Readthedocs initial commit

.readthedocs.yaml

@@ -10,23 +10,11 @@ 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
+   configuration: docs/source/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
+python:
+  install:
+  - requirements: docs/requirements.txt
\ No newline at end of file

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

+sphinx==7.1.2
+sphinx-rtd-theme==1.3.0rc1
+numpy
+pandas
+wget
+scipy
+networkx
+torch>=1.12
+matplotlib
+seaborn
+tqdm
+scikit-learn
+pytorch-lightning==1.9.0
+torchmetrics
+biopython
+fair-esm
\ No newline at end of file

docs/source/api.rst

+API
+===
+
+.. autosummary::
+   :toctree: generated

docs/source/conf.py

+# Configuration file for the Sphinx documentation builder.
+
+# -- Project information
+
+project = 'SENSE-PPI'
+copyright = '2023, Konstantin Volzhenin, Lucie Bittner, Alessandra Carbone'
+author = 'Konstantin Volzhenin, Lucie Bittner, Alessandra Carbone'
+
+release = '0.1'
+version = '0.1.0'
+
+# -- General configuration
+
+extensions = [
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+]
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+}
+intersphinx_disabled_domains = ['std']
+
+templates_path = ['_templates']
+
+# -- Options for HTML output
+
+html_theme = 'sphinx_rtd_theme'
+
+# -- Options for EPUB output
+epub_show_urls = 'footnote'

docs/source/index.rst

+Welcome to SENSE-PPI documentation!
+===================================
+
+**SENSE-PPI** is a Deep Learning model for predicting physical protein-protein interactions based on amino acid sequences.
+It is based on embeddings generated by ESM2 and uses Siamese RNN architecture to perform a binary classification.
+
+
+Check out the :doc:`usage` section for further information, including
+how to :ref:`installation` the project.
+
+.. note::
+
+   This project is under active development.
+
+Contents
+--------
+
+.. toctree::
+
+   usage
+   api

docs/source/usage.rst

+Usage
+=====
+
+.. _installation:
+
+Installation
+------------
+
+To use SENSE-PPI, first install it using pip:
+
+.. code-block:: console
+
+   (.venv) $ pip install senseppi
+
+Commands
+------------
+
+There are 5 commands available in the package:
+
+- `train`: trains SENSE-PPI on a given dataset
+- `test`: computes test metrics (AUROC, AUPRC, F1, MCC, Presicion, Recall, Accuracy) on a given dataset
+- `predict`: predicts interactions for a given dataset
+- `predict_string`: predicts interactions for a given dataset using STRING database: the interactions are taken from the STRING database (based on seed proteins). Predictions are compared with the STRING database. Optionally, the graphs can be constructed.
+- `create_dataset`: creates a dataset from the STRING database based on the taxonomic ID of the organism.
+
+

pyproject.toml

+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "senseppi"
+authors = [{name = "Konstantin Volzhenin", email = "konstantin_v_v@outlook.com"}]
+dynamic = ["version", "description"]