Tool

CBMPy Metadraft: a flexible and extensible genome-scale model reconstruction tool

CBMPy Metadraft: a flexible and extensible, GUI-based genome-scale model reconstruction tool that supports multiple Systems Biology standards. MetaDraft version 0.9.2 now defaults to the 2019-1 template library, if you are working directly in a cloned repository please initialise the new template library: cd cbmpy-metadraft git submodule update –init –remote — modeldb/2019-1/ If you want to switch back to the 2018-1 library and results please edit the _metadraft.cfg file and change the value of the “metadraft_db_version” key to “2018-1” (it is […]

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Command-line Tools

Zap: The delightful package manager for AppImages

Zap Looking for the older Zap v1 (Python) implementation? Head over to v1 branch. Getting Started ✨ For system-wide installation (needs sudo) sudo wget https://github.com/srevinsaju/zap/releases/download/continuous/zap-amd64 -O /usr/local/bin/zap sudo chmod +x /usr/local/bin/zap zap –help For local installation, (requires ~/.local/bin to be on $PATH) mkdir -p ~/.local/bin wget https://github.com/srevinsaju/zap/releases/download/continuous/zap-amd64 -O ~/.local/bin/zap chmod +x ~/.local/bin/zap zap –help NOTE: Replace amd64 with your machine architecture. Supported architectures are listed in the release page Installing AppImages All AppImages from the AppImage Catalog and AppImage catalog […]

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Console

Enlighten Progress Bar: a console progress bar library for Python

Enlighten Progress Bar Enlighten Progress Bar is a console progress bar library for Python. The main advantage of Enlighten is it allows writing to stdout and stderr without any redirection or additional code. Just print or log as you normally would. Enlighten also includes experimental support for Jupyter Notebooks. The code for this animation can be found in demo.py in examples. Documentation https://python-enlighten.readthedocs.io Installation PIP $ pip install enlighten RPM Fedora and EL8 (RHEL/CentOS) (EPEL repositories must be configured for […]

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Converter

A python scripts for importing Source 1 assets such as materials, models, and particle effects into Source 2

Set of scripts for importing Source 1 assets such as materials, models, and particle effects into Source 2. Inspired by Valve’s own source1import.exe (written in C++ and Perl), this one is in Python. Requires: Python 3.9python -m pip install -r requirements.txt Installing: Download as ZIP and ExtractOpen folder, press Ctrl + L, enter cmd and run the following commands python -m pip install -r requirements.txt cd utils All set. Use python materials_import.py –help or read below examples to get started. […]

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Checker

pylic – Python license checker

Reads pylic configuration in pyproject.toml and checks licenses of installed packages recursively. Principles: Every license has to be allowed explicitly (case-insensitive comparison). All installed packages without a license are considered unsafe and have to be listed as such. Only installed packages are checked for licenses. Packages/dependencies listed in pyproject.toml are ignored. Installation pip install pylic Configuration pylic needs be run in the directory where your pyproject.toml file is located. You can configure safe_licenses: All licenses you concider safe for usage. […]

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Natural Language Processing

GreynirCorrect: Spelling and grammar correction for Icelandic

GreynirCorrect: Spelling and grammar correction for Icelandic Overview GreynirCorrect is a Python 3 (>= 3.6) package and command line tool for checking and correcting spelling and grammar in Icelandic text. GreynirCorrect relies on the Greynir package, by the same authors, to tokenize and parse text. GreynirCorrect is documented in detail here. The software has three main modes of operation, described below. Token-level correction GreynirCorrect can tokenize text and return an automatically corrected token stream. This catches token-level errors, such as […]

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Analysis

Package for uncertainty analysis in Python

Currently in rewriting phase. Package for uncertainty analysis in Python.It was developed while I was doing my Bachelor in physics.The functionality is based on the lab courses. Warnings The function exec is used within some functionalities.This can cause harm if exploited. General introduction The main classes of the package are Data, Table and Formula.The package holds functionality for: Error/Uncertainty propagation in equations Create tables and calculate different types of averages including arithmetic, geometric, modus, … Normal and simplified gauss propagation […]

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Python

Using Podman with BuildKit, the better Docker image builder

BuildKit is a new and improved tool for building Docker images: it’s faster, has critical features missing from traditional Dockerfiles like build secrets, plus additionally useful features like cache mounting. So if you’re building Docker images, using BuildKit is in general a good idea. And then there’s Podman: Podman is a reimplemented, compatible version of the Docker CLI and API. It does not however implement all the BuildKit Dockerfile extensions. On its own, then, Podman isn’t as good as Docker […]

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