updated devcontainer

.devcontainer/devcontainer.json

@@ -0,0 +1,27 @@
+{
+    "name": "ont_preprocess",
+    "image": "mcr.microsoft.com/devcontainers/python:0-3.9",
+    "postCreateCommand": "bash .devcontainer/setup.sh",
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "GitHub.copilot",
+                "eamodio.gitlens",
+                "codezombiech.gitignore",
+                "ms-python.python",
+                "Gruntfuggly.todo-tree",
+                "ms-azuretools.vscode-docker",
+                "ms-vscode-remote.remote-ssh"
+            ]
+        }
+	},
+    "features": {
+        "ghcr.io/mamba-org/devcontainer-features/micromamba:1": {
+            "version": "latest",
+            "channels": "conda-forge,bioconda"
+        },
+        "ghcr.io/withfig/features/fig:1": {
+            "version": "latest"
+        }
+    }
+}

.devcontainer/setup.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# OS install
+sudo apt-get update -y
+## tools
+sudo apt-get install -y tree screen curl python3.8
+
+# dependencies
+#mamba install python=3.8 bioconda::hmmer scipy pandas numpy matplotlib
+micromamba env create -f conda_env.yml -y
+
+# package install
+python -m pip install --upgrade pip
+pip install pytest pytest-dependency pytest-console-scripts
+pip install .

conda_env.yml

@@ -0,0 +1,11 @@
+name: traitar3
+channels:
+- conda-forge
+- bioconda
+dependencies:
+- pip
+- matplotlib=3.7.0
+- numpy=1.24.2
+- pandas=1.5.3
+- scipy=1.10.1
+- hmmer=3.3.2