From 50210a884dc68ed5fbbb159d2f004dcbd4e27d9b Mon Sep 17 00:00:00 2001
From: Harrison <yunyangdeng@gmail.com>
Date: Fri, 21 Apr 2023 13:54:57 -0500
Subject: [PATCH] Fixed deployed CLI import paths

---
 bmlsa/aligner.py     | 5 ++---
 bmlsa/cli.py         | 4 ++--
 bmlsa/persistence.py | 3 ++-
 setup.cfg            | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/bmlsa/aligner.py b/bmlsa/aligner.py
index f85df25..a7bdfdf 100644
--- a/bmlsa/aligner.py
+++ b/bmlsa/aligner.py
@@ -1,7 +1,6 @@
 from Bio.Align import PairwiseAligner, substitution_matrices
-from exceptions import UnexpectedAlignmentResult
-
-from datatypes import AlignedSequence
+from bmlsa.datatypes import AlignedSequence
+from bmlsa.exceptions import UnexpectedAlignmentResult
 
 
 def protein_align_many_to_one_ssw(sequence: str, queries: dict[str, AlignedSequence]):
diff --git a/bmlsa/cli.py b/bmlsa/cli.py
index 424dfcd..a082cae 100644
--- a/bmlsa/cli.py
+++ b/bmlsa/cli.py
@@ -1,9 +1,9 @@
 import os
 import argparse
 from Bio import SeqIO
-from aligner import protein_align_many_to_one_ssw
+from bmlsa.aligner import protein_align_many_to_one_ssw
 
-from persistence import read_annotations_from_csv, save_alignments_to_csv
+from bmlsa.persistence import read_annotations_from_csv, save_alignments_to_csv
 
 
 def main():
diff --git a/bmlsa/persistence.py b/bmlsa/persistence.py
index fa4dc9f..a63a070 100644
--- a/bmlsa/persistence.py
+++ b/bmlsa/persistence.py
@@ -1,5 +1,6 @@
 import csv
-from datatypes import AlignedSequence
+
+from bmlsa.datatypes import AlignedSequence
 
 
 def read_annotations_from_csv(
diff --git a/setup.cfg b/setup.cfg
index e04dfc9..be41ec5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = bmlsa
-version = 0.0.1
+version = 0.0.2
 
 [options]
 packages = bmlsa