readme and docstrings

README.md

@@ -1,17 +1,28 @@
 [![](https://img.shields.io/badge/Python-3.10-blue.svg)]()
-[![](https://img.shields.io/badge/Documentation-unfinished-orange.svg)]()
-[![](https://img.shields.io/badge/build-passing-green.svg)]()
+[![](https://img.shields.io/badge/Python-3.11-blue.svg)]()
+[![](https://img.shields.io/badge/Python-3.12-blue.svg)]()
+[![](https://img.shields.io/badge/documentation-unfinished-orange.svg)]()
 
-# GFAgraphs
+# GFAGraphs - A Python GFA library
 
-This package aims to be an abstraction layer for GFA file format.
+This Python library aims to be an abstraction layer for GFA file format.
+Two implementations are proposed:
++ a legacy one, which will remain until deprecated, in `gfagraphs/`
++ a new, cleaner and faster implementation, in `pgGraphs/`
 
-Its a simple, convinient but lack-luster library to extract informations from GFA files, be it as the graph or line level.
+> [!WARNING]\
+> Moving forward, features will only be added to `pgGraphs`, while `gfagraphs` will remain as it, until full migration is done in [pancat](https://github.com/Tharos-ux/pancat) tool.
 
-Main features are :
-+ **Record** (line-level) and **Graph** (file-level) abstractions
-+ Full decoding of **GFA tags** (standard+optional)
-+ **pip**-installable (`pip install gfagraphs`)
-+ **networkx** integration
+## Package pgGraphs
 
+![](https://media.discordapp.net/attachments/874430800802754623/1179353568105467964/library.png)
+
+The package is organized in 4 modules:
++ `pgGraphs.abstractions` contains abstractions over GFA formats
++ `pgGraphs.gfaparser` contains an abstract class for parsing and saving GFA file format
++ `pgGraphs.graph` contains the main `Graph` class that represents a GFA graph in memory, and edit functions
++ `pgGraphs.networkx` conains an abstract class for visualization and modelization of GFA in a NetworkX object
+
+> [!NOTE]\
+> Want to contribute? Feel free to open a PR on an issue about a missing, buggy or incomplete feature!
 

pgGraphs/gfaparser.py

@@ -1,4 +1,4 @@
-""
+"Abstract class for parsing and saving GFA file format"
 from re import match, sub
 from typing import Callable
 from json import loads, dumps

pgGraphs/networkx.py

@@ -1,3 +1,4 @@
+"Abstract class for visualization and modelization of GFA in a NetworkX object"
 from networkx import MultiDiGraph, DiGraph
 from pgGraphs.graph import Graph
 from tharospytools.matplotlib_tools import get_palette

test_pggraphs.py

@@ -2,4 +2,7 @@
 
 
 def test_init_empty_graph() -> None:
+    """
+        Tests the initialization of an empty graph
+    """
     graph: Graph = Graph()