Merge branch 'master' into develop

.vscode/launch.json

@@ -8,7 +8,7 @@
             "name": "Run Fasta Filter",
             "type": "python",
             "request": "launch",
-            "program": "${workspaceFolder}/filterfasta/filterfasta.py",
+            "module": "filterfasta.cli",
             "args": [
                 "reference_standards.fas",
                 "reference_standards_filtered.fas",

Jenkinsfile

@@ -8,7 +8,8 @@ pipeline {
         }
         stage("install") {
             steps {
-                sh 'mamba env update --file environment.yml --prefix ./env || mamba env create --force --file environment.yml --prefix ./env'
+                sh 'mamba env update --file environment.yml'
+                sh 'echo "mamba activate filterfasta" >> ~/.bashrc'
             }
         }
         stage("build") {
@@ -24,7 +25,7 @@ pipeline {
         }
         stage("archive") {
             steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl'
             }
         }
         stage("publish") {

environment.yml

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

setup.cfg

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