Update docs build

docs/Makefile

@@ -1,9 +1,10 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build
 

docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -16,7 +16,7 @@
 import sys
 from unittest.mock import MagicMock
 
-from sphinx.apidoc import main as run_apidoc
+from sphinx.ext.apidoc import main as run_apidoc
 
 __location__ = os.path.abspath(os.path.join(os.path.dirname(__file__)))
 sys.path.insert(0, os.path.join(__location__, "..", "..", "src"))
@@ -66,12 +66,11 @@ def __getattr__(cls, name):
 
 run_apidoc(
     [
-        "sphinx-apidoc",
-        "-M",
-        "-o",
-        output_dir,
-        module_dir,
         "--force",
+        "--module-first",
+        "--output-dir",
+        output_dir,
+        module_dir
     ]
 )
 
@@ -80,7 +79,7 @@ def __getattr__(cls, name):
 
 # Extra styles, found in _static
 def setup(app):
-    app.add_stylesheet("theme_tweaks.css")
+    app.add_css_file("theme_tweaks.css")
 
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -93,8 +92,9 @@ def setup(app):
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
-    "m2r2",
+    "myst_parser",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -112,7 +112,7 @@ def setup(app):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/source/getting_started.rst

@@ -2,6 +2,7 @@
 Getting Started
 ===============
 
-.. mdinclude:: ../../README.md
-   :start-line: 63
-   :end-line: 78
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
+   :start-line: 56
+   :end-line: 72

docs/source/index.rst

@@ -13,41 +13,57 @@ a spatial networks toolkit
     :target: https://opensource.org/licenses/MIT
     :alt: License
 
-.. image:: https://travis-ci.com/tomalrussell/snkit.png?branch=master
-    :target: https://travis-ci.com/tomalrussell/snkit
-    :alt: Build Status
+.. image:: https://github.com/tomalrussell/snkit/actions/workflows/test.yml/badge.svg
+    :target: https://github.com/tomalrussell/snkit/actions/workflows/test.yml
+    :alt: Build
 
 .. image:: https://img.shields.io/pypi/v/snkit.svg
     :target: https://pypi.org/project/snkit/
     :alt: PyPI version
 
+.. image:: https://anaconda.org/conda-forge/snkit/badges/version.svg
+   :target: https://anaconda.org/conda-forge/snkit
+   :alt: Conda Forge version
+
+.. image:: https://img.shields.io/badge/poster-10.6084%2Fm9.figshare.11864826.v1-purple
+    :target: https://doi.org/10.6084/m9.figshare.11864826.v1
+    :alt: Poster
+
+.. image:: https://zenodo.org/badge/129739785.svg
+    :target: https://doi.org/10.5281/zenodo.3269518
+    :alt: DOI
+
 
 /ˈsnɪkɪt/ – sounds like `[snicket] <https://en.oxforddictionaries.com/definition/snicket>`_
 (noun, Northern English) A narrow passage between houses; an alleyway. Alternatively, a python
 package to help clean spatial networks data.
 
 
-.. mdinclude:: ../../README.md
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
    :start-line: 17
-   :end-line: 26
+   :end-line: 22
 
 .. image:: _static/unconnected-network.png
    :alt: Unconnected network
 
-.. mdinclude:: ../../README.md
-   :start-line: 28
-   :end-line: 39
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
+   :start-line: 25
+   :end-line: 35
 
 .. image:: _static/connected-network.png
    :alt: Connected network
 
-.. mdinclude:: ../../README.md
-   :start-line: 41
-   :end-line: 59
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
+   :start-line: 38
+   :end-line: 54
 
-.. mdinclude:: ../../README.md
-   :start-line: 78
-   :end-line: 107
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
+   :start-line: 113
+   :end-line: 138
 
 
 .. toctree::