Refresh README and remove ctags artifacts

.gitignore

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 # Compiled RRA artifacts
 rra/src/*.o
 rra/bin/RRA
+
+# Editor / ctags artifacts
+tags

README.md

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-
 # MAGeCK2: Model-based Analysis of CRISPR screens
 
+[![CI](https://github.com/davidliwei/mageck2/actions/workflows/ci.yml/badge.svg)](https://github.com/davidliwei/mageck2/actions/workflows/ci.yml)
+[![License: BSD-3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](LICENSE)
+
 MAGeCK2 is a new computational tool, built upon MAGeCK, for CRISPR screening analysis.
 
 Compared with MAGeCK, MAGeCK2 highlights the following additional functionalities:
@@ -9,32 +11,70 @@ Compared with MAGeCK, MAGeCK2 highlights the following additional functionalitie
 * Processing and analyzing screens with UMIs
 * Processing and analyzing paired-guide screens
 
-More functions to be added.
+See [ROADMAP.md](ROADMAP.md) for the planned direction of the project.
+
+
+# Installation
+
+MAGeCK2 requires Python ≥ 3.7 and a C++ compiler (used to build the bundled RRA
+component). The Python dependencies (numpy, scipy, pandas, matplotlib, statsmodels) are
+installed automatically.
+
+Install the latest version directly from GitHub:
+
+    pip install git+https://github.com/davidliwei/mageck2.git
+
+or from a local clone:
+
+    git clone https://github.com/davidliwei/mageck2.git
+    cd mageck2
+    pip install .
+
+For detailed instructions, see [mageck2-doc](https://github.com/davidliwei/mageck2-doc).
+
+
+# Quick start
+
+Run a statistical test from a count table:
+
+    mageck2 test -k count_table.txt -t treatment_samples -c control_samples -n output_prefix
+
+Runnable example datasets are available in the [mageck2-demo](https://github.com/davidliwei/mageck2-demo) repository.
 
 
 # Documentation
 
 For instructions on installation, usage and running examples, see [mageck2-doc](https://github.com/davidliwei/mageck2-doc).
 
-# Demo
-
-You can run the example datasets of MAGeCK2 from GitHub [mageck2-demo](https://github.com/davidliwei/mageck2-demo) repository.
 
 # MAGeCK
 
 The older version of MAGeCK can be accessed via [sourceforge](https://sourceforge.net/projects/mageck/) or [bitbucket](https://bitbucket.org/liulab/mageck/src/master/).
 
+
+# Contributing
+
+Contributions are welcome. See [CONTRIBUTING.md](CONTRIBUTING.md) for how to get started,
+[GOVERNANCE.md](GOVERNANCE.md) for how the project is run, and [ROADMAP.md](ROADMAP.md) for
+where it is headed.
+
+
 # Questions
 
 Questions? Bug? Recommendations? Here are a few ways:
 
-* Join our [Google group](https://groups.google.com/g/mageck?hl=en); 
-* Create an [issue](https://github.com/davidliwei/mageck2/issues) in the github repository. Issues from demo or documentations will need to posted to [mageck2-demo](https://github.com/davidliwei/mageck2-demo) or [mageck2-doc](https://github.com/davidliwei/mageck2-doc), respectively.
-
+* Join our [Google group](https://groups.google.com/g/mageck?hl=en);
+* Create an [issue](https://github.com/davidliwei/mageck2/issues) in the github repository. Issues from demo or documentations will need to be posted to [mageck2-demo](https://github.com/davidliwei/mageck2-demo) or [mageck2-doc](https://github.com/davidliwei/mageck2-doc), respectively.
 
 
 # Version history
 
+## 2026 — Packaging modernization
+
+* Migrated packaging to `pyproject.toml`; MAGeCK2 is now pip-installable on Python 3.7+ (including 3.12 and 3.13).
+* Added continuous integration and a smoke-test suite.
+* Added project governance and contribution documentation.
+
 ## 2020.12.01 Version 0.1
 
 * Add paired-guide support in count command