Merge branch 'develop' of https://git.reslate.systems/ydeng/msa-splitter into develop

.devcontainer/Dockerfile

@@ -1,11 +0,0 @@
-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

@@ -1,35 +0,0 @@
-// 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

@@ -1,3 +0,0 @@
-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

@@ -1,31 +1,27 @@
 pipeline {
-    agent {
+    agent any
-        kubernetes {
-            cloud 'Reslate Systems'
-            defaultContainer 'conda'
-        }
-    }
     stages {
+        stage("clean") {
+            steps {
+                sh 'rm -rf ./dist/*'
+            }
+        }
         stage("install") {
             steps {
-                sh 'conda update conda -y -q'
+                sh 'mamba env update --file environment.yml'
-                sh 'conda env update -n base --file environment.yml'
+                sh 'echo "mamba activate splitmsa" >> ~/.bashrc'
             }
         }
         stage("build") {
             steps {
-                sh "conda run -n base python -m build"
+                sh "python -m build"
+                sh "splitmsa -h"
             }
         }
         stage("test") {
             steps {
-                sh "conda run -n base pip install dist/*.whl"
+                sh "pip install dist/*.whl"
-                sh "conda run -n base splitmsa -h"
+                sh "splitmsa -h"
-            }
-        }
-        stage("archive") {
-            steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl'
             }
         }
         stage("publish") {
@@ -34,7 +30,7 @@ pipeline {
             }
             steps {
                 withCredentials([usernamePassword(credentialsId: 'rs-git-package-registry-ydeng', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
-                    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 ${PASS} --non-interactive --disable-progress-bar --verbose dist/*'
+                    sh "python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
                 }
             }
         }

environment.yml

@@ -4,6 +4,6 @@ channels:
 dependencies:
   - build=0.7.0
   - pytest=7.2.2
-  - twine
+  - twine=4.0.2
   - biopython=1.81
   - python=3.9

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = splitmsa
-version = 0.0.4
+version = 0.0.2
 
 [options]
 packages = splitmsa
@@ -9,4 +9,4 @@ install_requires =
 
 [options.entry_points]
 console_scripts =
-    splitmsa = splitmsa.splitmsa:main
+    splitmsa = splitmsa.cli:main