Version 0.1.1 (minor edits + requirements)

.gitignore

+# Editors
+.vscode/
+.idea/
+
+# Vagrant
+.vagrant/
+
+# Mac/OSX
+.DS_Store
+
+# Windows
+Thumbs.db
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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
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+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
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+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
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+# Flask stuff:
+instance/
+.webassets-cache
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+# Scrapy stuff:
+.scrapy
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+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
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+# Spyder project settings
+.spyderproject
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+# Rope project settings
+.ropeproject
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+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
 /esm2_embs_3B
-*.sh
\ No newline at end of file
+*.sh
+draft.py
\ No newline at end of file

senseppi/__init__.py

-__version__ = "0.1.0"
+__version__ = "0.1.1"
 __author__ = "Konstantin Volzhenin"
 
 from . import model, commands, esm2_model, dataset, utils, network_utils

senseppi/commands/predict_string.py

-import os
-
 from torch.utils.data import DataLoader
 import pytorch_lightning as pl
 from torchmetrics import AUROC, Accuracy, Precision, Recall, F1Score, MatthewsCorrCoef
@@ -9,7 +7,7 @@ import matplotlib
 from matplotlib.lines import Line2D
 from scipy.cluster.hierarchy import linkage, fcluster
 from matplotlib.patches import Rectangle
-
+import argparse
 import matplotlib.pyplot as plt
 import glob
 
@@ -225,12 +223,12 @@ def main(params):
                 node_color=[G.nodes[node]['color'] for node in G.nodes()])
 
         legend_elements = [
-            Line2D([0], [0], marker='_', color='darkblue', label='PP from training data', markerfacecolor='darkblue',
-                   markersize=10),
+            # Line2D([0], [0], marker='_', color='darkblue', label='PP from training data', markerfacecolor='darkblue',
+            #        markersize=10),
             Line2D([0], [0], marker='_', color='limegreen', label='PP', markerfacecolor='limegreen', markersize=10),
-            Line2D([0], [0], marker='_', color='red', label='FP', markerfacecolor='red', markersize=10)]
-            # Line2D([0], [0], marker='_', color='black', label='FN - based on STRING', markerfacecolor='black',
-            #        markersize=10, linestyle='dotted')]
+            Line2D([0], [0], marker='_', color='red', label='FP', markerfacecolor='red', markersize=10),
+            Line2D([0], [0], marker='_', color='black', label='FN - based on STRING', markerfacecolor='black',
+                   markersize=10, linestyle='dotted')]
         plt.legend(handles=legend_elements, loc='upper right', bbox_to_anchor=(1.2, 0.0), ncol=1, fontsize=8)
 
         savepath = '{}_graph_{}_{}.pdf'.format(params.output, '_'.join(params.genes), params.species)
@@ -277,6 +275,7 @@ def add_args(parser):
     add_esm_args(parser)
     return parser
 
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser = add_args(parser)

setup.py

@@ -21,6 +21,8 @@ setup(
         "numpy",
         "pandas",
         "wget",
+        "scipy",
+        "networkx",
         "torch>=1.12",
         "matplotlib",
         "seaborn",