibility with Python 2.5 and (currently) has significant performance advantages, even without using the optional C extension for speedups. Simplejson is also supported on Python 3.3+.

The mercantile module provides ul(xtile, ytile, zoom) and bounds(xtile, ytile, zoom) functions that respectively return the upper left corner and bounding longitudes and latitudes for XYZ tiles, a xy(lng, lat) function that returns spherical mercator x and y coordinates, a tile(lng, lat, zoom) function that returns the tile containing a given point, and quadkey conversion functions quadkey(xtile, ytile, zoom) and quadkey_to_tile(quadkey) for translating between quadkey and tile coordinates.

This package is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. This software package can assign both genomes and MAGs to SGBs. PhyloPhlAn can reconstruct strain-level phylogenies using clade- specific maximally informative phylogenetic markers, and can also scale to very large phylogenies comprising >17,000 microbial species.

This package contains a plugin that provides specializations for type hinting stub files, especially interesting for linting typeshed. It adds the .pyi extension to the default value of the --filename command-line argument to Flake8. This means stubs are linted by default with this plugin enabled, without needing to explicitly list every file. It modifies PyFlakes runs for .pyi files to defer checking type annotation expressions after the entire file has been read. This enables support for first-class forward references that stub files use.

pandapower is an easy to use network calculation program aimed to automate the analysis and optimization of power systems. It uses the data analysis library pandas and is compatible with the commonly used MATPOWER / PYPOWER case format. pandapower allows using different solvers including an improved Newton-Raphson power flow implementation, all PYPOWER solvers, the C++ library solvers for fast steady-state distribution power system analysis of PowerGridModel, the Newton-Raphson power flow solvers in the C++ library lightsim2grid, and the PowerModels.jl library.

The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms. From a high-level description of the form, it generates efficient low-level C++ code that can be used to assemble the corresponding discrete operator (tensor). In particular, a bilinear form may be assembled into a matrix and a linear form may be assembled into a vector. FFC may be used either from the command line (by invoking the ffc command) or as a Python module (import ffc).

FFC is part of the FEniCS Project.

Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line.

Key features:

• Hierarchical configuration composable from multiple sources

• Configuration can be specified or overridden from the command line

• Dynamic command line tab completion

• Run your application locally or launch it to run remotely

• Run multiple jobs with different arguments with a single command

clustimage is a Python library to detect natural groups or clusters of images. Multiple steps are pipelined where images are processed, features extracted, and the clusters evaluated across the feature space. The optimal number of clusters is determined using methods such as silhouette, dbindex, and derivatives in combination with clustering methods, such as agglomerative, kmeans, dbscan and hdbscan. clustimage allows you to determine the most robust clustering by efficiently searching across the parameters and by evaluating the clusters. Besides clustering of images, clustimage can also find the most similar images for a new, unseen sample.

NestedText is a file format for holding data that is to be entered, edited, or viewed by people. It allows data to be organized into a nested collection of dictionaries, lists, and strings. In this way it is similar to JSON and YAML, but without the complexity and risk of YAML and without the syntactic clutter of JSON. NestedText is both simple and natural. Only a small number of concepts and rules must be kept in mind when creating it. It is easily created, modified, or viewed with a text editor and easily understood and used by both programmers and non-programmers.

term-image is a library and program to display images on compatible terminals.

Features:

1. Multiple image formats (basically all formats supported by PIL.Image.open())

2. Multiple image source types: PIL image instance, local file, URL

3. Multiple image render styles (with automatic support detection)

4. Support for multiple terminal graphics protocols, including Kitty

5. Transparency support (with multiple options)

6. Animated image support (including transparent ones)

7. Integration into various TUI / terminal-based output libraries

8. Terminal size awareness

9. Automatic and manual image sizing

10. Horizontal and vertical alignment

11. Automatic and manual font ratio adjustment (to preserve image aspect ratio)

This package provides discretization tools for finite volume and inverse problems.

The vision is to create a package for finite volume simulation with a focus on large scale inverse problems. This package has the following features:

• modular with respect to the spacial discretization

• built with the inverse problem in mind

• supports 1D, 2D and 3D problems

• access to sparse matrix operators

• access to derivatives to mesh variables

Currently, discretize supports:

• Tensor Meshes (1D, 2D and 3D)

• Cylindrically Symmetric Meshes

• QuadTree and OcTree Meshes (2D and 3D)

• Logically Rectangular Meshes (2D and 3D)

• Triangular (2D) and Tetrahedral (3D) Meshes

This package provides information about the Euclid space telescope and survey that is needed to produce simulations using GalSim. Some of the information provided is approximate, aimed towards fast simulations rather than full accuracy in representation of Euclid images. Places where the information is only approximate are flagged and described in the docstring, and we particularly highlight that the PSF is only approximate; for details, see the docstring of the getPSF() method. This library should enable generation of Euclid-like images of sufficient fidelity for preliminary exploration of object detection, photometry, deblending, and joint analysis with ground-based observatories. For applications requiring high precision such as weak lensing, the higher fidelity simulations available within the Euclid Consortium should be used.

about-time is a helper for tracking time and throughput of code blocks, with beautiful human friendly renditions.

Key feature are:

• measure the duration of two or more blocks at the same time, including the whole duration

• instrument a code to cleanly retrieve durations in one line, to log or send to time series databases

• easily see human friendly durations in s (seconds), ms (milliseconds), µs (microseconds) and even ns (nanoseconds)

• easily see human friendly counts with SI prefixes like k, M, G, T, etc

• measure the actual throughput of a block

• easily see human friendly throughputs in /second, /minute, /hour or even /day, including SI prefixes

The package allows you to enter Python code within a LaTeX document, execute the code, and access its output in the original document. There is also support for Bash, JavaScript, Julia, Octave, Perl, R, Raku (Perl 6), Ruby, Rust, and SageMath. Code is only executed when it has been modified, or when it meets user-specified criteria. Code may be divided into user-defined sessions, which automatically run in parallel. Errors and warnings are synchronized with the LaTeX document, so that they refer to the document's line numbers. External dependencies can be tracked, so that code is re-executed when the data it depends on is modified. PythonTeX also provides syntax highlighting for code in LaTeX documents via the Pygments syntax highlighter.

The package also provides a depythontex utility. This creates a copy of the document in which all Python code has been replaced by its output. This is useful for journal submissions, sharing documents, and conversion to other formats.

Bindings for FUSE.

Mock data generation factories.

Fuzzy Finder implemented in Python.

Software Heritage Deposit Server

Convert matplotlib figures into TikZ/PGFPlots