Merge branch 'master' into develop

Wrong package name given in 'setup.cfg' is now fixed.

.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>

.devcontainer/devcontainer.json

@@ -0,0 +1,35 @@
+// 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"
+	},
+	"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.
+	// "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"
+}

.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.

Jenkinsfile

@@ -1,15 +1,31 @@
 pipeline {
-    agent any
+    agent {
+        kubernetes {
+            cloud 'Reslate Systems'
+            defaultContainer 'conda'
+        }
+    }
     stages {
         stage("install") {
             steps {
-                sh 'mamba env update --file environment.yml'
+                sh 'conda update conda -y -q'
-                sh 'echo "mamba activate splitmsa" >> ~/.bashrc'
+                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 "conda run -n base pip install dist/*.whl"
+                sh "conda run -n base splitmsa -h"
+            }
+        }
+        stage("archive") {
+            steps {
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
             }
         }
         stage("publish") {
@@ -18,7 +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 ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
+                    sh returnStatus: true, script: 'conda run -n base python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*'
                 }
             }
         }

environment.yml

@@ -4,7 +4,7 @@ channels:
 dependencies:
   - build=0.7.0
   - pytest=7.2.2
-  - twine=4.0.2
+  - twine
   - biopython=1.81
-  - gooey=1.0.8.1
   - python=3.9
+prefix: ./env

requirements.txt

@@ -1 +0,0 @@
-Bio==1.5.6

setup.cfg

@@ -1,13 +1,12 @@
 [metadata]
 name = splitmsa
-version = 0.0.1
+version = 0.0.4
 
 [options]
 packages = splitmsa
 install_requires =
-    gooey
+    biopython ==1.81; python_version == "3.9"
-    Bio; python_version == "3.9"
 
 [options.entry_points]
 console_scripts =
-    splitmsa = splitmsa.splitmsa:main
+    splitmsa = splitmsa.splitmsa:main

splitmsa/splitmsa.py

@@ -14,7 +14,6 @@ import os
 from Bio import SeqIO, SeqRecord
 from Bio.Seq import Seq
 import csv
-from gooey import Gooey
 
 
 def read_genes_from_csv(batch_genes_csv_path: str):
@@ -309,7 +308,6 @@ def run(args):
         info(f"Completed gene {gene_name} ({start} - {end})")
 
 
-@Gooey
 def main():
     parser = argparse.ArgumentParser(
         prog="splitmsa",