MAINT: add/update dunder attributes for metadata

reneo/workflow/scripts/combineJunctionPickles.py

@@ -4,7 +4,7 @@
 from collections import defaultdict
 
 __author__ = "Michael Roach"
-__copyright__ = "Copyright 2022, Reneo Project"
+__copyright__ = "Copyright 2023, Reneo Project"
 __license__ = "MIT"
 __version__ = "0.5.0"
 __maintainer__ = "Vijini Mallawaarachchi"

reneo/workflow/scripts/reneo.py

@@ -23,7 +23,7 @@
 )
 
 __author__ = "Vijini Mallawaarachchi"
-__copyright__ = "Copyright 2022, Reneo Project"
+__copyright__ = "Copyright 2023, Reneo Project"
 __license__ = "MIT"
 __version__ = "0.5.0"
 __maintainer__ = "Vijini Mallawaarachchi"

reneo/workflow/scripts/reneo_utils/FD_Inexact.py

@@ -1,12 +1,23 @@
+#!/usr/bin/env python3
+
 # Source: https://github.com/algbio/MFD-ILP
 
 import logging
 
 import more_itertools
 import networkx as nx
 
-# create logger
-logger = logging.getLogger("reneo 0.5.0")
+__author__ = "Vijini Mallawaarachchi"
+__copyright__ = "Copyright 2023, Reneo Project"
+__license__ = "MIT"
+__version__ = "0.5.0"
+__maintainer__ = "Vijini Mallawaarachchi"
+__email__ = "[email protected]"
+__status__ = "Development"
+
+
+# Create logger
+logger = logging.getLogger(f"reneo {__version__}")
 
 
 def read_input(graphfile, number_subpath):

reneo/workflow/scripts/reneo_utils/component_utils.py

@@ -1,3 +1,14 @@
+#!/usr/bin/env python3
+
+__author__ = "Vijini Mallawaarachchi"
+__copyright__ = "Copyright 2023, Reneo Project"
+__license__ = "MIT"
+__version__ = "0.5.0"
+__maintainer__ = "Vijini Mallawaarachchi"
+__email__ = "[email protected]"
+__status__ = "Development"
+
+
 def get_components(**kwargs):
     """
     Get connected components with VOGs and no SMGs.

reneo/workflow/scripts/reneo_utils/coverage_utils.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import glob
 import os
 import pickle
@@ -7,6 +9,14 @@
 
 import pysam
 
+__author__ = "Vijini Mallawaarachchi"
+__copyright__ = "Copyright 2023, Reneo Project"
+__license__ = "MIT"
+__version__ = "0.5.0"
+__maintainer__ = "Vijini Mallawaarachchi"
+__email__ = "[email protected]"
+__status__ = "Development"
+
 
 def get_unitig_coverage(coverage):
     """

reneo/workflow/scripts/reneo_utils/edge_graph_utils.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import copy
 import logging
 from collections import defaultdict
@@ -6,8 +8,17 @@
 from Bio.Seq import Seq
 from igraph import *
 
+__author__ = "Vijini Mallawaarachchi"
+__copyright__ = "Copyright 2023, Reneo Project"
+__license__ = "MIT"
+__version__ = "0.5.0"
+__maintainer__ = "Vijini Mallawaarachchi"
+__email__ = "[email protected]"
+__status__ = "Development"
+
+
 # Create logger
-logger = logging.getLogger("reneo 0.5.0")
+logger = logging.getLogger(f"reneo {__version__}")
 
 
 class BidirectionalError(Exception):

reneo/workflow/scripts/reneo_utils/flow_utils.py

@@ -1,9 +1,18 @@
-import tempfile
+#!/usr/bin/env python3
 
+import tempfile
 import networkx as nx
 
 from .FD_Inexact import SolveInstances
 
+__author__ = "Vijini Mallawaarachchi"
+__copyright__ = "Copyright 2023, Reneo Project"
+__license__ = "MIT"
+__version__ = "0.5.0"
+__maintainer__ = "Vijini Mallawaarachchi"
+__email__ = "[email protected]"
+__status__ = "Development"
+
 
 def get_source_sink_circular(G_edge, graph_unitigs, minlength, self_looped_nodes):
     """

reneo/workflow/scripts/reneo_utils/gene_utils.py

@@ -1,6 +1,16 @@
+#!/usr/bin/env python3
+
 from collections import defaultdict
 from pathlib import Path
 
+__author__ = "Vijini Mallawaarachchi"
+__copyright__ = "Copyright 2023, Reneo Project"
+__license__ = "MIT"
+__version__ = "0.5.0"
+__maintainer__ = "Vijini Mallawaarachchi"
+__email__ = "[email protected]"
+__status__ = "Development"
+
 
 def get_smg_unitigs(hmmout, mg_frac):
     """

reneo/workflow/scripts/reneo_utils/genome_utils.py

@@ -1,3 +1,14 @@
+#!/usr/bin/env python3
+
+__author__ = "Vijini Mallawaarachchi"
+__copyright__ = "Copyright 2023, Reneo Project"
+__license__ = "MIT"
+__version__ = "0.5.0"
+__maintainer__ = "Vijini Mallawaarachchi"
+__email__ = "[email protected]"
+__status__ = "Development"
+
+
 # Class for genome path
 class GenomePath:
     def __init__(

reneo/workflow/scripts/reneo_utils/output_utils.py

@@ -1,9 +1,19 @@
+#!/usr/bin/env python3
+
 import os
 import subprocess
 
-FASTA_LINE_LEN = 60
+__author__ = "Vijini Mallawaarachchi"
+__copyright__ = "Copyright 2023, Reneo Project"
+__license__ = "MIT"
+__version__ = "0.5.0"
+__maintainer__ = "Vijini Mallawaarachchi"
+__email__ = "[email protected]"
+__status__ = "Development"
 
 
+FASTA_LINE_LEN = 60
+
 def write_unitigs(nodes, unitig_names, graph_unitigs, filename, output):
     """
     Write unitigs to FASTA file

reneo/workflow/scripts/sampleJunctions.py

@@ -7,7 +7,7 @@
 from reneo_utils.coverage_utils import read_pair_generator
 
 __author__ = "Michael Roach"
-__copyright__ = "Copyright 2022, Reneo Project"
+__copyright__ = "Copyright 2023, Reneo Project"
 __license__ = "MIT"
 __version__ = "0.5.0"
 __maintainer__ = "Vijini Mallawaarachchi"