updated github test, sphynx docs generation, notebooks, readthedoc.ya…

…ml and README

.github/workflows/sphinx_autodoc.yaml

@@ -12,6 +12,8 @@ jobs:
             uses: actions/setup-python@v2
             with:
                 python-version: 3.10.13
+        -   name: Install pandoc
+            run: sudo apt-get install -y pandoc
         -   name: Load cached Poetry installation
             uses: actions/cache@v2
             with:

.readthedocs.yaml

@@ -1,22 +1,12 @@
 version: 2
-
-sphinx:
-    builder: html
-    configuration: docs/source/conf.py
-    fail_on_warning: true
-
-formats:
--   htmlzip
--   pdf
-
 build:
-    os: ubuntu-22.04
-    tools:
-        python: 3.10
-
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+sphinx:
+  configuration: docs/src/conf.py
 python:
-    install:
-    -   method: pip
-        path: .
-        extra_requirements:
-        -   docs
+  install:
+  - method: pip
+    path: .
+  - requirements: docs/src/requirements.txt

README.rst

@@ -0,0 +1,24 @@
+==================
+Neko
+==================
+
+   :target: /~https://github.com/sysbio-curie/Neko/actions/workflows/test.yml
+   :alt: Tests
+
+.. image:: https://img.shields.io/readthedocs/omniflow_project
+   :target: https://neko.readthedocs.io
+   :alt: Documentation
+
+Package to extract, visualize, convert and study interactions from database into executable activity flow based model.
+Neko, is based on `Omnipath </~https://github.com/saezlab/omnipath>`_, `Pypath </~https://github.com/saezlab/pypath>`_ and `Atopo </~https://github.com/druglogics/atopo>`_.
+
+This is a work-in-progress package made in collaboration with Dénes Turei and Asmund Flobak.
+
+CURRENT FEATURES:
+
+version 0.9.0
+--------------
+
+- Network creation and manipulation: The package allows for the creation of a network of nodes and edges, with various methods for enrichment analysis. This includes adding and removing nodes and edges, loading a network from a SIF (Simple Interaction Format) file, and adding paths to the edge list of the network.
+- Connection of nodes: The package provides several methods to connect nodes in the network. This includes connecting all nodes, connecting a subgroup of nodes, connecting all nodes of a network object, and connecting subcomponents of a network object.
+- Connection of genes to phenotype: The package provides a method to connect genes to a phenotype based on provided parameters. This includes retrieving phenotype markers, identifying unique Uniprot genes, and connecting them to the network. There is also an option to compress the network by substituting specified genes with the phenotype name.

docs/src/conf.py

@@ -17,52 +17,59 @@
 here = pathlib.Path(__file__).parent
 sys.path.insert(0, str(here.parent))
 
-import neko  # noqa: E402
+from neko._metadata import __version__, __author__  # noqa: E402
 
 # -- Project information -----------------------------------------------------
 
 project = 'neko'
-version = neko.__version__
-author = ', '.join(neko.__author__)
+version = __version__
+author = ', '.join(__author__)
 years = '-'.join(sorted({'2022', f'{datetime.now():%Y}'}))
-copyright = f'{years}, Saez Lab'
-repository_url = '/~https://github.com/sysbio-curie/neko'
+copyright = f'{years}, Sysbio-Curie'
+repository_url = '/~https://github.com/sysbio-curie/Neko'
+
+# thank you stupid sphinx, thank you stupid github :((( <-- directly taken from conf.py of Pypath XD
+readme_lines = []
+readme = pathlib.Path().absolute().parents[1].joinpath('README.rst')
+
+if readme.exists():
+
+    with readme.open('r') as fp:
+
+        readme_lines = fp.readlines()[4:]
+
+with open('index.rst', 'w') as fp:
+
+    fp.write('==================\n Neko \n==================\n\n')
+    fp.write(''.join(readme_lines))
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named "sphinx.ext.*") or your custom
 # ones.
 extensions = [
-    'myst_parser',
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
     'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
     'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.todo',  # not for output but to remove warnings
-    'sphinx.ext.githubpages',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.ifconfig',
-    'sphinxcontrib.bibtex',
-    'sphinx_autodoc_typehints',
-    'sphinx.ext.mathjax',
-    'sphinx_copybutton',
-    'sphinx_last_updated_by_git',
-    'sphinxcontrib.fulltoc',
-    'sphinx_remove_toctrees',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.autosectionlabel',
+    'numpydoc',
     'nbsphinx',
-    'IPython.sphinxext.ipython_console_highlighting',
+    'IPython.sphinxext.ipython_console_highlighting'
 ]
 
 autosummary_generate = True
 autodoc_member_order = 'groupwise'
 default_role = 'literal'
 napoleon_google_docstring = False
 napoleon_numpy_docstring = True
+numpydoc_show_class_members = False # don't show class members in both class and __init__ docstrings
 napoleon_include_init_with_doc = False
 napoleon_use_rtype = True  # having a separate entry generally helps readability
 napoleon_use_param = True
-
+nbsphinx_execute = 'never'
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -73,10 +80,12 @@
 # Usually you set "language" from the command line for these cases.
 language = 'en'
 
+# Add bibtex files
+bibtex_bibfiles = ['references.bib']
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
 
 # The master toctree document.
 master_doc = 'contents'
@@ -99,11 +108,12 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 
-html_theme = 'pydata_sphinx_theme'
-html_theme_options = {
-    'navigation_depth': 2,
-    'collapse_navigation': True,
-}
+html_theme = 'sphinx_rtd_theme'
+
+html_theme_options = dict(
+    logo_only=True,
+    display_version=True,
+)
 html_context = {
     'display_github': True,  # Integrate GitHub
     'github_user': 'sysbio-curie',  # Username

docs/src/contents.rst

@@ -0,0 +1,22 @@
+Contents
+========
+
+.. toctree::
+   :maxdepth: 3
+
+   index
+   api
+
+Notebooks
+=========
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Notebooks
+
+   notebooks/1_network_building
+   notebooks/2_add_resources
+   notebooks/3_build_phosphosite_network
+   notebooks/4_Connect_upstream
+   notebooks/5_ontology
+   notebooks/6_tissue_mapping

docs/src/index.rst

@@ -1,30 +1,24 @@
-############
-Introduction
-############
+==================
+Neko
+==================
 
-Created from a project template. Please write the docs of your project here,
-and remove the parts below (or edit ``README.rst`` in the project root).
+   :target: /~https://github.com/sysbio-curie/Neko/actions/workflows/test.yml
+   :alt: Tests
 
-.. include:: ../../README.rst
+.. image:: https://img.shields.io/readthedocs/omniflow_project
+   :target: https://neko.readthedocs.io
+   :alt: Documentation
 
-#########
-Reference
-#########
+Package to extract, visualize, convert and study interactions from database into executable activity flow based model.
+Neko, is based on `Omnipath </~https://github.com/saezlab/omnipath>`_, `Pypath </~https://github.com/saezlab/pypath>`_ and `Atopo </~https://github.com/druglogics/atopo>`_.
 
-project_name
-============
+This is a work-in-progress package made in collaboration with Dénes Turei and Asmund Flobak.
 
-.. automodule:: project_name
-   :members:
+CURRENT FEATURES:
 
-###########################
-Indices, Tables, and Search
-###########################
+version 0.9.0
+--------------
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
-
-.. toctree::
-   :maxdepth: 4
+- Network creation and manipulation: The package allows for the creation of a network of nodes and edges, with various methods for enrichment analysis. This includes adding and removing nodes and edges, loading a network from a SIF (Simple Interaction Format) file, and adding paths to the edge list of the network.
+- Connection of nodes: The package provides several methods to connect nodes in the network. This includes connecting all nodes, connecting a subgroup of nodes, connecting all nodes of a network object, and connecting subcomponents of a network object.
+- Connection of genes to phenotype: The package provides a method to connect genes to a phenotype based on provided parameters. This includes retrieving phenotype markers, identifying unique Uniprot genes, and connecting them to the network. There is also an option to compress the network by substituting specified genes with the phenotype name.