Explicitly select sphinx_rtd_theme and update Sphinx

Update to Sphinx 7.x now that there is a sphinx_rtd_theme release
that supports it. Update MANIFEST.in and remove duplicate entries.

MANIFEST.in

@@ -9,7 +9,7 @@ include NEWS
 include INSTALL
 include KNOWN_BUGS
 include THANKS
-include requirements.txt
+include requirements-dev.txt
 include pysam/libc*.pxd
 include pysam/libc*.pyx
 include pysam/libc*.c
@@ -45,9 +45,6 @@ include htslib/configure htslib/version.sh
 include htslib/Makefile htslib/*.mk
 exclude htslib/config.mk htslib/htscodecs.mk
 
-include cy_build.py
-include requirements.txt
-
 # documentation
 include doc/*.py doc/*.rst
-include doc/Makefile doc/make.bat
+include doc/Makefile doc/make.bat doc/requirements-rtd.txt

doc/conf.py

@@ -125,7 +125,7 @@
 
 # The theme to use for HTML and HTML Help pages.  Major themes that come with
 # Sphinx are currently 'default' and 'sphinxdoc'.
-html_theme = 'default'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

doc/requirements-rtd.txt

@@ -1,2 +1,2 @@
-sphinx==6.2.1
-sphinx-rtd-theme==1.2.2
+sphinx==7.2.5
+sphinx-rtd-theme==1.3.0