Merge pull request #3 from m-jahn/style_options

feat: expose more options to style DAGs formatting and creating module based python package.

Author: skchronicles

.github/workflows/release-please.yaml

@@ -0,0 +1,20 @@
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  pull-requests: write
+  issues: write
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: googleapis/release-please-action@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          release-type: python # this will auto-increment versions in the pyproject.toml and snakevision/__init__.py files

.github/workflows/testing.yaml

@@ -0,0 +1,44 @@
+name: Testing
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Formatting
+        uses: super-linter/super-linter@v8
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_YAML_PRETTIER: true
+          VALIDATE_MARKDOWN_PRETTIER: true
+          VALIDATE_PYTHON_BLACK: true
+
+  Testing:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.10", "3.12", "3.14"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: Test DAG visualization
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .
+          snakevision \
+              -s all multiqc \
+              -y scale=15.0 node_stroke=white edge_stroke_width=3 \
+              -o examples/atac_dag_test.svg \
+              examples/atac_rulegraph.dot

README.md

@@ -4,14 +4,16 @@
 
   **_An awesome tool to visualize Snakemake DAGs_**
 
-  [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/snakevision?color=brightgreen)](https://github.com/OpenOmics/snakevision/issues)  [![GitHub license](https://img.shields.io/github/license/OpenOmics/snakevision)](https://github.com/OpenOmics/snakevision/blob/main/LICENSE) 
-  
+[![GitHub issues](https://img.shields.io/github/issues/OpenOmics/snakevision?color=brightgreen)](https://github.com/OpenOmics/snakevision/issues)
+[![GitHub license](https://img.shields.io/github/license/OpenOmics/snakevision)](https://github.com/OpenOmics/snakevision/blob/main/LICENSE)
+
 </div>
 
 ## Overview
+
 Welcome to snakevision! Before getting started, we highly recommend reading through our documentation below.
 
-**`./snakevision`** provides a simplified command-line interface to visualize Snakemake DAGs or rule graphs. If you are familiar with other existing tools to visualize DAGs like [graphviz](https://graphviz.org/), getting started with `snakevision` should be a breeze. 
+**`./snakevision`** provides a simplified command-line interface to visualize Snakemake DAGs or rule graphs. If you are familiar with other existing tools to visualize DAGs like [graphviz](https://graphviz.org/), getting started with `snakevision` should be a breeze.
 
 ## Examples
 
@@ -36,40 +38,45 @@ Here are a few Snakemake rule graphs rendered by snakevision. These DAGs come fr
 </p>
 
 ## Dependencies
+
 **Requires:** `snakemake` `python>=3.7`
 
-At the current moment, the tool is designed to visualize rule graphs of existing snakemake pipelines. As so, [Snakemake<sup>1</sup>](https://snakemake.readthedocs.io/en/stable/) and any dependencies of the pipeline should be installed on the target system. This tool relies on a few 3rd-party pypi python packages which can be installed via pip from the provided [requirements.txt](https://github.com/OpenOmics/snakevision/blob/main/requirements.txt). 
+At the current moment, the tool is designed to visualize rule graphs of existing snakemake pipelines. As so, [Snakemake<sup>1</sup>](https://snakemake.readthedocs.io/en/stable/) and any dependencies of the pipeline should be installed on the target system. This tool relies on a few 3rd-party pypi python packages which can be installed via pip from the provided [requirements.txt](https://github.com/OpenOmics/snakevision/blob/main/requirements.txt).
 
 Please follow the instructions directly below to install snakevision on your local system.
 
 ## Installation
+
+### Github
+
 Please clone this repository to your local filesystem using the following command:
+
 ```bash
 # Clone Repository from Github
 git clone https://github.com/OpenOmics/snakevision.git
+
 # Change your working directory
 cd snakevision/
+
 # Create a python virtual environment
 # to install required python packages
 python -m venv .venv
+
 # Activate the virtual environment
 source .venv/bin/activate
+
 # Upgrade pip and install the list
 # of required python packages
 pip install -U pip
-pip install -r requirements.txt
-# Get check installation, get 
-# usage information of tool
-./bin/snakevision -h
-# Add snakevision to $PATH
-export PATH="${PATH}:$PWD/bin"
+pip install -e .
 ```
 
 ## Getting Started
 
 Snakevision can read an input snakemake rulegraph via an input file or via standard input directly from a pipe. To create an input rule graph to the `snakevision`, please run snakemake with the `--rulegraph` and `--forceall` options.
 
-Here is an basic example:
+### Basic example
+
 ```bash
 # Create a input file for snakevision
 snakemake  --configfile=$pipeline_outdir/config.json \
@@ -80,21 +87,38 @@ snakemake  --configfile=$pipeline_outdir/config.json \
 > pipeline_rulegraph.dot
 
 # Run snakevision, do not include
-# rule all and multiqc in the image, 
+# rule all and multiqc in the image,
 # makes final image less cluttered
 snakevision \
     -s all mutliqc \
     -o pipeline_rulegraph.svg \
     pipeline_rulegraph.dot
 ```
 
-## Contribute 
-This site is a living document, created for and by members like you. snakevision is maintained by the members of OpenOmics and is improved by continuous feedback! We encourage you to contribute new content and make improvements to existing content via pull requests to our [GitHub repository](https://github.com/OpenOmics/snakevision).
+### Customize DAG
+
+Snakevision provides a few options to customize the style of the DAG output.
+You can specify these options using the `-y` or `--styles` flag followed by the key-value pairs.
+Use `-y` multiple times to specify multiple style attributes.
+For example, you can change the size of the nodes and edges in the DAG by using the following command:
+
+```bash
+snakevision \
+    -y node_radius=10.0 \
+    -y edge_stroke_width=8.0 \
+    -o pipeline_rulegraph.svg \
+    pipeline_rulegraph.dot
+```
+
+For the full list of available options, run `snakevision -h`.
 
+## Contribute
+
+This site is a living document, created for and by members like you. snakevision is maintained by the members of OpenOmics and is improved by continuous feedback! We encourage you to contribute new content and make improvements to existing content via pull requests to our [GitHub repository](https://github.com/OpenOmics/snakevision).
 
 ## Cite
 
-If you use this software, please cite it as below:  
+If you use this software, please cite it as below:
 
 <details>
   <summary><b><i>@BibText</i></b></summary>
@@ -115,4 +139,5 @@ Citation coming soon!
 </details>
 
 ## References
-<sup>**1.**  Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.</sup>  
+
+<sup>**1.** Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.</sup>

bin/snakevision

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "snakevision"
+version = "0.1.0"
+description = "A tool to visualize Snakemake workflows."
+authors = [
+    { name = "Skyler Kuhn" },
+    { name = "Michael Jahn" },
+]
+readme = "README.md"
+requires-python = ">=3.7,<4"
+license = { file = "LICENSE" }
+keywords = ["snakemake", "workflow", "visualization", "graphviz", "bioinformatics"]
+classifiers = [
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+
+# Main package dependencies
+dependencies = [
+  "dagviz>=0.4.0,<1",
+  "networkx>=2.5.1,<4"
+]
+
+# Testing, linting, ci, and build dependencies
+[project.optional-dependencies]
+dev = [
+  "black>=24.0.0",
+  "pytest>=8.0.0",
+  "build>=1.2.0",
+  "twine>=5.0.0",
+]
+
+[project.urls]
+Repository = "https://github.com/OpenOmics/snakevision"
+Issues = "https://github.com/OpenOmics/snakevision/issues"
+
+# Main entry point for the command-line interface
+[project.scripts]
+snakevision = "snakevision.cli:main"
+
+[tool.setuptools]
+packages = ["snakevision"]

pyproject.toml

@@ -0,0 +1,14 @@
+"""Top-level package for snakevision.
+
+This package provides tools for parsing Snakemake rule graphs, constructing
+directed acyclic graph (DAG) representations, and rendering workflow
+visualizations. The package exposes the `SnakeVision` class as its primary
+public interface, along with other package metadata (such as the version).
+"""
+from .snakevision import SnakeVision
+from .version import __version__
+
+
+# Expose the SnakeVision class along
+# with its version information
+__all__ = ["SnakeVision", "__version__"]

requirements.txt

@@ -0,0 +1,27 @@
+"""Command-line entry point for the snakevision package.
+
+This module is executed when running `python -m snakevision`. The `main()`
+function from `cli.py` validates the Python version, parses command-line
+arguments, normalizes selected multi-value CLI options, constructs a
+`SnakeVision` DAG object from the provided Snakemake rule graph input,
+and writes the rendered DAG to an output file.
+
+This module is intended as an execution wrapper around the package's reusable
+library components and is not the primary location for core parsing or graph
+construction logic. Please see `snakevision.py` for the main implementation
+of the `SnakeVision` class. This contains the core logic for parsing Snakemake
+rule graph, building a DAG, and writing the resulting DAG as a snakevision
+image.
+
+To run the command-line interface, execute the following command in your terminal:
+    $ python -m snakevision [OPTIONS] snakemake_rulegraph
+
+For more information about available options and usage, run:
+    $ python -m snakevision --help
+"""
+# Local relative imports
+from .cli import main
+
+
+# Main entry-point to the command-line interface
+main()