Merge pull request #74 from GuignardLab/update_readme

Update readme

Author: leoguignard

README.md

@@ -24,66 +24,44 @@ and one can then load lineage trees the following way:
 For `.lT` files:
 
 ```python
-lT = lineageTree('path/to/file.lT')
+lT = lineageTree.load('path/to/file.lT')
 ```
 
 For ASTEC data:
 
 ```python
-lT = lineageTree('path/to/ASTEC.pkl', file_type='ASTEC')
+from LineageTree import read_from_ASTEC
+lT = read_from_ASTEC('path/to/ASTEC.pkl')
 ```
 
-or
+For MaMuT or TrackMate:
 
 ```python
-lT = lineageTree('path/to/ASTEC.xml', file_type='ASTEC')
-```
-
-For SVF:
-
-```python
-lT = lineageTree('path/to/SVF.bin')
-```
-
-For MaMuT:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='MaMuT')
-```
-
-For TrackMate:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='TrackMate')
+from LineageTree import read_from_mamut_xml
+lT = read_from_mamut_xml('path/to/MaMuT.xml')
 ```
 
 For TGMM:
 
 ```python
-lT = lineageTree('path/to/single_time_file{t:04d}.xml', tb=0, te=500, file_type='TGMM')
+from LineageTree import read_from_tgmm_xml
+lT = read_from_tgmm_xml('path/to/single_time_file{t:04d}.xml', tb=0, te=500)
 ```
 
 For Mastodon:
 
 ```python
-lT = lineageTree('path/to/Mastodon.mastodon', file_type='mastodon')
+from LineageTree import read_from_mastodon
+lT = read_from_mastodon('path/to/Mastodon.mastodon')
 ```
 
 or, for Mastodon csv file:
 
 ```python
-lT = lineageTree(['path/to/nodes.csv', 'path/to/links.csv'], file_type='mastodon')
+from LineageTree import read_from_mastodon_csv
+lT = read_from_mastodon_csv(['path/to/nodes.csv', 'path/to/links.csv'])
 ```
 
-## Dependencies
-
-Some dependecies are requiered:
-
-- general python dependecies:
-  - numpy, scipy
-- specific dependency:
-  - svgwrite if svg output is needed
-
 ## Quick install
 
 To quickly install the library together with its dependencies one can run:

src/LineageTree/lineageTreeManager.py

@@ -657,28 +657,28 @@ def plot_tree_distance_graphs(
                         matched_right.append(node_2)
                         l_node_2 = tree2.lT.get_chain_of_node(node_2)[-1]
                         matched_right.append(l_node_2)
-                        colors1[node_1] = (
-                            self.__calculate_distance_of_sub_tree(
-                                node_1,
-                                tree1.lT,
-                                node_2,
-                                tree2.lT,
-                                btrc,
-                                corres1,
-                                corres2,
-                                delta_tmp,
-                                self.norm_dict[norm],
-                                tree1.get_norm(node_1),
-                                tree2.get_norm(node_2),
-                            )
+                        colors1[
+                            node_1
+                        ] = self.__calculate_distance_of_sub_tree(
+                            node_1,
+                            tree1.lT,
+                            node_2,
+                            tree2.lT,
+                            btrc,
+                            corres1,
+                            corres2,
+                            delta_tmp,
+                            self.norm_dict[norm],
+                            tree1.get_norm(node_1),
+                            tree2.get_norm(node_2),
                         )
                         colors2[node_2] = colors1[node_1]
-                        colors1[tree1.lT.get_chain_of_node(node_1)[-1]] = (
-                            colors1[node_1]
-                        )
-                        colors2[tree2.lT.get_chain_of_node(node_2)[-1]] = (
-                            colors2[node_2]
-                        )
+                        colors1[
+                            tree1.lT.get_chain_of_node(node_1)[-1]
+                        ] = colors1[node_1]
+                        colors2[
+                            tree2.lT.get_chain_of_node(node_2)[-1]
+                        ] = colors2[node_2]
 
                         if tree1.lT.get_chain_of_node(node_1)[-1] != node_1:
                             matched_left.append(

src/LineageTree/test/test_lineageTree.py

@@ -2,7 +2,6 @@
 
 import numpy as np
 import pytest
-
 from LineageTree import (
     lineageTree,
     lineageTreeManager,