Merge branch 'master' into develop

.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"
+}

Jenkinsfile

@@ -1,15 +1,15 @@
 pipeline {
-    agent any
-    stages {
-        stage("clean") {
-            steps {
-                sh 'rm -rf ./dist/*'
-            }
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
         }
+    }
+    stages {
         stage("install") {
             steps {
-                sh 'mamba env update --file environment.yml'
-                sh 'echo "mamba activate filterfasta" >> ~/.bashrc'
+                sh 'pip install -r requirements.txt'
             }
         }
         stage("build") {
@@ -25,7 +25,7 @@ pipeline {
         }
         stage("archive") {
             steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl'
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
             }
         }
         stage("publish") {
@@ -33,8 +33,8 @@ pipeline {
                 branch '**/master'
             }
             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 ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
+                withCredentials([usernamePassword(credentialsId: '4d6f64be-d26d-4f95-8de3-b6a9b0beb311', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
+                    sh returnStdout: true, script: "python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
                 }
             }
         }

environment.yml

@@ -7,3 +7,4 @@ dependencies:
   - twine=4
   - biopython=1.81
   - python=3.11
+prefix: ./env

requirements.txt

@@ -1 +1,5 @@
 Bio==1.5.6
+build
+pytest
+twine
+biopython==1.81

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = filterfasta
-version = 0.0.2
+version = 0.0.3
 
 [options]
 packages = filterfasta