update docs

lmdu · Sep 7, 2023 · bef1a95 · bef1a95
1 parent 707e3fa
commit bef1a95
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Showing 15 changed files with 51 additions and 83 deletions.
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
diff --git a/docs/Makefile b/docs/Makefile
@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

diff --git a/docs/source/acknowledgements.rst → docs/acknowledgements.rst b/docs/source/acknowledgements.rst → docs/acknowledgements.rst
diff --git a/docs/source/advance.rst → docs/advance.rst b/docs/source/advance.rst → docs/advance.rst
diff --git a/docs/source/api_reference.rst → docs/api_reference.rst b/docs/source/api_reference.rst → docs/api_reference.rst
@@ -403,7 +403,7 @@ New in ``pyfastx`` 0.4.0
 
 		get read quality ascii string
 
-	.. py:attriubte:: quali
+	.. py:attribute:: quali
 
 		get read quality integer value (ascii - phred), return a list
 

diff --git a/docs/source/changelog.rst → docs/changelog.rst b/docs/source/changelog.rst → docs/changelog.rst
@@ -240,7 +240,7 @@ Version 0.6.0 (2020-01-02)
 - Disabled export gzip index when building memory index
 
 Version 0.5.10 (2019-11-20)
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Added identifier filter function
 - Remove tp_new for Read, Sequence and Identifier
@@ -335,7 +335,7 @@ Version 0.4.0 (2019-09-29)
 - Added random access to reads from FASTQ
 
 Version 0.3.10 (2019-09-27)
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Fixed GC skew exception caused by mixing unsigned with signed for division  
 
@@ -409,12 +409,12 @@ Version 0.3.0 (2019-09-07)
 - removed support for Python34
 
 Version 0.2.11 (2019-08-31)
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Support for Python 3.4
 
 Version 0.2.10 (2019-08-28)
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Changed fseek and fread into gzseek and gzread
 - Fixed sequence cache name comparision

diff --git a/docs/source/commandline.rst → docs/commandline.rst b/docs/source/commandline.rst → docs/commandline.rst
@@ -13,7 +13,7 @@ New in ``pyfastx`` 0.5.0
 
     optional arguments:
       -h, --help     show this help message and exit
-      -v, --version  show program's version number and exit
+      -v, --version  show program version number and exit
 
     Commands:
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -0,0 +1,36 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+
+project = 'pyfastx'
+copyright = '2023, Lianming Du'
+author = 'Lianming Du'
+
+with open(os.path.join(os.path.abspath('..'), 'src', 'version.h')) as fh:
+	__version__ = fh.read().split()[2].strip('"')
+
+version = __version__
+
+release = __version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+#html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
diff --git a/docs/source/drawbacks.rst → docs/drawbacks.rst b/docs/source/drawbacks.rst → docs/drawbacks.rst
diff --git a/docs/source/index.rst → docs/index.rst b/docs/source/index.rst → docs/index.rst
diff --git a/docs/source/installation.rst → docs/installation.rst b/docs/source/installation.rst → docs/installation.rst
diff --git a/docs/make.bat b/docs/make.bat
@@ -7,10 +7,8 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=source
-set BUILDDIR=build
-
-if "%1" == "" goto help
+set SOURCEDIR=.
+set BUILDDIR=_build
 
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
@@ -21,10 +19,12 @@ if errorlevel 9009 (
 	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/
+	echo.https://www.sphinx-doc.org/
 	exit /b 1
 )
 
+if "%1" == "" goto help
+
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 goto end
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1 +1,2 @@
-sphinx>=2.1.2
+sphinx>=7.2.5
+sphinx-rtd-theme>=1.3.0
diff --git a/docs/source/conf.py b/docs/source/conf.py
diff --git a/docs/source/usage.rst → docs/usage.rst b/docs/source/usage.rst → docs/usage.rst