added .readthedocs.yaml + minor edits

.readthedocs.yaml

+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#    install:
+#    - requirements: docs/requirements.txt
\ No newline at end of file

README.md

@@ -35,7 +35,7 @@ Predictions are compared with the STRING database. Optionally, the graphs can be
 
 The original SENSE-PPI repository contains two models (checkpoints with weights) pretrained on human PPIs: `senseppi.ckpt` and `dscript.ckpt` pretrained on SENSE-PPI and DSCRIPT human datasets respectively.
 
-- `senseppi.ckpt` (preferred) : Download from [here](http://gitlab.lcqb.upmc.fr/Konstvv/SENSE-PPI/raw/master/pretrained_models/senseppi.ckpt)
+- `senseppi.ckpt`: Download from [here](http://gitlab.lcqb.upmc.fr/Konstvv/SENSE-PPI/raw/master/pretrained_models/senseppi.ckpt)
 - `dscript.ckpt` : Download from [here](http://gitlab.lcqb.upmc.fr/Konstvv/SENSE-PPI/raw/master/pretrained_models/dscript.ckpt)
 
 The package already comes with preinstalled model `senseppi.ckpt` that is used by default if model path is not specified.

senseppi/commands/predict_string.py

 import numpy as np
-from torchmetrics import AUROC, Accuracy, Precision, Recall, F1Score, MatthewsCorrCoef
 import networkx as nx
 import seaborn as sns
 import matplotlib