Update

CHANGELOG.md

@@ -8,9 +8,9 @@
 * Added a Docker container
 * Changed tests to pytest
 * Updated versions of dependencies
-* Perform code optimizations and clean ups
+* Performed code optimizations and clean ups
 * Added more tests for almost full coveragge
-* Bump taggd to 0.4.0
+* Bumped taggd to 0.4.0
 * Changed documentation
 * Added --demultiplex-chunk-size option
 

CONTRIBUTING.md

@@ -54,7 +54,8 @@ git clone git@github.com:jfnavarro/st_pipeline.git
 ```
 
 3. Ensure [poetry](https://python-poetry.org/docs/) is installed.
-4. Install dependencies and start your virtualenv:
+4. Ensure [STAR](https://github.com/alexdobin/STAR) is installed.
+5. Install dependencies and start your virtualenv:
 
 ``` console
 poetry install -E test -E doc -E dev
@@ -67,30 +68,30 @@ changing the default behaviour in poetry with this command:
 poetry config virtualenvs.create false
 ```
 
-5. Create a branch for local development:
+6. Create a branch for local development:
 
 ``` console
 git checkout -b name-of-your-bugfix-or-feature
 ```
 
 Now you can make your changes locally.
 
-6. When you're done making changes, check that your changes pass the
+7. When you're done making changes, check that your changes pass the
    tests, including testing other Python versions, with pytest:
 
 ``` console
 poetry run pytest
 ```
 
-7. Commit your changes and push your branch to GitHub:
+8. Commit your changes and push your branch to GitHub:
 
 ``` console
 git add .
 git commit -m "Your detailed description of your changes."
 git push origin name-of-your-bugfix-or-feature
 ```
 
-8. Submit a pull request through the GitHub website.
+9. Submit a pull request through the GitHub website.
 
 ## Pull Request Guidelines
 
@@ -116,35 +117,35 @@ Replace test_your_module.py with the actual name of your test file.
 
 ## Makefile
 
-A `makefile`is included in the repo with the following actions:
+A `makefile` is included in the repo with the following actions:
 
 To run formatting tools
 
-```bash
+``` console
 make format
 ```
 
 To run linting tools
 
-```bash
+``` console
 make lint
 ```
 
 To run the tests
 
-```bash
+``` console
 make unittet
 ```
 
 To run the tests with coverage
 
-```bash
+``` console
 make coverage
 ```
 
 To clean the temporary files and cache
 
-```bash
+``` console
 make clean
 ```
 

README.md

@@ -46,7 +46,7 @@ The ST pipeline will also output a log file with useful stats and information.
 
 For users see [install](docs/installation.md)
 
-For developers [contributing](docs/contributing.md)
+For developers [contributing](CONTRIBUTING.md)
 
 ## Usage
 

stpipeline/common/stats.py

@@ -43,7 +43,7 @@ def __str__(self) -> str:
         Returns a string representation of the Stats object.
 
         Returns:
-            str: A formatted string of all stats attributes.
+            A formatted string of all stats attributes.
         """
         return "\n".join(f"{field_name}: {getattr(self, field_name)}" for field_name in self.__dataclass_fields__)
 
@@ -52,7 +52,7 @@ def write_json(self, filename: str) -> None:
         Writes the stats to a JSON file.
 
         Args:
-            filename (str): The path to the JSON file to write.
+            filename: The path to the JSON file to write.
         """
         with open(filename, "w") as file:
             json.dump(asdict(self), file, indent=2, separators=(",", ": "))
@@ -63,10 +63,10 @@ def from_json(cls, filename: str) -> "Stats":
         Creates a Stats object from a JSON file.
 
         Args:
-            filename (str): The path to the JSON file to read.
+            filename: The path to the JSON file to read.
 
         Returns:
-            Stats: A Stats object populated with data from the JSON file.
+            A Stats object populated with data from the JSON file.
         """
         with open(filename, "r") as file:
             data = json.load(file)

stpipeline/scripts/st_pipeline_run.py

@@ -12,7 +12,7 @@
 an a dataset name.
 
 The ST Pipeline has many parameters and options, you can see a description of them
-by typing : st_pipeline_run.py --help
+by typing : st_pipeline_run --help
 
 @Author Jose Fernandez Navarro <jc.fernandez.navarro@gmail.com>
 """