From 603c962a67e95dc90c586424df53aae3469d4ef3 Mon Sep 17 00:00:00 2001
From: Tharos <dubois.siegfried@gmail.com>
Date: Wed, 29 Nov 2023 10:44:13 +0100
Subject: [PATCH] readme and docstrings

---
 README.md             | 31 +++++++++++++++++++++----------
 pgGraphs/gfaparser.py |  2 +-
 pgGraphs/networkx.py  |  1 +
 test_pggraphs.py      |  3 +++
 4 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index a8dfdc3..1419703 100644
--- a/README.md
+++ b/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!
 
diff --git a/pgGraphs/gfaparser.py b/pgGraphs/gfaparser.py
index 178222c..fa753fe 100644
--- a/pgGraphs/gfaparser.py
+++ b/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
diff --git a/pgGraphs/networkx.py b/pgGraphs/networkx.py
index a5a0361..74c5dca 100644
--- a/pgGraphs/networkx.py
+++ b/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
diff --git a/test_pggraphs.py b/test_pggraphs.py
index 87fe8e1..659607d 100644
--- a/test_pggraphs.py
+++ b/test_pggraphs.py
@@ -2,4 +2,7 @@
 
 
 def test_init_empty_graph() -> None:
+    """
+        Tests the initialization of an empty graph
+    """
     graph: Graph = Graph()