From 0eae5be21ac3ab3ac7aa770a3931e2977e37b909 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Wed, 30 Oct 2024 23:09:06 +1300 Subject: [PATCH] Consistently capitalise PyPI thus [minor] --- INSTALL | 8 ++++---- MANIFEST.in | 3 +-- NEWS | 2 +- README.rst | 4 ++-- doc/conf.py | 2 +- doc/installation.rst | 8 ++++---- 6 files changed, 13 insertions(+), 14 deletions(-) diff --git a/INSTALL b/INSTALL index 5016dcc7..6dd0163f 100644 --- a/INSTALL +++ b/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 ============ diff --git a/MANIFEST.in b/MANIFEST.in index adb23683..47e77029 100644 --- a/MANIFEST.in +++ b/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 diff --git a/NEWS b/NEWS index 83ee8032..86c0df57 100644 --- a/NEWS +++ b/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. diff --git a/README.rst b/README.rst index e71eea43..89a51f3c 100644 --- a/README.rst +++ b/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 -`_. To install, type:: +Pysam is available through `PyPI `_. +To install, type:: pip install pysam diff --git a/doc/conf.py b/doc/conf.py index 40081eb4..053c8a72 100644 --- a/doc/conf.py +++ b/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/ diff --git a/doc/installation.rst b/doc/installation.rst index a659f9da..6282fb5d 100644 --- a/doc/installation.rst +++ b/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 ============