style: Update pre-commit configs and CLI help message

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
       - id: cargo-check
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.6.9"
+    rev: "v0.7.0"
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
@@ -62,7 +62,7 @@ repos:
 
   # md formatting
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.18
     hooks:
       - id: mdformat
         args: ["--number"]

README.md

@@ -86,7 +86,7 @@ Below are the compatibility matrices for PyPI installations:
 |      3.11      |      ✅      |     ✅      |         ✅          | ✅             |
 |      3.12      |      ✅      |     ✅      |         ✅          | ✅             |
 
-🆘 Trouble installing? Check our [Troubleshooting Guide](./docs/troubleshooting.md) or [open an issue](https://github.com/ylab-hi/DeepChopper/issues).
+🆘 Trouble installing? Check our [Troubleshooting Guide](https://github.com/ylab-hi/DeepChopper/blob/main/documentation/tutorial.md#troubleshooting) or [open an issue](https://github.com/ylab-hi/DeepChopper/issues).
 
 ## 🛠️ Usage
 
@@ -103,7 +103,7 @@ DeepChopper offers three main commands: `encode`, `predict`, and `chop`.
    deepchopper encode <input.fq>
    ```
 
-2. **Predict** chimeric reads:
+2. **Predict** chimera artifacts:
 
    ```bash
    deepchopper predict <input.parquet> --output predictions
@@ -115,7 +115,7 @@ DeepChopper offers three main commands: `encode`, `predict`, and `chop`.
    deepchopper predict <input.parquet> --output predictions --gpus 2
    ```
 
-3. **Chop** the chimeric reads:
+3. **Chop** chimera artifacts:
 
    ```bash
    deepchopper chop <predictions> raw.fq

deepchopper/cli.py

@@ -223,7 +223,7 @@ def version_callback(value: bool):
 app = typer.Typer(
     cls=OrderCommands,
     context_settings={"help_option_names": ["-h", "--help"]},
-    help="DeepChopper: A genomic lanuage model to identify artificial sequenes.",
+    help="DeepChopper: A genomic lanuage model to identify artificial sequences.",
 )