Jenkinsfile

@@ -28,7 +28,7 @@ pipeline {
             }
             steps {
                 withCredentials([usernamePassword(credentialsId: 'rs-git-package-registry-ydeng', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
-                    sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*'
+                    sh "python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
                 }
             }
         }

bmlsa/aligner.py

@@ -1,6 +1,7 @@
 from Bio.Align import PairwiseAligner, substitution_matrices
-from bmlsa.datatypes import AlignedSequence
+from exceptions import UnexpectedAlignmentResult
-from bmlsa.exceptions import UnexpectedAlignmentResult
+
+from datatypes import AlignedSequence
 
 
 def protein_align_many_to_one_ssw(sequence: str, queries: dict[str, AlignedSequence]):
@@ -35,7 +36,7 @@ def protein_align_many_to_one_ssw(sequence: str, queries: dict[str, AlignedSeque
                 alignment.query,
                 query.name,
                 query.description,
-                int(aligned_start) + 1,
+                aligned_start,
                 aligned_end,
                 score,
             )

bmlsa/cli.py

@@ -1,9 +1,9 @@
 import os
 import argparse
 from Bio import SeqIO
-from bmlsa.aligner import protein_align_many_to_one_ssw
+from aligner import protein_align_many_to_one_ssw
 
-from bmlsa.persistence import read_annotations_from_csv, save_alignments_to_csv
+from persistence import read_annotations_from_csv, save_alignments_to_csv
 
 
 def main():

bmlsa/persistence.py

@@ -1,6 +1,5 @@
 import csv
-
+from datatypes import AlignedSequence
-from bmlsa.datatypes import AlignedSequence
 
 
 def read_annotations_from_csv(

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = bmlsa
-version = 0.0.3
+version = 0.0.1
 
 [options]
 packages = bmlsa