docs: Add bumpversion configuration file

.bumpversion.toml

@@ -0,0 +1,32 @@
+# bump-my-version bump minor --allow-dirty        
+
+[tool.bumpversion]
+current_version = "1.1.0"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = false
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = false
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+
+[[tool.bumpversion.files]]
+filename = "Cargo.toml"
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+
+[[tool.bumpversion.files]]
+filename = "./py_cli/pyproject.toml"

.github/workflows/release-python-cli.yml

@@ -13,11 +13,11 @@ on:
     tags:
       - "*"
   pull_request:
+    branches:
+      - main
+      - master
   workflow_dispatch:
 
-env:
-  PythonVersion: "3.10"
-
 # Add this concurrency configuration
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -34,23 +34,24 @@ jobs:
         platform:
           - runner: ubuntu-latest
             target: x86_64
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PythonVersion }}
+          python-version: ${{ matrix.python-version }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release -b bin --out dist  -i "python3.10"
+          args: --release -b bin --out dist  -i python${{ matrix.python-version }}
           sccache: "true"
           manylinux: auto
           working-directory: ./py_cli
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels-linux-${{ matrix.platform.target }}
+          name: wheels-linux-${{ matrix.platform.target }}-py${{ matrix.python-version }}
           path: ./py_cli/dist
       - name: pytest
         if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
@@ -84,7 +85,6 @@ jobs:
         run: |
           echo "Build failed. Debugging information:"
           ls -R
-          cat Cargo.toml
           cat pyproject.toml
 
   musllinux:
@@ -94,23 +94,24 @@ jobs:
         platform:
           - runner: ubuntu-latest
             target: x86_64
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PythonVersion }}
+          python-version: ${{ matrix.python-version }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release -b bin --out dist  -i "python3.10"
+          args: --release -b bin --out dist  -i python${{ matrix.python-version }}
           sccache: "true"
           manylinux: musllinux_1_2
           working-directory: ./py_cli
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels-musllinux-${{ matrix.platform.target }}
+          name: wheels-musllinux-${{ matrix.platform.target }}-py${{ matrix.python-version }}
           path: ./py_cli/dist
 
   windows:
@@ -122,23 +123,24 @@ jobs:
             target: x64
           - runner: windows-latest
             target: x86
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PythonVersion }}
+          python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.platform.target }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release -b bin --out dist
+          args: --release -b bin --out dist -i python${{ matrix.python-version }}
           sccache: "true"
           working-directory: ./py_cli
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels-windows-${{ matrix.platform.target }}
+          name: wheels-windows-${{ matrix.platform.target }}-py${{ matrix.python-version }}
           path: ./py_cli/dist
       - name: pytest
         if: ${{ !startsWith(matrix.platform.target, 'aarch64') }}
@@ -160,22 +162,23 @@ jobs:
             target: x86_64
           - runner: macos-14
             target: aarch64
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PythonVersion }}
+          python-version: ${{ matrix.python-version }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release -b bin --out dist
+          args: --release -b bin --out dist -i python${{ matrix.python-version }}
           sccache: "true"
           working-directory: ./py_cli
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels-macos-${{ matrix.platform.target }}
+          name: wheels-macos-${{ matrix.platform.target }}-py${{ matrix.python-version }}
           path: ./py_cli/dist
       - name: pytest
         run: |

.github/workflows/release-python.yml

@@ -13,6 +13,9 @@ on:
     tags:
       - "*"
   pull_request:
+    branches:
+      - main
+      - master
   workflow_dispatch:
 
 # Add this concurrency configuration
@@ -31,22 +34,23 @@ jobs:
         platform:
           - runner: ubuntu-latest
             target: x86_64
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: ${{ matrix.python-version }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release --out dist
+          args: --release --out dist -i python${{ matrix.python-version }}
           sccache: "true"
           manylinux: auto
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels-linux-${{ matrix.platform.target }}
+          name: wheels-linux-${{ matrix.platform.target }}-py${{ matrix.python-version }}
           path: dist
       - name: pytest
         if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
@@ -80,22 +84,23 @@ jobs:
         platform:
           - runner: windows-latest
             target: x64
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.platform.target }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release --out dist
+          args: --release --out dist -i python${{ matrix.python-version }}
           sccache: "true"
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels-windows-${{ matrix.platform.target }}
+          name: wheels-windows-${{ matrix.platform.target }}-py${{ matrix.python-version }}
           path: dist
       - name: pytest
         if: ${{ !startsWith(matrix.platform.target, 'aarch64') }}
@@ -106,7 +111,6 @@ jobs:
           source .venv/Scripts/activate
           pip install deepchopper --find-links dist --force-reinstall
           pip install pytest
-          # python -c "import deepchopper"
           deepchopper -h
 
   macos:
@@ -118,21 +122,22 @@ jobs:
             target: x86_64
           - runner: macos-14
             target: aarch64
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: ${{ matrix.python-version }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release --out dist
+          args: --release --out dist  -i python${{ matrix.python-version }}
           sccache: "true"
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels-macos-${{ matrix.platform.target }}
+          name: wheels-macos-${{ matrix.platform.target }}-py${{ matrix.python-version }}
           path: dist
       - name: pytest
         run: |
@@ -141,7 +146,6 @@ jobs:
           source .venv/bin/activate
           pip install deepchopper --find-links dist --force-reinstall
           pip install pytest
-          # python -c "import deepchopper"
           deepchopper -h
   sdist:
     runs-on: ubuntu-latest

.gitignore

@@ -592,3 +592,5 @@ scripts/*.json
 *overlap_results*.json
 *stats_*.json
 !build.rs
+.ruff_cache
+hg_deepchopper

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "deepchopper"
-version = "1.0.1"
+version = "1.1.0"
 edition = "2021"
 authors = ["Yangyang Li <yangyang.li@northwestern.edu>"]
 description = "A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing"

README.md

@@ -1,8 +1,16 @@
 # <img src="./documentation/logo.webp" alt="logo" height="100"/> **DeepChopper** [![social](https://img.shields.io/github/stars/ylab-hi/DeepChopper?style=social)](https://github.com/ylab-hi/DeepChopper/stargazers)
 
+[![pypi](https://img.shields.io/pypi/v/deepchopper.svg)](https://pypi.python.org/pypi/deepchopper)
+[![license](https://img.shields.io/pypi/l/deepchopper.svg)](https://github.com/ylab-hi/DeepChopper/blob/main/LICENSE)
+[![pypi version](https://img.shields.io/pypi/pyversions/deepchopper.svg)](https://pypi.python.org/pypi/deepbiop)
+[![Actions status](https://github.com/ylab-hi/DeepChopper/actions/workflows/release-python.yml/badge.svg)](https://github.com/ylab-hi/DeepChopper/actions)
+[![platform](https://img.shields.io/badge/platform-linux%20%7C%20osx%20%7C%20win-blue)](https://pypi.org/project/deepchopper/#files)
+[![Space](https://huggingface.co/datasets/huggingface/badges/resolve/main/open-in-hf-spaces-md.svg)](https://huggingface.co/spaces/yangliz5/deepchopper)
+
 <!--toc:start-->
 
 - [ **DeepChopper** ](#-deepchopper-)
+  - [Quick Start: Try DeepChopper Online](#quick-start-try-deepchopper-online)
   - [Install](#install)
   - [Usage](#usage)
     - [Command-Line Interface](#command-line-interface)
@@ -17,6 +25,25 @@
 DeepChopper leverages language model to accurately detect and chop artificial sequences which may cause chimeric reads, ensuring higher quality and more reliable sequencing results.
 By integrating seamlessly with existing workflows, DeepChopper provides a robust solution for researchers and bioinformatics working with NanoPore direct-RNA sequencing data.
 
+## Quick Start: Try DeepChopper Online
+
+Experience DeepChopper instantly through our user-friendly web interface. No installation required!
+
+Simply click the button below to launch the web application and start exploring DeepChopper's capabilities:
+
+[![Open in Hugging Face Spaces](https://huggingface.co/datasets/huggingface/badges/resolve/main/open-in-hf-spaces-md.svg)](https://huggingface.co/spaces/yangliz5/deepchopper)
+
+This online version provides a convenient way to:
+
+- Upload your sequencing data
+- Run DeepChopper's analysis
+- Visualize results
+- Experiment with different parameters
+
+It's perfect for quick tests or when you want to showcase DeepChopper's functionality without local setup.
+However, for more extensive analyses or custom workflows, we recommend installing DeepChopper on your machine.
+Because the online version is limited to one FASTQ record at a time, it may not be suitable for large-scale projects.
+
 ## Install
 
 DeepChopper can be installed using pip, the Python package installer. Follow these steps to install:
@@ -42,18 +69,6 @@ DeepChopper can be installed using pip, the Python package installer. Follow the
    deepchopper --help
    ```
 
-5. DeepChopper include a Rust command line tool for faster performance.
-
-```bash
-cargo install deepchopper-chop
-```
-
-For GPU support, ensure you have CUDA installed on your system, then install the GPU version:
-
-```bash
-pip install deepchopper[gpu]
-```
-
 Note: If you encounter any issues, please check our GitHub repository for troubleshooting guides or to report a problem.
 
 ## Usage
@@ -107,6 +122,12 @@ model = deepchopper.DeepChopper.from_pretrained("yangliz5/deepchopper")
 
 ## Cite
 
+If you use DeepChopper in your research, please cite the following paper:
+
+```bibtex
+
+```
+
 ## 🤜 Contribution
 
 ### Build Environment