From 9d98d5d8d1424a69b0fcc71c107f637145a9daf0 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Thu, 14 Nov 2024 19:57:55 +0000
Subject: [PATCH] Updated CI to new serverside config and added devcontainer
 config

---
 .devcontainer/devcontainer.json | 22 ++++++++++++++++++++++
 Jenkinsfile                     | 11 +++++++++--
 requirements.txt                |  6 ++++++
 3 files changed, 37 insertions(+), 2 deletions(-)
 create mode 100644 .devcontainer/devcontainer.json
 create mode 100644 requirements.txt

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..8c6f3fb
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,22 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python 3",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye"
+
+	// 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": "pip3 install --user -r requirements.txt",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}
diff --git a/Jenkinsfile b/Jenkinsfile
index f44b283..3d25256 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -1,9 +1,16 @@
 pipeline {
-    agent any
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
+        }
+    }
+
     stages {
         stage("install") {
             steps {
-                sh 'mamba env update --file environment.yml --prefix ./env || mamba env create --force --file environment.yml --prefix ./env'
+                sh 'pip install -r requirements.txt'
             }
         }
         stage("unit tests") {
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..4ad03b3
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,6 @@
+biopython==1.81
+pytest
+hypothesis
+twine
+python-build
+setuptools