Write report by default; fix report path (double .ms2rescore)

.gitignore

@@ -1,5 +1,7 @@
 # Others
-data/*
+nbs/
+.prettierrc
+data/
 steps.txt
 old_files/
 prepare_pin_files.py

examples/xtandem-ms2rescore.json

@@ -0,0 +1,16 @@
+{
+    "ms2rescore": {
+        "psm_file": "examples/data/search/xtandem/pyro.t.xml",
+        "psm_file_type": "xtandem",
+        "spectrum_path": "examples/data/spectra/Velos005137.mgf",
+        "psm_id_pattern": "(\\S+).*",
+        "modification_mapping": {
+            "+57.022": "U:Carbamidomethyl",
+            "+15.994": "U:Oxidation",
+            "+39.9954": "U:Pyro-carbamidomethyl",
+            "+42.0106": "U:Acetyl",
+            "-17.0266": "U:Gln->pyro-Glu",
+            "-18.0106": "U:Glu->pyro-Glu"
+        }
+    }
+}

ms2rescore/package_data/config_default.json

@@ -35,6 +35,6 @@
         "processes": -1,
         "rename_to_usi": false,
         "fasta_file": null,
-        "write_report": false
+        "write_report": true
     }
 }

ms2rescore/report/generate.py

@@ -221,8 +221,6 @@ def _get_overview_context(confidence_before, confidence_after) -> dict:
 
 
 def _get_target_decoy_context(psm_list) -> dict:
-    # fasta_file = "../../examples/fasta/uniprot-proteome-human-contaminants.fasta"
-    # confidence_estimates = _get_confidence_estimates(psm_list, fasta_file)
     logger.debug("Generating target-decoy charts...")
     psm_df = psm_list.to_dataframe()
     return {
@@ -363,7 +361,7 @@ def _get_log_context(files: Dict[str, Path]) -> dict:
 
 def _render_and_write(output_path_prefix: str, **context):
     """Render template with context and write to HTML file."""
-    report_path = Path(output_path_prefix + ".ms2rescore.report.html").resolve()
+    report_path = Path(output_path_prefix + ".report.html").resolve()
     logger.info("Writing report to %s", report_path.as_posix())
     template_dir = Path(__file__).parent / "templates"
     env = Environment(loader=FileSystemLoader(template_dir, encoding="utf-8"))