diff --git a/.devcontainer.json b/.devcontainer.json new file mode 100644 index 00000000..df947074 --- /dev/null +++ b/.devcontainer.json @@ -0,0 +1,41 @@ +// 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" +} diff --git a/README.md b/README.md index 5d02fab3..8b80faef 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,7 @@ [![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) +[](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.