fixing ruff problems

notebooks/Basics_of_lineageTree.ipynb

@@ -131,11 +131,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# lT.plot_nodes(list(lT.roots)[3])"
+    "# lT.plot_nodes(list(lT.roots)[3])  # noqa: ERA001\n"
    ]
   },
   {
@@ -556,7 +556,7 @@
    "source": [
     "selected_root = list(lT.roots)[0]\n",
     "lT.get_subtree_nodes(selected_root)  # returns all the nodes spawned by a node\n",
-    "lT.all_chains  # returns a list of lists that contains each chain of the dataset\n",
+    "lT.all_chains  # returns a list of lists that contains each chain of the dataset  # noqa: B018\n",
     "lT.get_all_chains_of_subtree(\n",
     "    selected_root\n",
     ")  # returns a list of lists that contains each chain of the subtree of a node"
@@ -568,8 +568,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lT.nodes  # all the nodes present on the lT object\n",
-    "lT.roots  # all the roots of the object\n",
+    "lT.nodes  # all the nodes present on the lT object  # noqa: B018\n",
+    "lT.roots  # all the roots of the object  # noqa: B018\n",
     "lT.successor  # dictionary that connects an id to a list of successors, can be used to find all edges."
    ]
   },

notebooks/Easy_clustermaps.ipynb

@@ -46,8 +46,8 @@
     "\n",
     "try:\n",
     "    import seaborn as sns\n",
-    "except:\n",
-    "    !pip install seaborn\n",
+    "except ModuleNotFoundError:\n",
+    "    %pip install seaborn\n",
     "finally:\n",
     "    from itertools import combinations\n",
     "\n",
@@ -77,7 +77,7 @@
     "\n",
     "### Or load a manager###\n",
     "\n",
-    "# lTm = lineageTreeManager.load(\"path_to/Manager.ltM\")"
+    "# lTm = lineageTreeManager.load(\"path_to/Manager.ltM\")  # noqa: ERA001"
    ]
   },
   {
@@ -195,7 +195,7 @@
    "outputs": [],
    "source": [
     "comparison = {}\n",
-    "for i, (n1, n2) in enumerate(combs):\n",
+    "for n1, n2 in combs:\n",
     "    comparison[n1, n2] = lTm.cross_lineage_edit_distance(\n",
     "        names[n1][1],\n",
     "        names[n1][0],\n",
@@ -247,8 +247,8 @@
    "source": [
     "g = sns.clustermap(\n",
     "    hierarchy,\n",
-    "    xticklabels=[label for label in labels],  # labels,\n",
-    "    yticklabels=[label for label in labels],\n",
+    "    xticklabels=list(labels),\n",
+    "    yticklabels=list(labels),\n",
     "    cmap=\"viridis\",\n",
     "    row_linkage=linkage_data,\n",
     "    col_linkage=linkage_data,\n",

src/LineageTree/lineageTree.py

@@ -3497,7 +3497,7 @@ def __init__(
                     f"Attribute `starting_time` was a `{type(starting_time)}`, has been casted as an `int`.",
                     stacklevel=2,
                 )
-            self._time = {node: starting_time for node in self.roots}
+            self._time = dict.fromkeys(self.roots, starting_time)
             queue = list(self.roots)
             for node in queue:
                 for succ in self._successor[node]:

src/LineageTree/loaders.py

@@ -393,7 +393,7 @@ def read_from_binary(fname: str, name: None | str = None) -> lineageTree:
                     )
                 )
             )
-            is_root = {c: True for c in tmp}
+            is_root = dict.fromkeys(tmp, True)
             done = True
     while (
         i < len(number_sequence) and not done
@@ -635,7 +635,7 @@ def read_from_txt_for_celegans_BAO(
         ids = list(range(unique_id, unique_id + len(lc)))
         successor.update({ids[i]: [ids[i + 1]] for i in range(len(ids) - 1)})
         properties["expression"].update(dict(zip(ids, lc, strict=True)))
-        properties["_labels"].update({id_: c for id_ in ids})
+        properties["_labels"].update(dict.fromkeys(ids, c))
         to_link[c] = (unique_id, unique_id + len(lc) - 1)
         unique_id += len(lc)
 

src/LineageTree/test/test_lineageTree.py

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