ylab-hi · cauliyang · Oct 25, 2023 · Oct 25, 2023 · Oct 25, 2023 · Oct 25, 2023
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -30,6 +30,7 @@ repos:
     rev: 1.16.0
     hooks:
       - id: blacken-docs
+        exclude: docs/tutorial.md
 
   - repo: https://github.com/crate-ci/typos
     rev: typos-dict-v0.11.2

diff --git a/README.md b/README.md
@@ -7,7 +7,8 @@ _An Efficient and Ergonomic Python Binding Library for BLAT_
 [![c](https://img.shields.io/badge/C-A8B9CC.svg?style=for-the-badge&logo=C&logoColor=black)](https://www.gnu.org/software/gnu-c-manual/)
 [![pypi](https://img.shields.io/pypi/v/pxblat.svg?style=for-the-badge)][pypi]
 [![conda](https://img.shields.io/conda/vn/bioconda/pxblat?style=for-the-badge)][conda]
-![platform](https://img.shields.io/static/v1?style=for-the-badge&label=platform&message=macos%20%7C%20linux&color=brightgreen)
+![Linux](https://img.shields.io/badge/-Linux-grey?logo=linux&style=for-the-badge)
+![macOS](https://img.shields.io/badge/-OSX-black?logo=apple&style=for-the-badge)
 [![pyversion](https://img.shields.io/pypi/pyversions/pxblat?style=for-the-badge)][pypi]
 [![tests](https://img.shields.io/github/actions/workflow/status/cauliyang/pxblat/tests.yml?style=for-the-badge&logo=github&label=Tests)](https://github.com/cauliyang/pxblat/actions/workflows/tests.yml)
 [![Codecov](https://img.shields.io/codecov/c/github/cauliyang/pxblat/main?style=for-the-badge)](https://app.codecov.io/gh/cauliyang/pxblat)

diff --git a/docs/_templates/base.html b/docs/_templates/base.html
@@ -1,6 +1,5 @@
 {% extends "!base.html" %} {% block announce %}
 <p>
-  Now
   <a href="https://github.com/ylab-hi/pxblat#-citation">Please Cite Me</a>
   v0.3.10
 </p>

diff --git a/docs/conf.py b/docs/conf.py
@@ -82,6 +82,7 @@
 # so a file named 'default.css' will overwrite the builtin 'default.css'.
 html_static_path = ["_static"]
 
+
 myst_heading_anchors = 3
 myst_enable_extensions = [
     "dollarmath",

diff --git a/docs/installation.md b/docs/installation.md
@@ -1,95 +1,74 @@
-# Install
+# **Installation Guide**
 
-## **Prerequisites**
+Welcome to the installation guide for **PxBLAT**!
+Below, you'll find straightforward instructions on how to install **PxBLAT** on your system.
+You can choose between `CONDA` and `PyPI` for installation, depending on your preference.
 
-```{tip}
-I highly recommend to install `PxBLAT` via `CONDA` such that you do not need to
-install dependencies [goto ➡️](#get-started).
-```
+## Get started
 
-Before you begin with the installation and use of **PxBLAT**, there are certain prerequisites that need to be met.
-The following sections detail the necessary software, hardware, and knowledge prerequisites that you should have before you start.
-**PxBLAT** has been tested and runs on the following operating systems **Linux** and **MacOS**.
-Choosing appropriate dependencies manager according to the operating systems.
-You should have an active and stable internet connection for downloading and installing the software:
+Installing **PxBLAT** is a breeze, whether you prefer using `CONDA` or `PyPI`.
+Simply follow the tabs below to choose your preferred installation method.
 
 `````{md-tab-set}
 
-````{md-tab-item} Brew
+````{md-tab-item} Pip
+
+To install using `pip`, run the following command in your terminal:
+
 ```{code-block} bash
-brew install htslib openssl
+pip install pxblat
 ```
+
+This will fetch the latest version of **PxBLAT** and install it on your system.
 ````
 
 ````{md-tab-item} Conda
+
+To install using `conda`, execute the following command:
+
 ```{code-block} bash
-conda install htslib openssl
-```
-````
-````{md-tab-item} Apt-get
-```{code-block} bash
-apt-get update && apt-get install libhts-dev libssl-dev
+conda install pxblat
 ```
+This command will install **PxBLAT** from the [conda] repository.
 ````
 
 `````
 
-## **Get Started**
+## Compatibility and Support
 
-Installing **PxBLAT** via `CONDA` **do not requires** the prerequisites.
-Installing **PxBLAT** via `PyPI` requires the prerequisites.
-Once you have confirmed the prerequisites, you can proceed with the software installation:
+Below is a compatibility matrix that shows the support status of **PxBLAT** across different platforms and Python versions.
 
-`````{md-tab-set}
+### [Conda Support][conda]
 
-````{md-tab-item} Conda
-```{code-block} bash
-conda install pxblat
-```
-````
-
-````{md-tab-item} Pip
-```{code-block} bash
-pip install pxblat
-```
-````
-
-`````
+| Python Version | Linux x86_64 | macOS Intel |
+| :------------: | :----------: | :---------: |
+|      3.9       |      ✅      |     ✅      |
+|      3.10      |      ✅      |     ✅      |
+|      3.11      |      ✅      |     ✅      |
+|      3.12      |      ⚫      |     ⚫      |
 
-``````{warning}
-You meet the issue _*.h cannot found_ or _undefined symbol **_ If you install `pxblat` by `pip`.
-If you have installed the prerequisites, the problem is caused by incorrect environment variable {envvar}`CFLAGS`, `CXXFLAGS`,
-and `LDFLAGS`, which direct compiler and linker find right location of
-dependencies so as to compile and link code properly.
-**The easy solution** is to install  **PxBLAT**  via `conda`.
-You can also set proper environment variable if `conda` is not accessible.
+### [PyPI Support][pypi]
 
+| Python Version | Linux x86_64 | macOS Intel | macOS Apple Silicon |
+| :------------: | :----------: | :---------: | :-----------------: |
+|      3.9       |      ✅      |     ✅      |         ✅          |
+|      3.10      |      ✅      |     ✅      |         ✅          |
+|      3.11      |      ✅      |     ✅      |         ✅          |
+|      3.12      |      ⚫      |     ⚫      |         ⚫          |
 
-`````{md-tab-set}
+## Frequently Asked Questions (FAQ)
 
-````{md-tab-item} Bash/Zsh
-```{code-block} bash
-export CFLAGS="-Idependencies"
-export CXXFLAGS="-Idependencies"
-...
-```
-````
+- **Q1**: I'm unable to install `PxBLAT` via `Conda` on my macOS device with an Arm-based processor (M1 or M2). What should I do?
 
-````{md-tab-item} Fish
-```{code-block} fish
-set -x CFLAGS="-Idependencies"
-set -x CXXLAGS="-Idependencies"
-...
-```
-````
-`````
+  > **A**: Currently, `Conda` provides **PxBLAT** built for x86 architectures. For Arm-based macOS devices, we recommend installing **PxBLAT** via `PyPI` instead:
 
-``````
+  ```bash
+  pip install pxblat
+  ```
 
-## **FAQ (Frequently Asked Questions)**
+You've successfully installed **PxBLAT**! Feel free to dive into a real usage case ({doc}`tutorial`) to start exploring its functionalities.
 
-1. I cannot download `PxBLAT` via `Conda` in MacOS with Arm (M1 or M2).
+<!-- links -->
 
-A: So far, conda build `PxBLAT` in x86 instead of arrch64.
-Hence we can install [prerequisites](#prerequisites) manually via `brew` or `Conda`.
-Then, we can use `pip install pxblat` to install `PxBLAT`.
+[conda]: https://anaconda.org/bioconda/pxblat
+[pypi]: https://pypi.org/project/pxblat/