add LICENSE

python/LICENSE

@@ -0,0 +1,9 @@
+The MIT License (MIT)
+
+Copyright (c) 2024-2024 Kai Zhang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

python/README.md

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+# Single-cell genomics preprocessing package
+
+This tool is an automated pipeline for preprocessing single-cell genomics data.
+It is designed to take raw data (fastq files) from a variety of single-cell genomics
+platforms and a seqspec file as input, and output a count matrix (RNA) or a fragment file (ATAC)
+for downstream analysis. The seqspec files for common platforms can be found here: https://github.com/IGVF/seqspec.
+
+## Installation
+
+### Stable version
+
+```
+pip install precellar
+```
+
+### Development version
+
+```
+pip install 'git+https://github.com/regulatory-genomics/precellar.git#egg=precellar&subdirectory=python'
+```
+
+For more information, please refer to the documentation: https://lab.kaizhang.org/precellar/.

python/pyproject.toml

@@ -4,12 +4,26 @@ build-backend = "maturin"
 
 [project]
 name = "precellar"
-requires-python = ">=3.8"
+authors = [
+    {name = "Kai Zhang", email = "zhangkai33@westlake.edu.cn"}
+]
+description = "precellar: Single-cell epigenomics preprocessing toolkit"
+readme = "README.md"
+license = {file = "LICENSE"}
 classifiers = [
     "Programming Language :: Rust",
     "Programming Language :: Python :: Implementation :: CPython",
     "Programming Language :: Python :: Implementation :: PyPy",
 ]
+requires-python = ">=3.9, <3.13"
 dynamic = ["version"]
+
 [tool.maturin]
 features = ["pyo3/extension-module"]
+
+[project.urls]
+Homepage = "https://lab.kaizhang.org/precellar/"
+Documentation = "https://lab.kaizhang.org/precellar/"
+Repository = "https://github.com/regulatory-genomics/precellar"
+Issues = "https://github.com/regulatory-genomics/precellar/issues"
+Changelog = "https://lab.kaizhang.org/precellar/version/dev/changelog.html"