From 6953f3c82e09a7c07fbdfae52b9dc13403169c8a Mon Sep 17 00:00:00 2001
From: Istvan Albert <istvan.albert@gmail.com>
Date: Tue, 2 Apr 2024 11:55:13 -0400
Subject: [PATCH] fixing linting errors

---
 pyproject.toml         | 7 +++++++
 src/genescape/tree.py  | 2 +-
 src/genescape/utils.py | 2 +-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e1f2be0..93c7df3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -117,6 +117,10 @@ skip-string-normalization = true
 [tool.ruff]
 target-version = "py39"
 line-length = 120
+exclude = [
+    # This a vendored third-party library.
+    "src/genescape/bottle.py",
+]
 select = [
   "A",
   "ARG",
@@ -153,6 +157,9 @@ ignore = [
   "S105", "S106", "S107",
   # Ignore complexity
   "C901", "PLR0911", "PLR0912", "PLR0913", "PLR0915",
+
+  # Pet peevees
+  "Q000", "C402",  "F401", "E401",  "T201",
 ]
 unfixable = [
   # Don't touch unused imports
diff --git a/src/genescape/tree.py b/src/genescape/tree.py
index 39ab54e..b52b5da 100644
--- a/src/genescape/tree.py
+++ b/src/genescape/tree.py
@@ -22,7 +22,7 @@ def build_onto_graph(index):
     terms = data[utils.IDX_OBO]
 
     # Add all nodes to Graph
-    for name, node in terms.items():
+    for key, node in terms.items():
         oid = node["id"]
         name = node["name"]
         text = textwrap.fill(name, width=20)
diff --git a/src/genescape/utils.py b/src/genescape/utils.py
index d9137f4..34ed979 100644
--- a/src/genescape/utils.py
+++ b/src/genescape/utils.py
@@ -1,4 +1,4 @@
-import logging, functools, time, functools
+import logging, time, functools
 import os, gzip, json, csv
 import sys, pathlib
 from logging import DEBUG, ERROR, INFO, WARNING