Add a Tutorial in the Documentation

docs/api/api_ref.md

@@ -3,6 +3,5 @@
 ```{toctree}
 :maxdepth: 2
 binette
-indice_and_table
 ```
 

docs/api/binette.md

@@ -20,15 +20,6 @@
    :show-inheritance:
 ```
 
-## binette.binette module
-
-```{eval-rst}
-.. automodule:: binette.binette
-   :members:
-   :undoc-members:
-   :show-inheritance:
-```
-
 ## binette.cds module
 
 ```{eval-rst}
@@ -65,10 +56,10 @@
    :show-inheritance:
 ```
 
-## Module contents
+## binette.main module
 
 ```{eval-rst}
-.. automodule:: binette
+.. automodule:: binette.main
    :members:
    :undoc-members:
    :show-inheritance:

docs/conf.py

@@ -18,35 +18,58 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-    "myst_parser",
+    #  
     # "sphinxcontrib.jquery",
     "sphinx.ext.duration",
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.autodoc",
-    'sphinx_search.extension'
+    'sphinx_search.extension',
+     'sphinx_togglebutton',
+    # "myst_nb",
+    "myst_parser",
+    'nbsphinx',
+    'nbsphinx_link', 
+    # 'sphinx.ext.napoleon',
+    # 'sphinx.ext.viewcode',
+    'sphinxcontrib.mermaid'
+]
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "replacements",
+    "smartquotes",
+    "strikethrough",
+    "substitution",
+    "tasklist",
 ]
-
 
 source_suffix = {
-    '.md': 'markdown'
+    '.md': 'markdown',
 }
 
 
 templates_path = ['_templates']
 
-
+nb_execution_mode = "off"
+nbsphinx_execute = 'never'
 # Prefix document path to section labels, to use:
 # `path/to/file:heading` instead of just `heading`
 autosectionlabel_prefix_document = True
 
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'build', "jupyter_execute"]
 
 
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme' #'alabaster' # 
+# html_theme = 'sphinx_rtd_theme' #'alabaster' # 
+html_theme = 'sphinx_rtd_theme' #'sphinx_book_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -55,3 +78,40 @@
 
 
 
+
+
+# Include the Plotly JavaScript in the HTML output
+nbsphinx_requirejs_path = ""
+
+# Ensures that the `require.js` is loaded for Plotly to function correctly
+nbsphinx_requirejs_options = {
+    'paths': {
+        'plotly': 'https://cdn.plot.ly/plotly-latest.min'
+    },
+    'shim': {
+        'plotly': {
+            'exports': 'Plotly'
+        }
+    }
+}
+
+# Specify the default language for syntax highlighting in Sphinx
+highlight_language = 'python'
+
+# -- Options for HTML output -------------------------------------------------
+
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add plotly renderer options
+nbsphinx_prolog = r"""
+.. raw:: html
+
+    <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
+"""
+
+
+

docs/contributing.md

@@ -26,7 +26,7 @@ For minor changes like fixing typos or making small edits, create a new Pull Req
    - Clone your forked repository to your local machine.
 
 2. **Get an Environment:**
-   Create an environment with all Binette prerequisites installed by following the installation instructions [here](./installation.md#installing-from-source-code-within-a-conda-environnement).
+   Create an environment with all Binette prerequisites installed by following the installation instructions [here](./installation.md#from-the-source-code-within-a-conda-environnement).
 
 3. **Install in Editable Mode:**
    To enable code editing and testing of new functionality, you can install Binette in editable mode using the following command:

docs/index.md

@@ -31,14 +31,18 @@ Binette is inspired from the metaWRAP bin-refinement tool but it effectively sol
 - Enhanced Speed: Binette significantly improves the speed of the refinement process. It achieves this by launching the initial steps of CheckM2, such as Prodigal and Diamond runs, only once on all contigs. These intermediate results are then utilized to assess the quality of any given bin, eliminating redundant computations and accelerating the refinement process.
 - No Limit on Input Bin Sets: Unlike its predecessor, Binette is not constrained by the number of input bin sets. It can handle and process multiple bin sets simultaneously.
 
+
+
+
 ```{toctree}
 :caption: 'Documentation'
 :maxdepth: 2
 
 installation
 usage
+tutorial/tutorial_main
 contributing
-tests.md
+tests
 api/api_ref
 ```
 

docs/tests.md

@@ -8,7 +8,7 @@ Tests have been implemented to ensure the correctness of Binette.
 Unit tests have been implmented in the tests directory using pytest. 
 
 
-To run the test suit you would need to  have install Binette from the source code.  For that, you can follow installation instructions [here](./installation.md#installing-from-source-code-within-a-conda-environnement).
+To run the test suit you would need to  have install Binette from the source code.  For that, you can follow installation instructions [here](./installation.md#from-the-source-code-within-a-conda-environnement).
 
 
 To install pytest in you environement you can run :