Development

.coveragerc

@@ -0,0 +1,6 @@
+[run]
+source = .
+omit = tests/*, setup.py
+
+[report]
+omit = tests/*, setup.py

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+max-line-length = 88  # Black standard
+exclude = .git,__pycache__,build,dist  # Ignore folders and files
+max-complexity = 10  # Set the maximum complexity allowed
+ignore =
+    ; E203,  # space before ':'
+    ; W503,  # line break before binary operator
+    ; W191,  # indentation contains tabs
+    ; E101,  # indentation contains mixed spaces and tabs
+
+    ; be more restrictive after the refactor code

.github/workflows/ci.yml

@@ -0,0 +1,37 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - development
+  pull_request:
+    branches:
+    - development
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checkout the code
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      # Set up Python environment
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+
+      # Run the tests
+      - name: Run tests with pytest
+        run: |
+          pytest --maxfail=5 --disable-warnings
+

.github/workflows/format.yml

@@ -0,0 +1,31 @@
+name: Code Formatting
+
+on: 
+  push:
+    branches:
+      - development
+  pull_request:
+    branches:
+      - master
+      - development
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install black
+      run: |
+        pip install black
+
+    - name: Run black check
+      run: |
+        black --check .

.gitignore

@@ -1 +1,33 @@
 **/*.pyc
+.pytest_cache/
+.python-version
+venv
+build
+dist
+LOKI.egg-info
+.vscode
+.temp/
+loki.db
+.venv
+.db
+.temp
+.tmp
+.tmp/
+.DS_Store
+tests/*.db
+tests/loki_test.db
+sources_mint.tar.gz
+
+# Temp/cache locais
+.tmp/
+sources_*.tar.gz
+
+# Bancos locais
+*.db
+*.sqlite
+
+# Ruídos comuns
+.DS_Store
+__pycache__/
+.venv/
+.pytest_cache/

.vscode/launch.json

@@ -1,5 +1,17 @@
 {
+    "version": "0.2.0",
     "configurations": [
+        {
+            "name": "Debug Pytest",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${workspaceFolder}/tests",  // Caminho para seus arquivos de teste
+            "console": "integratedTerminal",
+            "justMyCode": true,  // Define como false se você quiser depurar bibliotecas externas
+            "args": [
+                "-m", "pytest"
+            ]
+        },
         {
             "name": "Docker: Python - General",
             "type": "docker",

.vscode/settings.json

@@ -1,3 +1,8 @@
 {
-    "python.analysis.typeCheckingMode": "basic"
+    "python.analysis.typeCheckingMode": "basic",
+    "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python",
+    "python.testing.pytestEnabled": true,
+    "python.testing.unittestEnabled": false,
+    "python.testing.nosetestsEnabled": false,
+    "python.testing.pytestArgs": ["tests"]
 }

CHANGELOG

@@ -1,6 +1,10 @@
 CHANGELOG
 
-3.0.0
+3.0.1-dev
+- 
+
+
+3.0.0-dev (2024-10-03)
 - added disease category for groups
 - added sub-categories for groups
 - added data source like disgenet, gaad, and kegg disease

README.md

@@ -0,0 +1,114 @@
+# LOKI: Library of Knowledge Integration
+
+[![Build Status](https://img.shields.io/badge/build-passing-brightgreen.svg)](https://github.com/yourusername/loki)
+[![Python Version](https://img.shields.io/badge/python-3.8%2B-blue.svg)](https://www.python.org/downloads/release/python-380/)
+[![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)
+
+## Overview
+
+LOKI (Library of Knowledge Integration) is a bioinformatics data integration platform designed to aggregate and manage data from various genomic, genetic, and biological databases. It serves as a local repository that can be used to quickly access structured biological knowledge for downstream analysis, such as filtering, annotating, and modeling gene-gene or SNP-SNP interactions. 
+
+By working with local data instead of issuing real-time queries to external databases, LOKI enables faster and more flexible data processing, improving efficiency in bioinformatic pipelines.
+
+## Key Features
+
+- **Data Integration**: Merges data from multiple external sources into a unified local database.
+- **Flexible Data Queries**: Supports querying different data types like SNPs, genes, proteins, pathways, and ontological categories.
+- **Annotation and Filtering**: Facilitates the annotation of data sets with biological context and filtering based on genomic criteria.
+- **Interaction Modeling**: Allows for gene-gene and SNP-SNP interaction modeling to reduce computational burden and enhance statistical analysis.
+- **No Internet Dependency**: Works offline by using a pre-built local database.
+
+## Installation
+
+### Requirements
+
+- **Python 3.8+**
+- **SQLite3** (or another supported database)
+- **Git**
+
+### Installing via PyPI
+
+To install LOKI via [PyPI](https://pypi.org/project/loki):
+
+```bash
+pip install loki
+```
+
+### Installing from Source
+
+Alternatively, clone the repository and install the dependencies manually:
+
+```bash
+git clone https://github.com/yourusername/loki.git
+cd loki
+pip install -r requirements.txt
+```
+
+### Setting Up the Database
+
+LOKI requires the creation of a local database that aggregates external biological data sources. You can generate the database with the following command:
+
+```bash
+python loki_db.py --build
+```
+
+This process may take some time depending on the amount of data being imported.
+
+## Usage
+
+### Basic Commands
+
+1. **Database Querying**: To query the LOKI database for SNPs related to a specific gene:
+
+```bash
+python loki_query.py --gene A1BG
+```
+
+2. **Filtering SNP Data**: You can filter a dataset by genomic location or gene association:
+
+```bash
+python loki_filter.py --input mydata.txt --filter genes --output filtered_data.txt
+```
+
+3. **Interaction Modeling**: For generating SNP-SNP interaction models:
+
+```bash
+python loki_model.py --input snps.txt --model snp-snp --output models.txt
+```
+
+### Configuration
+
+You can configure LOKI using a `config.yaml` file located in the project root. This file contains settings for database paths, default filters, and other preferences.
+
+## Project Structure
+
+```plaintext
+loki/
+│
+├── loki_db.py             # Database creation and management
+├── loki_query.py          # Query interface for accessing the LOKI database
+├── loki_filter.py         # Filtering logic for datasets
+├── loki_model.py          # Interaction modeling tools
+├── data/                  # External source data
+├── tests/                 # Unit and integration tests
+└── README.md              # Project documentation
+```
+
+## Contributing
+
+We welcome contributions! To get started:
+
+1. Fork the repository.
+2. Create a new branch for your feature or bugfix.
+3. Submit a pull request with a clear explanation of your changes.
+
+Please ensure that your code adheres to [PEP8](https://pep8.org/) and includes tests for any new functionality.
+
+## License
+
+This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.
+
+## Contact
+
+For any questions, feel free to contact the project maintainers at `email@email.com`.
+

__init__.py

@@ -1,2 +1,9 @@
-__all__ = ["loki-build","loki/loki_db","loki/loki_source","loki/loki_updater","loki/loaders","loki/util"]
-__version__ = "3.0.0"
+__all__ = [
+    "loki-build",
+    "loki/loki_db",
+    "loki/loki_source",
+    "loki/loki_updater",
+    "loki/loaders",
+    "loki/util",
+]
+__version__ = "3.0.0"