doc: improve TOCs

docs/source/_static/css/custom.css

@@ -0,0 +1,10 @@
+body {
+    --themecolor: #4f4f4f;
+}
+
+.wy-side-nav-search {
+    background-color: var(--themecolor);
+}
+.wy-nav-top {
+    background-color: var(--themecolor);
+}

docs/source/cli/index.rst

@@ -3,6 +3,84 @@
 CLI Reference
 =============
 
+.. toctree::
+  :maxdepth: 1
+
+Contents
+--------
+
+.. program:: momics
+.. code-block:: shell
+
+    momics [OPTIONS] COMMAND [ARGS]...
+
+.. list-table::
+    :widths: 25 100
+    :align: left
+    :header-rows: 1
+
+    * - Data management
+      -
+    * - `momics create <#momics-create>`_
+      - Create a repository
+    * - `momics delete <#momics-delete>`_
+      - Delete a repository
+    * - `momics ingest <#momics-ingest>`_
+      - Ingest datasets
+    * - `momics cp <#momics-cp>`_
+      - Copy datasets
+    * - `momics remove <#momics-remove>`_
+      - Remove datasets
+    * - `momics ls <#momics-ls>`_
+      - List tables
+
+
+.. list-table::
+    :widths: 25 100
+    :align: left
+    :header-rows: 1
+
+    * - Data query engine
+      -
+    * - `momics query <#momics-query>`_
+      - Query a repository
+
+
+.. list-table::
+    :widths: 25 100
+    :align: left
+    :header-rows: 1
+
+    * - Cloud configuration
+      -
+    * - `momics config <#momics-config>`_
+      - Create a repository
+
+.. list-table::
+    :widths: 25 100
+    :align: left
+    :header-rows: 1
+
+    * - Momics utils
+      -
+    * - `momics tree <#momics-tree>`_
+      - List repository content
+    * - `momics binnify <#momics-binnify>`_
+      - Binnify a genome
+
+.. rubric:: Options
+
+.. option:: -v, --version
+
+    Show the version and exit.
+
+.. option:: -h, --help
+
+    Show help menu and exit.
+
+
+----
+
 .. click:: momics.cli:cli
   :prog: momics
   :nested: full

docs/source/conf.py

@@ -35,7 +35,6 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.ifconfig",
     "sphinx.ext.viewcode",
-    "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinx_click.ext",
     "myst_parser",
@@ -45,7 +44,6 @@
 myst_heading_anchors = 2
 source_suffix = [".rst", ".md"]
 
-autosummary_generate = True
 numpydoc_show_class_members = True
 napoleon_use_rtype = True
 autodoc_typehints = "description"
@@ -60,6 +58,7 @@
 html_static_path = ["_static"]
 html_logo = "_static/logo.svg"
 html_favicon = "_static/logo.svg"
+html_css_files = ["css/custom.css"]
 html_sourcelink_suffix = ""
 html_last_updated_fmt = ""
 htmlhelp_basename = "momicsdoc"
@@ -72,6 +71,7 @@
 html_theme_options = {
     "use_edit_page_button": True,
     "external_links": "",
+    "logo_only": False,
     "github_url": "https://github.com/js2264/momics/",
     "show_prev_next": False,
     "search_bar_text": "Search the docs ...",
@@ -83,6 +83,8 @@
     "footer_start": ["copyright"],
     "footer_center": ["sphinx-version"],
     "content_footer_items": ["last-updated"],
+    "rightsidebar": "false",
+    "relbarbgcolor": "black",
 }
 html_context = {
     "github_url": "https://github.com/js2264/momics/",
@@ -93,11 +95,11 @@
 }
 html_static_path = ["_static"]
 
-autosummary_generate = True
-
 # -- Options for autoapi -------------------------------------------------------
 autoapi_type = "python"
 autoapi_dirs = ["../../src/momics"]
+autoapi_ignore = ["*/cli*"]
+autoapi_exclude = ["*/cli*"]
 autoapi_options = [
     "members",
     "undoc-members",

docs/source/index.md

@@ -18,10 +18,12 @@ The `momics` package aims to facilitate:
 Follow `momics` development on [GitHub](https://github.com/js2264/momics).
 
 ```{toctree}
-:caption: Table of content
-:maxdepth: 3
+:caption: Contents
+:maxdepth: 1
 
-user_guide/index
+user_guide/get-started
+user_guide/api
+user_guide/cli
 api/index
 cli/index
 ```

docs/source/user_guide/api.md

@@ -1,6 +1,10 @@
 # Introduction to `momics` API
 
-## Introduction
+```{danger}
+This package is still under active development, and we make no promises
+about the stability of any specific class, function, etc.
+Pin versions if you're worried about breaking changes!
+```
 
 The `momics` package provides a Python API for creating and interacting with the `momics` data
 model. This API is designed to be simple and intuitive, and is built on top of
@@ -91,13 +95,13 @@ print(mom.tracks())
 
 ## Querying `momics` repositories
 
-The `momics` package provides a dedicated `MultiRangeQuery` class,
+The `momics` package provides a dedicated `MomicsQuery` class,
 to register query ranges, run queries and export results.
 
 ### Registering a query
 
 ```python
-q = momics.MultiRangeQuery(mom, "I:10-1000")
+q = momics.MomicsQuery(mom, "I:10-1000")
 ```
 
 ### Running a query
@@ -126,7 +130,7 @@ q.query_tracks(threads = 4)
 ### Exporting query results
 
 The query results can be coerced into generic bioinformatic data objects and
-exported to output files using dedicated methods of the `MultiRangeQuery` class.
+exported to output files using dedicated methods of the `MomicsQuery` class.
 
 ```python
 # Coerce queried sequences as a SeqRecord object

docs/source/user_guide/get-started.md

@@ -1,5 +1,11 @@
 # Get started with `momics`
 
+```{danger}
+This package is still under active development, and we make no promises
+about the stability of any specific class, function, etc.
+Pin versions if you're worried about breaking changes!
+```
+
 ## Installation
 
 With python `3.8` and higher, you can install `momics`  from [PyPI](https://pypi.org/project/momics) using `pip`.