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

README.md

@@ -170,6 +170,54 @@ 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

@@ -35,6 +35,36 @@ 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

@@ -2,6 +2,7 @@
 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,
@@ -69,9 +70,28 @@ 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..."
@@ -95,6 +115,7 @@ def cli():
             args.analysis_output,
             verbose=args.verbose,
             notes_output=args.notes_output,
+            analysis_config=analysis_config,
         )
 
     else:
@@ -110,37 +131,51 @@ 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}")
-                run_somef_single(
+                success = 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}")
-                run_somef_batch(
+                success = 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

@@ -1,7 +1,11 @@
 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
@@ -40,7 +44,89 @@
 from rsmetacheck.scripts.warnings.w010 import detect_git_remote_shorthand_pitfall
 
 
-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):
+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,
+):
     """
     Detect all software repository pitfalls in SoMEF output files using modular detectors.
     Now also generates individual JSON-LD files for each repository.
@@ -49,12 +135,21 @@ def detect_all_pitfalls(json_files: Iterable[Path], pitfalls_output_dir: Union[s
     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": {
@@ -321,6 +416,13 @@ def detect_all_pitfalls(json_files: Iterable[Path], pitfalls_output_dir: Union[s
                 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)
 
@@ -330,8 +432,16 @@ def detect_all_pitfalls(json_files: Iterable[Path], pitfalls_output_dir: Union[s
             repo_pitfall_results = []
 
             for idx, (detector_func, pitfall_code) in enumerate(pitfall_detectors):
+                if config.is_ignored(pitfall_code):
+                    continue
+
                 try:
-                    detector_results = detector_func(somef_data, json_file.name)
+                    detector_results = _run_detector_with_parameters(
+                        detector_func,
+                        somef_data,
+                        json_file.name,
+                        config.get_parameters(pitfall_code),
+                    )
                     if not isinstance(detector_results, list):
                         detector_results = [detector_results]
 
@@ -500,7 +610,15 @@ def detect_all_pitfalls(json_files: Iterable[Path], pitfalls_output_dir: Union[s
         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):
+def main(
+    input_dir=None,
+    somef_json_paths=None,
+    pitfalls_dir=None,
+    analysis_output=None,
+    verbose=False,
+    notes_output=None,
+    analysis_config: AnalysisConfig = None,
+):
     """
     Main function to run all pitfall detections.
 
@@ -541,7 +659,14 @@ def main(input_dir=None, somef_json_paths=None, pitfalls_dir=None, analysis_outp
         print("No JSON files found for analysis.")
         return
 
-    detect_all_pitfalls(json_files, pitfalls_directory, output_file, verbose, notes_output)
+    detect_all_pitfalls(
+        json_files,
+        pitfalls_directory,
+        output_file,
+        verbose,
+        notes_output,
+        analysis_config=analysis_config,
+    )
 
 if __name__ == "__main__":
     main()