Consistently capitalise PyPI thus [minor]

Author: jmarshall

INSTALL

@@ -5,7 +5,7 @@ http://pysam.readthedocs.io/en/latest/installation.html
 Installing pysam
 ================
 
-Pysam can be installed through conda_, pypi_ and from the repository.
+Pysam can be installed through conda_, PyPI_ and from the repository.
 The recommended way to install pysam is through conda/bioconda.
 
 Conda installation
@@ -22,7 +22,7 @@ makes sure that dependencies are installed. Also, compilation flags
 will be set automatically, which will potentially save a lot of
 trouble on OS X.
 
-Pypi installation
+PyPI installation
 =================
 
 Pysam provides a python interface to the functionality contained
@@ -32,7 +32,7 @@ can be combined, ``builtin`` and ``external``.
 Builtin
 -------
 
-The typical installation will be through pypi_::
+The typical installation will be through PyPI_::
 
    pip install pysam
 
@@ -86,7 +86,7 @@ To install from repository, type::
 
     python setup.py install
 
-For compilation options, see the section on Pypi installation above.
+For compilation options, see the section on PyPI installation above.
 
 Requirements
 ============

MANIFEST.in

@@ -19,8 +19,7 @@ exclude pysam/config.py
 
 include win32/*.[ch]
 
-# exclude tests from pypi tar-ball - they
-# require additional data
+# exclude tests from sdist tarball as they require additional data
 prune tests/
 
 # samtools

NEWS

@@ -39,7 +39,7 @@ Release 0.22.0
 This pysam release wraps htslib/samtools/bcftools 1.18 (PR #1208).
 
 It has been tested with Python versions 3.6 through 3.12, and wheels are
-available via pypi_ for all of those Python versions. Python versions 3.6
+available via PyPI_ for all of those Python versions. Python versions 3.6
 and 3.7 are end-of-life; particularly if you use pysam with either of
 these versions, please vote in the version survey at issue #1230.
 

README.rst

@@ -27,8 +27,8 @@ lot of trouble.
 
 The current version of pysam wraps 3rd-party code from htslib-1.21, samtools-1.21, and bcftools-1.21.
 
-Pysam is available through `pypi
-<https://pypi.python.org/pypi/pysam>`_. To install, type::
+Pysam is available through `PyPI <https://pypi.org/project/pysam/>`_.
+To install, type::
 
    pip install pysam
 

doc/conf.py

@@ -64,7 +64,7 @@
 .. _Galaxy: https://main.g2.bx.psu.edu/
 .. _cython: https://cython.org/
 .. _python: https://www.python.org/
-.. _pypi: https://pypi.org/
+.. _PyPI: https://pypi.org/
 .. _pip: https://pip.pypa.io/
 .. _pyximport: https://github.com/cython/cython/tree/master/pyximport
 .. _conda: https://conda.io/docs/

doc/installation.rst

@@ -4,7 +4,7 @@
 Installing pysam
 ================
 
-Pysam can be installed through conda_, pypi_ and from the repository.
+Pysam can be installed through conda_, PyPI_ and from the repository.
 The recommended way to install pysam is through conda/bioconda.
 
 Conda installation
@@ -21,7 +21,7 @@ makes sure that dependencies are installed. Also, compilation flags
 will be set automatically, which will potentially save a lot of
 trouble on OS X.
 
-Pypi installation
+PyPI installation
 =================
 
 Pysam provides a python interface to the functionality contained
@@ -31,7 +31,7 @@ can be combined, ``builtin`` and ``external``.
 Builtin
 -------
 
-The typical installation will be through pypi_::
+The typical installation will be through PyPI_::
 
    pip install pysam
 
@@ -89,7 +89,7 @@ To install from repository, type::
 
     python setup.py install
 
-For compilation options, see the section on Pypi installation above.
+For compilation options, see the section on PyPI installation above.
 
 Requirements
 ============