From a50b1e9999e12e9010eb1b7709de742cb7851d64 Mon Sep 17 00:00:00 2001
From: Vijini Mallawaarachchi <viji.mallawaarachchi@gmail.com>
Date: Wed, 4 Sep 2024 12:10:45 +0930
Subject: [PATCH] MAINT: add/update dunder attributes for metadata

---
 reneo/workflow/scripts/combineJunctionPickles.py  |  2 +-
 reneo/workflow/scripts/reneo.py                   |  2 +-
 reneo/workflow/scripts/reneo_utils/FD_Inexact.py  | 15 +++++++++++++--
 .../scripts/reneo_utils/component_utils.py        | 11 +++++++++++
 .../scripts/reneo_utils/coverage_utils.py         | 10 ++++++++++
 .../scripts/reneo_utils/edge_graph_utils.py       | 13 ++++++++++++-
 reneo/workflow/scripts/reneo_utils/flow_utils.py  | 11 ++++++++++-
 reneo/workflow/scripts/reneo_utils/gene_utils.py  | 10 ++++++++++
 .../workflow/scripts/reneo_utils/genome_utils.py  | 11 +++++++++++
 .../workflow/scripts/reneo_utils/output_utils.py  | 12 +++++++++++-
 reneo/workflow/scripts/sampleJunctions.py         |  2 +-
 11 files changed, 91 insertions(+), 8 deletions(-)

diff --git a/reneo/workflow/scripts/combineJunctionPickles.py b/reneo/workflow/scripts/combineJunctionPickles.py
index 54e4b07..ebc075f 100644
--- a/reneo/workflow/scripts/combineJunctionPickles.py
+++ b/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"
diff --git a/reneo/workflow/scripts/reneo.py b/reneo/workflow/scripts/reneo.py
index de01552..8e76ab3 100644
--- a/reneo/workflow/scripts/reneo.py
+++ b/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"
diff --git a/reneo/workflow/scripts/reneo_utils/FD_Inexact.py b/reneo/workflow/scripts/reneo_utils/FD_Inexact.py
index 36d68b2..ebed488 100644
--- a/reneo/workflow/scripts/reneo_utils/FD_Inexact.py
+++ b/reneo/workflow/scripts/reneo_utils/FD_Inexact.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 # Source: https://github.com/algbio/MFD-ILP
 
 import logging
@@ -5,8 +7,17 @@
 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__ = "viji.mallawaarachchi@gmail.com"
+__status__ = "Development"
+
+
+# Create logger
+logger = logging.getLogger(f"reneo {__version__}")
 
 
 def read_input(graphfile, number_subpath):
diff --git a/reneo/workflow/scripts/reneo_utils/component_utils.py b/reneo/workflow/scripts/reneo_utils/component_utils.py
index bd7e79d..e48079a 100644
--- a/reneo/workflow/scripts/reneo_utils/component_utils.py
+++ b/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__ = "viji.mallawaarachchi@gmail.com"
+__status__ = "Development"
+
+
 def get_components(**kwargs):
     """
     Get connected components with VOGs and no SMGs.
diff --git a/reneo/workflow/scripts/reneo_utils/coverage_utils.py b/reneo/workflow/scripts/reneo_utils/coverage_utils.py
index 42cff10..9213a5a 100644
--- a/reneo/workflow/scripts/reneo_utils/coverage_utils.py
+++ b/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__ = "viji.mallawaarachchi@gmail.com"
+__status__ = "Development"
+
 
 def get_unitig_coverage(coverage):
     """
diff --git a/reneo/workflow/scripts/reneo_utils/edge_graph_utils.py b/reneo/workflow/scripts/reneo_utils/edge_graph_utils.py
index 05be7c5..565f09d 100644
--- a/reneo/workflow/scripts/reneo_utils/edge_graph_utils.py
+++ b/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__ = "viji.mallawaarachchi@gmail.com"
+__status__ = "Development"
+
+
 # Create logger
-logger = logging.getLogger("reneo 0.5.0")
+logger = logging.getLogger(f"reneo {__version__}")
 
 
 class BidirectionalError(Exception):
diff --git a/reneo/workflow/scripts/reneo_utils/flow_utils.py b/reneo/workflow/scripts/reneo_utils/flow_utils.py
index 623d344..135f8a8 100644
--- a/reneo/workflow/scripts/reneo_utils/flow_utils.py
+++ b/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__ = "viji.mallawaarachchi@gmail.com"
+__status__ = "Development"
+
 
 def get_source_sink_circular(G_edge, graph_unitigs, minlength, self_looped_nodes):
     """
diff --git a/reneo/workflow/scripts/reneo_utils/gene_utils.py b/reneo/workflow/scripts/reneo_utils/gene_utils.py
index 3915739..e27aff0 100644
--- a/reneo/workflow/scripts/reneo_utils/gene_utils.py
+++ b/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__ = "viji.mallawaarachchi@gmail.com"
+__status__ = "Development"
+
 
 def get_smg_unitigs(hmmout, mg_frac):
     """
diff --git a/reneo/workflow/scripts/reneo_utils/genome_utils.py b/reneo/workflow/scripts/reneo_utils/genome_utils.py
index 7f580d3..febdec3 100644
--- a/reneo/workflow/scripts/reneo_utils/genome_utils.py
+++ b/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__ = "viji.mallawaarachchi@gmail.com"
+__status__ = "Development"
+
+
 # Class for genome path
 class GenomePath:
     def __init__(
diff --git a/reneo/workflow/scripts/reneo_utils/output_utils.py b/reneo/workflow/scripts/reneo_utils/output_utils.py
index cbe79a8..a8fd7df 100644
--- a/reneo/workflow/scripts/reneo_utils/output_utils.py
+++ b/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__ = "viji.mallawaarachchi@gmail.com"
+__status__ = "Development"
 
 
+FASTA_LINE_LEN = 60
+
 def write_unitigs(nodes, unitig_names, graph_unitigs, filename, output):
     """
     Write unitigs to FASTA file
diff --git a/reneo/workflow/scripts/sampleJunctions.py b/reneo/workflow/scripts/sampleJunctions.py
index a4c8e97..618f048 100644
--- a/reneo/workflow/scripts/sampleJunctions.py
+++ b/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"