From ac77fe038ee034577af24eb9eac6fb1d1328a3e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Wed, 25 May 2022 13:16:31 +0100
Subject: [PATCH] update docs and bump version
---
docs/requirements.txt | 1 +
docs/source/conf.py | 13 +++++++++++++
docs/source/index.rst | 25 +++++--------------------
pyproject.toml | 2 +-
4 files changed, 20 insertions(+), 21 deletions(-)
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 577cdaf1..6b7abcb3 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,3 +1,4 @@
numpydoc>=1.3.1
aliby>=0.1.26
myst-parser
+sphinx-autodoc-hints
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 34583117..ba132177 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -35,10 +35,23 @@ release = "0.1.26"
extensions = [
"sphinx.ext.autodoc", # Core library for html generation from docstrings
"sphinx.ext.autosummary", # Create neat summary tables
+ "sphinx.ext.intersphinx", # Link to other project's documentation (see mapping below)
+ "sphinx.ext.viewcode", # Add a link to the Python source code for classes, functions etc.
+ "sphinx_autodoc_typehints", # Automatically document param types (less noise in class signature)
"numpydoc", # Play along with numpydoc format
"myst_parser", # Include markdown in rst files.
]
+
autosummary_generate = True # Turn on sphinx.ext.autosummary
+autoclass_content = "both" # Add __init__ doc (ie. params) to class summaries
+html_show_sourcelink = (
+ False # Remove 'view source code' from top of page (for html, not python)
+)
+autodoc_inherit_docstrings = True # If no docstring, inherit from base class
+set_type_checking_flag = True # Enable 'expensive' imports for sphinx_autodoc_typehints
+nbsphinx_allow_errors = True # Continue through Jupyter errors
+# autodoc_typehints = "description" # Sphinx-native method. Not as good as sphinx_autodoc_typehints
+add_module_names = False # Remove namespaces from class/method signatures
# Add any paths that contain templates here, relative to this directory.
diff --git a/docs/source/index.rst b/docs/source/index.rst
index b612c9c4..560b15f7 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -3,30 +3,15 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-ALIBY's guides and documentation
-=================================
.. toctree::
- :maxdepth: 3
+ :hidden:
+
+ Home page <self>
+ ALIBY reference <aliby>
+ extraction reference <extraction>
.. include:: ../../README.md
:parser: myst_parser.sphinx_
-
-Contributing
-============
-.. toctree::
- :maxdepth: 2
-
.. include:: ../../CONTRIBUTING.md
:parser: myst_parser.sphinx_
-
-
-API Reference
-============
-.. toctree::
-.. autosummary::
- :template: custom-module-template.rst
- :recursive:
-
- aliby
- extraction
diff --git a/pyproject.toml b/pyproject.toml
index 943828b4..8721f4fc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "aliby"
-version = "0.1.28"
+version = "0.1.29"
description = "Process and analyse live-cell imaging data"
authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
packages = [
--
GitLab