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build: add codespace config #231

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Dec 26, 2023
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41 changes: 41 additions & 0 deletions .devcontainer.json
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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
// README at: https://github.com/devcontainers/templates/tree/main/src/ubuntu
{
"name": "Ubuntu",
// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
"image": "mcr.microsoft.com/devcontainers/base:jammy",
"features": {
"ghcr.io/rocker-org/devcontainer-features/miniforge:1": {
"version": "latest",
"variant": "Mambaforge"
}
},

// Features to add to the dev container. More info: https://containers.dev/features.
// "features": {},

// Use 'forwardPorts' to make a list of ports inside the container available locally.
// "forwardPorts": [],

// Use 'postCreateCommand' to run commands after the container is created.
"postCreateCommand": "mamba create -y -n haptools -c conda-forge 'poetry>=1.1.15' 'python=3.7' && conda run -n haptools poetry install -E docs -E tests",

// Configure tool-specific properties.
"customizations": {
"vscode": {
"extensions": ["ms-python.python"],
"settings": {
"python.condaPath": "/opt/conda/condabin/conda",
"python.defaultInterpreterPath": "/opt/conda/envs/haptools/bin/python",
"python.terminal.activateEnvironment": true,
"python.terminal.activateEnvInCurrentTerminal": true,
"python.venvFolders": ["/opt/conda/envs"],
"terminal.integrated.environmentChangesRelaunch": true,
"terminal.integrated.hideOnStartup": "always"
}
}
}

// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
// "remoteUser": "root"
}
1 change: 1 addition & 0 deletions README.md
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[![image](https://anaconda.org/bioconda/haptools/badges/version.svg)](https://anaconda.org/bioconda/haptools)
[![license](https://img.shields.io/pypi/l/haptools)](LICENSE)
![status](https://github.com/CAST-genomics/haptools/workflows/Tests/badge.svg)
[<img src=https://github.com/codespaces/badge.svg width=160>](https://codespaces.new/CAST-genomics/haptools)

Haptools is a collection of tools for simulating and analyzing genotypes and phenotypes while taking into account haplotype information. Haptools supports fast simulation of admixed genomes (with `simgenotype`), visualization of admixture tracks (with `karyogram`), simulating haplotype- and local ancestry-specific phenotype effects (with `transform` and `simphenotype`), and computing a variety of common file operations and statistics in a haplotype-aware manner.

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