From 3de2fd771d92064c095147f6d18297599a7e5130 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Semid=C3=A1n=20Robaina=20Est=C3=A9vez?= Date: Fri, 19 Jun 2026 12:45:01 +0100 Subject: [PATCH] docs: pynteny is on PyPI - lead with `pip install pynteny` Now that v1.2.0 is published to PyPI: - Re-add the PyPI version badge to the README. - Make `pip install pynteny` the primary install command in README and docs/index.md, keeping the GitHub install as the "latest development version" option. - Colab example installs from PyPI again. Co-Authored-By: Claude Opus 4.8 --- README.md | 9 +++++---- docs/examples/example_api_colab.ipynb | 2 +- docs/index.md | 8 ++++---- 3 files changed, 10 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 548ca6a..f3cac1d 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,7 @@ ![license](https://img.shields.io/github/license/Robaina/Pynteny) ![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4) +[![PyPI version](https://img.shields.io/pypi/v/pynteny?logo=pypi&style=flat-square)](https://pypi.org/project/pynteny/) [![GitHub release](https://img.shields.io/github/release/Robaina/Pynteny.svg)](https://GitHub.com/Robaina/Pynteny/releases/) ![python](https://img.shields.io/badge/Python-3.9%20|%203.12-blue) @@ -36,16 +37,16 @@ binaries). All dependencies, including the HMMER and Prodigal engines, are provided by the pip packages [pyhmmer](https://github.com/althonos/pyhmmer) and [pyrodigal](https://github.com/althonos/pyrodigal). -Install the latest development version directly from GitHub: +Install with pip: ```bash -pip install git+https://github.com/Robaina/Pynteny.git +pip install pynteny ``` -Once released on PyPI, Pynteny will also be installable with: +Or install the latest development version directly from GitHub: ```bash -pip install pynteny +pip install git+https://github.com/Robaina/Pynteny.git ``` Check that the installation worked fine: diff --git a/docs/examples/example_api_colab.ipynb b/docs/examples/example_api_colab.ipynb index 435fcb4..6308683 100644 --- a/docs/examples/example_api_colab.ipynb +++ b/docs/examples/example_api_colab.ipynb @@ -45,7 +45,7 @@ "try:\n", " import google.colab\n", " # Pynteny is a pure-pip package (no conda / external binaries required).\n", - " !pip install -q git+https://github.com/Robaina/Pynteny.git\n", + " !pip install -q pynteny\n", " # Grab the bundled test data used throughout this example.\n", " !git clone -q https://github.com/Robaina/Pynteny.git\n", " !cp -r Pynteny/tests/ . && rm -rf Pynteny\n", diff --git a/docs/index.md b/docs/index.md index f5a9bd1..b49f276 100644 --- a/docs/index.md +++ b/docs/index.md @@ -18,16 +18,16 @@ binaries). The HMMER and Prodigal engines are provided by the pip packages [pyhmmer](https://github.com/althonos/pyhmmer) and [pyrodigal](https://github.com/althonos/pyrodigal). -Install the latest development version directly from GitHub: +Install with pip: ```bash -pip install git+https://github.com/Robaina/Pynteny.git +pip install pynteny ``` -Once released on PyPI, Pynteny will also be installable with: +Or install the latest development version directly from GitHub: ```bash -pip install pynteny +pip install git+https://github.com/Robaina/Pynteny.git ``` Check that installation worked fine: