Refactor version retrieval to use importlib.metadata for compatibility

Author: mdshw5

pisces/__init__.py

@@ -18,9 +18,13 @@
 from multiprocessing import Process
 from tempfile import NamedTemporaryFile, mkdtemp
 from functools import partial
-from pkg_resources import get_distribution
+try:
+    from importlib.metadata import version
+except ImportError:
+    from pkg_resources import get_distribution
+    version = lambda name: get_distribution(name).version
 
-__version__ = get_distribution("novartis_pisces").version
+__version__ = version("novartis-pisces")
 
 unique_id = ''.join(random.choice(string.digits) for _ in range(10))
 

pisces/cli.py

@@ -21,9 +21,13 @@
 from collections import OrderedDict, defaultdict
 from tqdm import tqdm
 from pisces import find_data_directory
-from pkg_resources import get_distribution
+try:
+    from importlib.metadata import version
+except ImportError:
+    from pkg_resources import get_distribution
+    version = lambda name: get_distribution(name).version
 
-__version__ = get_distribution("novartis_pisces").version
+__version__ = version("novartis-pisces")
 
 data_dir = find_data_directory()
 

pisces/fastq.py

@@ -12,7 +12,6 @@
 from subprocess import Popen, PIPE
 from io import TextIOWrapper
 import os.path
-from pkg_resources import get_distribution
 
 if PY2:
     import string

pisces/index.py

@@ -1,9 +1,13 @@
 import logging
 import os
 from pisces import find_data_directory
-from pkg_resources import get_distribution
+try:
+    from importlib.metadata import version
+except ImportError:
+    from pkg_resources import get_distribution
+    version = lambda name: get_distribution(name).version
 
-__version__ = get_distribution("novartis_pisces").version
+__version__ = version("novartis-pisces")
 
 def build_index(args, unknown_args):
     from pyfaidx import Fasta

pisces/qc.py

@@ -2,9 +2,6 @@
 from collections import OrderedDict, defaultdict
 from pisces import find_data_directory
 from subprocess import Popen, PIPE, call
-from pkg_resources import get_distribution
-
-__version__ = get_distribution("novartis_pisces").version
 
 data_dir = find_data_directory()
 

pisces/run.py

@@ -6,9 +6,13 @@
 from multiprocessing import Process
 from pisces import find_data_directory, long_substr
 from itertools import chain
-from pkg_resources import get_distribution
+try:
+    from importlib.metadata import version
+except ImportError:
+    from pkg_resources import get_distribution
+    version = lambda name: get_distribution(name).version
 
-__version__ = get_distribution("novartis_pisces").version
+__version__ = version("novartis-pisces")
 
 data_dir = find_data_directory()
 

pisces/submit.py

@@ -9,9 +9,13 @@
 import pickle
 import pandas as pd
 import time
-from pkg_resources import get_distribution
+try:
+    from importlib.metadata import version
+except ImportError:
+    from pkg_resources import get_distribution
+    version = lambda name: get_distribution(name).version
 
-__version__ = get_distribution("novartis_pisces").version
+__version__ = version("novartis-pisces")
 
 def _submit_drmaa(args, unknown_args):
     """ Submit multiple 'pisces run' jobs to the cluster using libdrmaa """