From ba4a5327844152c40643125d267456cb9800f4f5 Mon Sep 17 00:00:00 2001
From: Harrison <yunyangdeng@gmail.com>
Date: Mon, 24 Apr 2023 16:23:02 -0500
Subject: [PATCH 1/3] Bumped package version

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 014b452..48e2157 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = splitmsa
-version = 0.0.3
+version = 0.0.4
 
 [options]
 packages = splitmsa

From bfeec687565795fdf92d1701c23df1c009c755ae Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Sun, 21 Jul 2024 02:52:25 +0000
Subject: [PATCH 2/3] Added devcontainer to pipeline.

---
 .devcontainer/Dockerfile        | 11 +++++++++++
 .devcontainer/devcontainer.json | 24 ++++++++++++++++++++++++
 .devcontainer/noop.txt          |  3 +++
 Jenkinsfile                     | 24 ++++++++++++------------
 4 files changed, 50 insertions(+), 12 deletions(-)
 create mode 100644 .devcontainer/Dockerfile
 create mode 100644 .devcontainer/devcontainer.json
 create mode 100644 .devcontainer/noop.txt

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
new file mode 100644
index 0000000..2738918
--- /dev/null
+++ b/.devcontainer/Dockerfile
@@ -0,0 +1,11 @@
+FROM mcr.microsoft.com/devcontainers/anaconda:1-3
+
+# Copy environment.yml (if found) to a temp location so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
+RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+    && rm -rf /tmp/conda-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..70e91b2
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,24 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/anaconda
+{
+	"name": "Anaconda (Python 3)",
+	"build": { 
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	}
+
+	// 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": "python --version",
+
+	// 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/.devcontainer/noop.txt b/.devcontainer/noop.txt
new file mode 100644
index 0000000..dde8dc3
--- /dev/null
+++ b/.devcontainer/noop.txt
@@ -0,0 +1,3 @@
+This file copied into the container along with environment.yml* from the parent
+folder. This file is included to prevents the Dockerfile COPY instruction from 
+failing if no environment.yml is found.
\ No newline at end of file
diff --git a/Jenkinsfile b/Jenkinsfile
index 9166532..fe35108 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -1,26 +1,26 @@
 pipeline {
-    agent any
-    stages {
-        stage("clean") {
-            steps {
-                sh 'rm -rf ./dist/*'
-            }
+    agent {
+        kubernetes {
+            cloud 'Reslate Systems'
+            defaultContainer 'conda'
         }
+    }
+    stages {
         stage("install") {
             steps {
-                sh 'mamba env update --file environment.yml'
-                sh 'echo "mamba activate splitmsa" >> ~/.bashrc'
+                sh 'conda update conda -y -q'
+                sh 'conda env update -n base --file environment.yml'
             }
         }
         stage("build") {
             steps {
-                sh "python -m build"
+                sh "conda run -n base python -m build"
             }
         }
         stage("test") {
             steps {
-                sh "pip install dist/*.whl"
-                sh "splitmsa -h"
+                sh "conda run -n base pip install dist/*.whl"
+                sh "conda run -n base splitmsa -h"
             }
         }
         stage("archive") {
@@ -34,7 +34,7 @@ pipeline {
             }
             steps {
                 withCredentials([usernamePassword(credentialsId: 'rs-git-package-registry-ydeng', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
-                    sh "python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
+                    sh "conda run -n base python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
                 }
             }
         }

From 9d97ee6244631f1558fc3a9c430f00401a35776a Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Sun, 21 Jul 2024 02:54:01 +0000
Subject: [PATCH 3/3] Added some extensions for the devcontainer.

---
 .devcontainer/devcontainer.json | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 70e91b2..edc63c0 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -5,6 +5,17 @@
 	"build": { 
 		"context": "..",
 		"dockerfile": "Dockerfile"
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-python.debugpy",
+				"ms-python.python",
+				"ms-python.vscode-pylance",
+				"ms-python.black-formatter",
+				"ms-python.flake8"
+			]
+		}
 	}
 
 	// Features to add to the dev container. More info: https://containers.dev/features.