Added branch repo targeting, improved evidence report and started addresssing dynamic suggestions #65

Author: Anas-Elhounsri

.gitignore

@@ -129,4 +129,12 @@ coverage/
 
 # Data files (adjust depending on project)
 data/
-datasets/
+datasets/
+
+# uv
+uv.lock
+.python-version
+
+# Testing directory
+
+results/

README.md

@@ -1,7 +1,6 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18956787.svg)](https://doi.org/10.5281/zenodo.18956787)
 ![PyPI - Version](https://img.shields.io/pypi/v/rsmetacheck)
 
-
 # Research Software MetaCheck (a Pitfall/Warning Detection Tool)
 
 This project provides an automated tool for detecting common metadata quality issues (pitfalls & Warnings)
@@ -28,7 +27,7 @@ The tool detects the following categories of issues:
 
 ## Requirements
 
-- **Python 3.10**
+- **Python 3.11**
 - Required Python packages:
   - `requests` (for URL validation)
   - `pathlib` (built-in)
@@ -78,6 +77,14 @@ pip install git+https://github.com/SoftwareUnderstanding/RsMetaCheck.git
 poetry run rsmetacheck --input https://github.com/tidyverse/tidyverse
 ```
 
+#### Analyze a Specific Branch
+
+You can analyze a specific branch of a repository by using the `--branch` or `-b` flag:
+
+```bash
+poetry run rsmetacheck --input https://github.com/tidyverse/tidyverse --branch develop
+```
+
 #### Analyze Multiple Repositories from a JSON File
 
 ```bash

src/rsmetacheck/cli.py

@@ -39,6 +39,10 @@ def cli():
         default=0.8,
         help="SoMEF confidence threshold (default: 0.8). Only used when running SoMEF."
     )
+    parser.add_argument(
+        "-b", "--branch",
+        help="Branch of the repository to analyze. Overrides the default branch. Only used when running SoMEF."
+    )
 
     parser.add_argument(
         "--verbose",
@@ -76,10 +80,10 @@ def cli():
         for input_item in args.input:
             if input_item.startswith("http://") or input_item.startswith("https://"):
                 print(f"Processing repository URL: {input_item}")
-                run_somef_single(input_item, somef_output_dir, threshold)
+                run_somef_single(input_item, somef_output_dir, threshold, branch=args.branch)
             elif os.path.exists(input_item):
                 print(f"Processing repositories from file: {input_item}")
-                run_somef_batch(input_item, somef_output_dir, threshold)
+                run_somef_batch(input_item, somef_output_dir, threshold, branch=args.branch)
             else:
                 print(f"Warning: Skipping invalid input (not a URL or existing file): {input_item}")
 

src/rsmetacheck/run_somef.py

@@ -18,29 +18,29 @@ def ensure_somef_configured():
             return False
     return True
 
-def run_somef(repo_url, output_file, threshold):
+def run_somef(repo_url, output_file, threshold, branch=None):
     """Run SoMEF on a given repository and save results."""
+    cmd = ["somef", "describe", "-r", repo_url, "-o", output_file, "-t", str(threshold)]
+    if branch:
+        cmd.extend(["-b", branch])
     try:
-        subprocess.run(
-            ["somef", "describe", "-r", repo_url, "-o", output_file, "-t", str(threshold)],
-            check=True
-        )
+        subprocess.run(cmd, check=True)
         print(f"SoMEF finished for: {repo_url}")
         return True
     except subprocess.CalledProcessError as e:
         print(f"Error running SoMEF for {repo_url}: {e}")
         return False
 
-def run_somef_single(repo_url, output_dir="somef_outputs", threshold=0.8):
+def run_somef_single(repo_url, output_dir="somef_outputs", threshold=0.8, branch=None):
     """Run SoMEF for a single repository."""
     os.makedirs(output_dir, exist_ok=True)
     output_file = os.path.join(output_dir, "output_1.json")
 
     print(f"Running SoMEF for {repo_url}...")
-    success = run_somef(repo_url, output_file, threshold)
+    success = run_somef(repo_url, output_file, threshold, branch)
     return output_dir if success else None
 
-def run_somef_batch(json_file, output_dir="somef_outputs", threshold=0.8):
+def run_somef_batch(json_file, output_dir="somef_outputs", threshold=0.8, branch=None):
     """Run SoMEF for all repositories listed in a JSON file."""
     os.makedirs(output_dir, exist_ok=True)
 
@@ -58,7 +58,7 @@ def run_somef_batch(json_file, output_dir="somef_outputs", threshold=0.8):
     for idx, repo_url in enumerate(repos, start=1):
         output_file = os.path.join(output_dir, f"{base_name}_output_{idx}.json")
         print(f"[{idx}/{len(repos)}] {repo_url}")
-        run_somef(repo_url, output_file, threshold)
+        run_somef(repo_url, output_file, threshold, branch)
 
     print(f"Completed SoMEF for {base_name}. Results in {output_dir}")
     return True