Merge pull request #10 from BIONF/dev

Dev

README.md

@@ -3,7 +3,8 @@
 [![linting: pylint](https://img.shields.io/badge/linting-pylint-yellowgreen)](https://github.com/pylint-dev/pylint)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-<img src="/src/docs/img/logo.png" height="50%" width="50%">
+<img src="/docs/img/logo.png" height="50%" width="50%">
+
 <!-- start intro -->
 XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or sub-type level using [Bloom Filters] and a [Support Vector Machine]. It also identifies existing [blaOxa-genes] and provides a list of relevant research papers for further information.
 <br/><br/>
@@ -27,7 +28,7 @@ To install Xspect, please download the lastest 64 bit Python version and install
 ```
 pip install xspect
 ```
-Please note that Apple Silicon is currently not supported.
+Please note that Windows and Alpine Linux is currently not supported.
 
 ## Usage
 ### Get the Bloomfilters

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "XspecT"
-version = "0.2.3"
+version = "0.2.4"
 description = "Tool to monitor and characterize pathogens using Bloom filters."
 readme = {file = "README.md", content-type = "text/markdown"}
 license = {file = "LICENSE"}

src/xspect/main.py

@@ -2,6 +2,7 @@
 
 from pathlib import Path
 import datetime
+import uuid
 import click
 import uvicorn
 from xspect import fastapi
@@ -77,7 +78,7 @@ def classify(genus, path, meta, step):
     for idx, file_path in enumerate(file_paths):
         run = pipeline.run(file_path)
         time_str = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
-        save_path = get_xspect_runs_path() / f"run_{time_str}.json"
+        save_path = get_xspect_runs_path() / f"run_{time_str}_{uuid.uuid4()}.json"
         run.save(save_path)
         print(
             f"[{idx+1}/{len(file_paths)}] Run finished. Results saved to '{save_path}'."