From f29d352d1e37d400af77a500d2b564fb9a271edf Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Thu, 21 Dec 2023 19:48:13 +0000
Subject: [PATCH 1/4] start creating github codespace

---
 devcontainer.json | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 devcontainer.json

diff --git a/devcontainer.json b/devcontainer.json
new file mode 100644
index 00000000..14078735
--- /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"vi
+		}
+	},
+
+	// 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"
+}

From 7b669300d4144aa7c1be6e93b9622875e2d3e506 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Thu, 21 Dec 2023 19:55:03 +0000
Subject: [PATCH 2/4] rename devcontainer to .devcontainer

---
 devcontainer.json => .devcontainer.json | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename devcontainer.json => .devcontainer.json (100%)

diff --git a/devcontainer.json b/.devcontainer.json
similarity index 100%
rename from devcontainer.json
rename to .devcontainer.json

From 9e8552a9fc59e0caa989d2ae5e245b2cb99822c4 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Thu, 21 Dec 2023 19:55:34 +0000
Subject: [PATCH 3/4] fix typo in devcontainer

---
 .devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer.json b/.devcontainer.json
index 14078735..df947074 100644
--- a/.devcontainer.json
+++ b/.devcontainer.json
@@ -7,7 +7,7 @@
 	"features": {
 		"ghcr.io/rocker-org/devcontainer-features/miniforge:1": {
 			"version": "latest",
-			"variant": "Mambaforge"vi
+			"variant": "Mambaforge"
 		}
 	},
 

From 005355f4640fb40ce2a542e242d1cc921be92dd8 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Thu, 21 Dec 2023 20:41:12 +0000
Subject: [PATCH 4/4] add codespace badge

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

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)
+[<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.