v0.1.0

.github/workflows/test_python.yml

@@ -50,4 +50,21 @@ jobs:
 
   build-wheel:
     needs: build-and-test
-    uses: regulatory-genomics/precellar/.github/workflows/wheels.yml@main
+    uses: regulatory-genomics/precellar/.github/workflows/wheels.yml@main
+
+  publish:
+    needs: build-wheel
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    if: ${{ startsWith(github.ref, 'refs/tags') }}
+    steps:
+    - name: Download wheel files
+      uses: actions/download-artifact@v4
+      with:
+        path: dist
+        pattern: precellar-*
+        merge-multiple: true
+
+    - name: Publish to PyPI
+      uses: pypa/[email protected]

README.md

@@ -5,4 +5,18 @@ It is designed to take raw data (fastq files) from a variety of single-cell geno
 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/.

docs/index.rst

@@ -5,5 +5,6 @@ precellar: Single-cell genomics data preprocessing tools
    :maxdepth: 3
    :hidden:
 
-   api
-   tutorials/index
+   install
+   tutorials/index
+   api

docs/install.md

@@ -0,0 +1,52 @@
+Installation
+============
+
+Stable version
+--------------
+
+Stable versions of precellar are published on PyPI.
+Precompiled binaries are available for x86_64 Linux systems.
+So installing it is as simple as running:
+
+```
+pip install precellar
+```
+
+You may need the [Rust](https://www.rust-lang.org/tools/install) compiler during
+the installation process. The Rust compiler can be installed using:
+
+```
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+```
+
+Nightly build
+-------------
+
+The nightly build is the build from the latest source codes, which includes the
+latest features, enhancements, and bug fixes that haven't been released. 
+The nightly build can be unstable and include some untested features.
+
+The [nightly release](https://github.com/regulatory-genomics/precellar/releases/tag/nightly) page
+contains wheel files for the nightly build.
+Please download the corresponding wheel file for your platform and use `pip install` to install it.
+For example, if you are using a Linux system with Python 3.8, you can use the following command to install it:
+
+```
+pip install precellar-x.x.x-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+```
+
+Build from the latest source code 
+---------------------------------
+
+Building the precellar library requires the [Rust](https://www.rust-lang.org/tools/install) compiler.
+The Rust compiler can be installed using:
+
+```
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+```
+
+Once you have the Rust compiler properly installed, you can use pip to install the precellar library:
+
+```
+pip install 'git+https://github.com/regulatory-genomics/precellar.git#egg=precellar&subdirectory=python'
+```

python/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "precellar-py"
-version = "0.1.0-dev"
+version = "0.1.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html