Revert "Add root config file support for analysis tuning and improve SoMEF failure handling"

Author: Anas-Elhounsri

README.md

@@ -170,54 +170,6 @@ By default, the JSON-LD files generated by RsMetaCheck will only contain informa
 poetry run rsmetacheck --input https://github.com/tidyverse/tidyverse --verbose
 ```
 
-#### Configure Analysis with a Root Config File
-
-You can configure RsMetaCheck with a TOML file at the repository root named `.rsmetacheck.toml` (auto-detected), or pass a custom path with `--config`.
-
-Supported options:
-
-- `ignore`: warnings/pitfalls to ignore (e.g. `P001`, `W002`)
-- `exclude_files`: metadata sources to ignore (glob, filename, or substring match)
-- `parameters`: per-check parameters for configurable checks
-- `profiles`: alternate configurations such as `unstable` or `prerelease`
-
-Example:
-
-```toml
-ignore = ["W002"]
-exclude_files = ["**/generated/**", "tmp_metadata.json"]
-
-[parameters.P001]
-ahead_significant_diff = 2
-
-[parameters.W002]
-stale_after_days = 3
-
-[profiles.unstable]
-ignore = ["W002", "P017"]
-
-[profiles.unstable.parameters.P001]
-ahead_significant_diff = 10
-
-[profiles.prerelease]
-ignore = []
-
-[profiles.prerelease.parameters.P001]
-ahead_significant_diff = 1
-```
-
-Use a specific profile:
-
-```bash
-poetry run rsmetacheck --input https://github.com/example/repo --config-profile unstable
-```
-
-Use a custom config path:
-
-```bash
-poetry run rsmetacheck --input https://github.com/example/repo --config ./ci/rsmetacheck.toml
-```
-
 ### Output
 
 The tool will:

docs/usage.md

@@ -35,36 +35,6 @@ Run the analysis:
 poetry run rsmetacheck --input repositories.json
 ```
 
-### Configure Analysis Rules
-
-RsMetaCheck can load a root-level `.rsmetacheck.toml` file to customize analysis behavior.
-
-```toml
-ignore = ["W002"]
-exclude_files = ["tmp_metadata.json"]
-
-[parameters.P001]
-ahead_significant_diff = 10
-
-[profiles.prerelease]
-ignore = []
-
-[profiles.unstable]
-ignore = ["W002", "P017"]
-```
-
-Use a profile:
-
-```bash
-poetry run rsmetacheck --input https://github.com/example/repo --config-profile unstable
-```
-
-Use an explicit config path:
-
-```bash
-poetry run rsmetacheck --input https://github.com/example/repo --config ./ci/rsmetacheck.toml
-```
-
 ## GitHub Action
 
 You can integrate RSMetaCheck into your GitHub workflows:

src/rsmetacheck/cli.py

@@ -2,7 +2,6 @@
 import os
 from pathlib import Path
 
-from rsmetacheck.config import load_analysis_config
 from rsmetacheck.run_analyzer import run_analysis
 from rsmetacheck.run_somef import (
     ensure_somef_configured,
@@ -70,28 +69,9 @@ def cli():
         action="store_true",
         help="Include both detected AND undetected pitfalls in the output JSON-LD.",
     )
-    parser.add_argument(
-        "--config",
-        default=None,
-        help="Path to RsMetaCheck TOML config file (default: auto-detect .rsmetacheck.toml at repository root).",
-    )
-    parser.add_argument(
-        "--config-profile",
-        default=None,
-        help="Name of config profile to apply (e.g., unstable, prerelease).",
-    )
 
     args = parser.parse_args()
 
-    try:
-        analysis_config = load_analysis_config(
-            config_path=args.config,
-            profile=args.config_profile,
-        )
-    except (FileNotFoundError, ValueError, OSError, Exception) as exc:
-        print(f"Error loading config: {exc}")
-        return
-
     if args.skip_somef:
         print(
             f"Skipping SoMEF execution. Analyzing {len(args.input)} existing SoMEF output files..."
@@ -115,7 +95,6 @@ def cli():
             args.analysis_output,
             verbose=args.verbose,
             notes_output=args.notes_output,
-            analysis_config=analysis_config,
         )
 
     else:
@@ -131,51 +110,37 @@ def cli():
                 "Codemeta generation is ENABLED. Codemeta files will be created for each repository."
             )
 
-        any_somef_success = False
-
         for input_item in args.input:
             if input_item.startswith("http://") or input_item.startswith("https://"):
                 print(f"Processing repository URL: {input_item}")
-                success = run_somef_single(
+                run_somef_single(
                     input_item,
                     somef_output_dir,
                     threshold,
                     branch=args.branch,
                     generate_codemeta=generate_codemeta,
                 )
-                any_somef_success = any_somef_success or bool(success)
             elif os.path.exists(input_item):
                 print(f"Processing repositories from file: {input_item}")
-                success = run_somef_batch(
+                run_somef_batch(
                     input_item,
                     somef_output_dir,
                     threshold,
                     branch=args.branch,
                     generate_codemeta=generate_codemeta,
                 )
-                any_somef_success = any_somef_success or bool(success)
             else:
                 print(
                     f"Warning: Skipping invalid input (not a URL or existing file): {input_item}"
                 )
 
-        if not any_somef_success:
-            print(
-                "Error: SoMEF did not produce any outputs. Analysis is aborted."
-            )
-            print(
-                "Fix SoMEF/authentication issues and rerun, or run with --skip-somef on existing SoMEF JSON files."
-            )
-            return
-
         print(f"\nRunning analysis on outputs in {somef_output_dir}...")
         run_analysis(
             somef_output_dir,
             args.pitfalls_output,
             args.analysis_output,
             verbose=args.verbose,
             notes_output=args.notes_output,
-            analysis_config=analysis_config,
         )
 
 

src/rsmetacheck/detect_pitfalls_main.py

@@ -1,11 +1,7 @@
 import json
-import copy
-import fnmatch
-import inspect
 from pathlib import Path
 from typing import Iterable, Union
 from rsmetacheck.run_somef import CODEMETA_DEFAULT_NAME
-from rsmetacheck.config import AnalysisConfig
 from rsmetacheck.utils.pitfall_utils import extract_programming_languages
 from rsmetacheck.utils.json_ld_utils import create_pitfall_jsonld, save_individual_pitfall_jsonld
 from rsmetacheck.utils.somef_compat import normalize_somef_data
@@ -44,89 +40,7 @@
 from rsmetacheck.scripts.warnings.w010 import detect_git_remote_shorthand_pitfall
 
 
-def _source_matches_exclude_patterns(source_value: str, exclude_patterns: list[str]) -> bool:
-    source = str(source_value)
-    basename = Path(source).name
-
-    for pattern in exclude_patterns:
-        if fnmatch.fnmatch(source, pattern):
-            return True
-        if fnmatch.fnmatch(basename, pattern):
-            return True
-        if pattern in source:
-            return True
-
-    return False
-
-
-def _filter_somef_data_by_excluded_files(data, exclude_patterns: list[str]):
-    if isinstance(data, dict):
-        filtered_dict = {}
-
-        for key, value in data.items():
-            if key == "source":
-                if isinstance(value, list):
-                    kept_sources = [
-                        src for src in value if not _source_matches_exclude_patterns(src, exclude_patterns)
-                    ]
-                    if not kept_sources:
-                        return None
-                    filtered_dict[key] = kept_sources
-                else:
-                    if _source_matches_exclude_patterns(value, exclude_patterns):
-                        return None
-                    filtered_dict[key] = value
-                continue
-
-            filtered_value = _filter_somef_data_by_excluded_files(value, exclude_patterns)
-            if filtered_value is not None:
-                filtered_dict[key] = filtered_value
-
-        return filtered_dict
-
-    if isinstance(data, list):
-        filtered_list = []
-        for item in data:
-            filtered_item = _filter_somef_data_by_excluded_files(item, exclude_patterns)
-            if filtered_item is not None:
-                filtered_list.append(filtered_item)
-        return filtered_list
-
-    return data
-
-
-def _run_detector_with_parameters(detector_func, somef_data, file_name: str, parameters: dict):
-    if not parameters:
-        return detector_func(somef_data, file_name)
-
-    signature = inspect.signature(detector_func)
-    accepts_kwargs = any(
-        param.kind == inspect.Parameter.VAR_KEYWORD
-        for param in signature.parameters.values()
-    )
-
-    if accepts_kwargs:
-        return detector_func(somef_data, file_name, **parameters)
-
-    accepted_parameter_names = set(signature.parameters.keys()) - {"somef_data", "file_name"}
-    filtered_parameters = {
-        key: value for key, value in parameters.items() if key in accepted_parameter_names
-    }
-
-    if filtered_parameters:
-        return detector_func(somef_data, file_name, **filtered_parameters)
-
-    return detector_func(somef_data, file_name)
-
-
-def detect_all_pitfalls(
-    json_files: Iterable[Path],
-    pitfalls_output_dir: Union[str, Path],
-    output_file: Union[str, Path],
-    verbose: bool = False,
-    notes_output: Union[str, Path] = None,
-    analysis_config: AnalysisConfig = None,
-):
+def detect_all_pitfalls(json_files: Iterable[Path], pitfalls_output_dir: Union[str, Path], output_file: Union[str, Path], verbose: bool = False, notes_output: Union[str, Path] = None):
     """
     Detect all software repository pitfalls in SoMEF output files using modular detectors.
     Now also generates individual JSON-LD files for each repository.
@@ -135,21 +49,12 @@ def detect_all_pitfalls(
     pitfalls_output_dir = Path(pitfalls_output_dir)
     pitfalls_output_dir.mkdir(exist_ok=True, parents=True)
     json_files = list(json_files)
-    config = analysis_config or AnalysisConfig.empty()
 
     if not json_files:
         print("No JSON files found for analysis.")
         return
 
     print(f"Analyzing {len(json_files)} SoMEF JSON files...")
-    if config.source_path:
-        print(f"Using config file: {config.source_path}")
-    if config.profile:
-        print(f"Using config profile: {config.profile}")
-    if config.ignored_checks:
-        print(f"Ignoring checks: {', '.join(sorted(config.ignored_checks))}")
-    if config.exclude_files:
-        print(f"Excluded source patterns: {config.exclude_files}")
 
     results = {
         "summary": {
@@ -416,13 +321,6 @@ def detect_all_pitfalls(
                 somef_data = json.load(f)
 
             somef_data = normalize_somef_data(somef_data)
-            if config.exclude_files:
-                somef_data = _filter_somef_data_by_excluded_files(
-                    copy.deepcopy(somef_data),
-                    config.exclude_files,
-                )
-                if somef_data is None:
-                    somef_data = {}
 
             languages = extract_programming_languages(somef_data)
 
@@ -432,16 +330,8 @@ def detect_all_pitfalls(
             repo_pitfall_results = []
 
             for idx, (detector_func, pitfall_code) in enumerate(pitfall_detectors):
-                if config.is_ignored(pitfall_code):
-                    continue
-
                 try:
-                    detector_results = _run_detector_with_parameters(
-                        detector_func,
-                        somef_data,
-                        json_file.name,
-                        config.get_parameters(pitfall_code),
-                    )
+                    detector_results = detector_func(somef_data, json_file.name)
                     if not isinstance(detector_results, list):
                         detector_results = [detector_results]
 
@@ -610,15 +500,7 @@ def detect_all_pitfalls(
         print(f"Error writing output file: {e}")
 
 
-def main(
-    input_dir=None,
-    somef_json_paths=None,
-    pitfalls_dir=None,
-    analysis_output=None,
-    verbose=False,
-    notes_output=None,
-    analysis_config: AnalysisConfig = None,
-):
+def main(input_dir=None, somef_json_paths=None, pitfalls_dir=None, analysis_output=None, verbose=False, notes_output=None):
     """
     Main function to run all pitfall detections.
 
@@ -659,14 +541,7 @@ def main(
         print("No JSON files found for analysis.")
         return
 
-    detect_all_pitfalls(
-        json_files,
-        pitfalls_directory,
-        output_file,
-        verbose,
-        notes_output,
-        analysis_config=analysis_config,
-    )
+    detect_all_pitfalls(json_files, pitfalls_directory, output_file, verbose, notes_output)
 
 if __name__ == "__main__":
     main()