Merge pull request #11 from lotzma/mihaela_start

Mihaela start

.github/workflows/pylint.yml

@@ -0,0 +1,23 @@
+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint $(git ls-files '*.py')

.gitignore

@@ -0,0 +1,4 @@
+.DS_Store
+__pycache__/
+.venv/
+docs/build/

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/pylint-dev/pylint
+    rev: v3.3.1
+    hooks:
+      - id: pylint
+        name: pylint
+        entry: pylint
+        language: python
+        types: [python]
+        files: ^l2gv2/.*\.py$

.python-version

@@ -0,0 +1 @@
+3.12.0

.readthedocs.yaml

@@ -0,0 +1,17 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+sphinx:
+   configuration: docs/source/conf.py
+
+python:
+   install:
+   - requirements: docs/requirements.txt

README.md

@@ -1,2 +1,70 @@
-# l2gv2
-Local2Global
+
+[![linting: pylint](https://img.shields.io/badge/linting-pylint-yellowgreen)](https://github.com/pylint-dev/pylint)
+[![Pylint](https://github.com/lotzma/L2Gv2/actions/workflows/pylint.yml/badge.svg)](https://github.com/lotzma/L2Gv2/actions/workflows/pylint.yml)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+[![All Contributors](https://img.shields.io/badge/all_contributors-1-orange.svg?style=flat-square)](#contributors-)
+
+# l2gv2 - Local2Global
+
+## Overview
+
+## Documentation
+
+Full documentation available [here](https://l2gv2.readthedocs.io/en/latest/)
+
+
+## Setup
+
+
+**Supported Python Versions**: 3.10, 3.11, 3.12  
+**Supported Operating Systems**: macOS, Linux  
+
+Clone the repository on your machine
+
+```shell
+git clone https://github.com/lotzma/L2Gv2.git
+```
+
+Setup the virtual environment
+
+1. Create and activate a virtual environment
+   ```shell
+   python3 -m venv .venv
+   source .venv/bin/activate
+   ```
+
+2. Install the dependencies
+
+    ```shell
+    pip install -r requirements.txt
+    ```
+
+The unified `requirements.in` file includes both shared and platform-specific dependencies with version constraints where necessary. To update dependencies, modify `requirements.in` and then recompile `requirements.txt`
+
+```shell
+pip-compile requirements.in --verbose
+```
+
+## License
+
+## Contributors
+
+The following people contributed to this project ([emoji key](https://allcontributors.org/docs/en/emoji-key)). 
+
+<!-- ALL-CONTRIBUTORS-LIST:START -->
+<table>
+  <tbody>
+    <tr>
+      <td align="center">
+        <a href="https://github.com/lotzma">
+            <img src="https://avatars.githubusercontent.com/u/22026207?v=4?v=4?s=100" width="100px;" alt="Martin Lotz"/>
+            <br /><sub><b>Martin Lotz</b></sub>
+            <br />🤔 📆 💻 💡
+        </a>
+    </td>  
+    </tr>
+  </tbody>
+</table>
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification.

docs/Makefile

@@ -0,0 +1,20 @@
+# 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

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,9 @@
+#
+# A subset of requirements.txt for the use of ReadTheDocs
+
+
+-e .
+Sphinx==8.1.3
+sphinx-markdown-builder==0.6.7
+sphinx-rtd-theme==3.0.1
+sphinx-autobuild==2024.10.3

docs/source/code.rst

@@ -0,0 +1,65 @@
+Code documentation
+==================
+
+Anomaly detection
+-----------------
+
+.. automodule:: l2gv2.anomaly_detection
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Induced subgraph
+----------------
+
+.. automodule:: l2gv2.induced_subgraph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Manopt optimization
+-------------------
+
+.. automodule:: l2gv2.manopt_optimization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Models
+------
+
+.. automodule:: l2gv2.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. Embeddings
+.. ----------
+
+.. .. automodule:: l2gv2.embedding.embeddings
+..    :members:
+..    :undoc-members:
+..    :show-inheritance:
+
+Patch
+-----
+
+.. automodule:: l2gv2.patch.lazy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: l2gv2.patch.patch
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. .. automodule:: l2gv2.patch.patches
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
+
+.. .. automodule:: l2gv2.patch.utils
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:

docs/source/conf.py

@@ -0,0 +1,28 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "l2gv2"
+copyright = "2024"
+author = ""
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx_markdown_builder", "sphinx.ext.autodoc", "sphinx.ext.autosummary"]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+autodoc_mock_imports = ["optuna", "autograd", "pymanopt", "tqdm", "torch", "numpy", "pandas", "sklearn", "scipy", "community", "torch_geometric", "torch_scatter", "local2global", "raphtory", "local2global_embedding", "networkx", "matplotlib", "nfts", "polars"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

docs/source/index.rst

@@ -0,0 +1,14 @@
+.. l2gv2 documentation master file, created by
+   sphinx-quickstart on Mon Nov  4 11:00:53 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+l2gv2 documentation
+====================
+
+.. toctree::
+   :maxdepth: 4
+
+   intro
+   code
+