restructure package layout (#42)

* 🔥 remove old code in setup.py

* 🎨 src package layout

* 🐛 specify path correctly for module

* 🐛 Fix(report_config_micw2graph.yaml): Modify the component paths by adding "docs" to run vuegen from root

* 🐛 Fix(cdci.yml): Remove cd docs fro tests

* 🐛 Fix(cdci.yml): Add docs to the config paths

* 🎨 change to directory based execution

---------

Co-authored-by: sayalaruano <sebasar1245@gmail.com>

Author: enryH

.github/workflows/docs.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Build references
         run: |
             cd docs
-            sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../vuegen
+            sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuegen
       - name: Build documentation
         run: |
             cd docs

docs/README.md

@@ -26,7 +26,7 @@ Options:
 ```bash	
 # pwd: docs
 # apidoc
-sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../vuegen
+sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuegen
 # build docs
 sphinx-build -n -W --keep-going -b html ./ ./_build/
 ```

setup.py

@@ -1,54 +1,4 @@
 # builtin
-import setuptools
+from setuptools import setup
 
-def get_long_description():
-    with open("README.md", "r") as readme_file:
-        long_description = readme_file.read()
-    return long_description
-
-
-def get_requirements():
-    with open('requirements.txt') as f:
-        required = f.read().splitlines()
-    return required
-    
-
-def create_pip_wheel():
-    requirements = get_requirements()
-    setuptools.setup(
-        name="report_generator",
-        version="0.1.0",
-        license="MIT",
-        description="An open-source Python package for generating reports for Omics datasets",
-        long_description=get_long_description(),
-        long_description_content_type="text/markdown",
-        author="Multi-omics Network Analytics lab",
-        author_email="albsad@dtu.dk",
-        url="",
-        project_urls={
-            "Multi-omics Network Analytics": "",
-            "GitHub": "",
-            "ReadTheDocs": "",
-            "PyPi": "",
-            "Scientific paper": "https://www.nature.com/articles/s41587-021-01145-6",
-        },
-        keywords=["dashboard", "bioinformatics", "multi-omics",],
-        classifiers=[
-            "Intended Audience :: Science/Research",
-            "License :: OSI Approved :: MIT License",
-            "Operating System :: OS Independent",
-            "Programming Language :: Python :: 3",
-            "Topic :: Scientific :: Bioinformatics",
-        ],
-        packages=[
-            "report",
-        ],
-        include_package_data=True,
-        entry_points={},
-        install_requires=requirements,
-        python_requires=">=3.9,<4",
-    )
-
-
-if __name__ == "__main__":
-    create_pip_wheel()
+setup()