fix typing error in python v3.9

python v3.9 does not support "|", and `from __future__ import annotations` can solve this problem.

src/nplinker/genomics/aa_pred.py

@@ -3,6 +3,7 @@
 # TODO This module is used in bgc.py, referenced in gcf.py and then in misc.py,
 # NPLinker core business does not use it at all.
 
+from __future__ import annotations
 import argparse
 from Bio import SeqIO
 

src/nplinker/genomics/antismash/antismash_downloader.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import os
 import shutil
 from os import PathLike

src/nplinker/genomics/antismash/podp_antismash_downloader.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import json
 import re
 import time

src/nplinker/genomics/bigscape/runbigscape.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import os
 import subprocess
 import sys

src/nplinker/genomics/mibig/mibig_downloader.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import os
 import shutil
 from pathlib import Path

src/nplinker/metabolomics/gnps/gnps_annotation_loader.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import csv
 from os import PathLike
 from pathlib import Path

src/nplinker/metabolomics/gnps/gnps_extractor.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import os
 import zipfile
 from os import PathLike

src/nplinker/metabolomics/gnps/gnps_file_mapping_loader.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import csv
 from os import PathLike
 from pathlib import Path

src/nplinker/metabolomics/gnps/gnps_format.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import zipfile
 from enum import Enum
 from enum import unique

src/nplinker/metabolomics/gnps/gnps_molecular_family_loader.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import csv
 from os import PathLike
 from nplinker.metabolomics.abc import MolecularFamilyLoaderBase

src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 from os import PathLike
 from pyteomics import mgf
 from nplinker.logconfig import LogConfig

src/nplinker/metabolomics/utils.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import json
 from os import PathLike
 from pathlib import Path

src/nplinker/parsers/kcb.py

@@ -12,6 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
 import json
 import os
 import re

src/nplinker/scoring/linking/link_likelihood.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 from deprecated import deprecated
 from nplinker.logconfig import LogConfig
 from nplinker.scoring.linking.utils import calc_likelihood_matrix

src/nplinker/strain/utils.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import json
 from os import PathLike
 from jsonschema import validate

tests/integration/conftest.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import os
 import shutil
 import tempfile