Make running reports optional

Author: adelavega

autonima/cli.py

@@ -356,13 +356,15 @@ def validate(config: str, output_folder: str | None, debug: bool):
               type=click.Path(exists=True, dir_okay=False),
               default=None,
               help='Path to text file with study IDs/PMIDs to include (one per line)')
+@click.option('--run-reports', is_flag=True,
+              help='Generate NiMARE HTML reports (disabled by default to reduce memory use)')
 @click.option('--fail-fast', is_flag=True,
               help='Stop at the first failing annotation column')
 @click.option('--debug', is_flag=True,
               help='Enable debug mode; fail fast and enter post-mortem debugging on errors')
 def meta(output_folder: str, estimator: str, estimator_args: str,
          corrector: str, corrector_args: str, include_ids: str,
-         fail_fast: bool, debug: bool):
+         run_reports: bool, fail_fast: bool, debug: bool):
     """
     Run meta-analyses on Autonima output using NiMARE.
 
@@ -378,6 +380,7 @@ def meta(output_folder: str, estimator: str, estimator_args: str,
         --corrector              Corrector to use (fdr, montecarlo, bonferroni)
         --corrector-args         JSON string of arguments for the corrector
         --include-ids            Path to newline-delimited study IDs/PMIDs for post-hoc filtering
+        --run-reports            Generate NiMARE HTML reports (default: off)
         --fail-fast              Stop on the first failing annotation column
         --debug                  Enable fail-fast post-mortem debugging (ipdb/pdb)
 
@@ -424,6 +427,7 @@ def meta(output_folder: str, estimator: str, estimator_args: str,
             include_ids=include_ids,
             fail_fast=(fail_fast or debug),
             debug=debug,
+            generate_reports=run_reports,
         )
 
         print(f"Completed meta-analyses for {len(results)} columns")

autonima/meta.py

@@ -197,6 +197,7 @@ def run_meta_analysis_for_column(
     corrector_name="fdr",
     corrector_args=None,
     include_ids=None,
+    generate_reports=False,
 ):
     """Run meta-analysis for a specific annotation column."""
     del annotation  # kept for backward compatibility with existing call sites
@@ -276,7 +277,8 @@ def run_meta_analysis_for_column(
     )
 
     meta_results = workflow.fit(first_dataset)
-    run_reports(meta_results, str(output_dir))
+    if generate_reports:
+        run_reports(meta_results, str(output_dir))
 
     return meta_results
 
@@ -294,6 +296,7 @@ def run_meta_analyses_from_files(
     columns=None,
     fail_fast=False,
     debug=False,
+    generate_reports=False,
 ):
     """
     Run meta-analyses from explicit studyset + annotation file paths.
@@ -315,6 +318,8 @@ def run_meta_analyses_from_files(
         If True, re-raise on the first column-level exception instead of continuing.
     debug : bool
         If True and fail_fast is enabled, enter post-mortem debugging on error.
+    generate_reports : bool
+        If True, run NiMARE HTML report generation for each completed column.
     """
     include_ids_set = _normalize_include_ids(include_ids)
 
@@ -356,6 +361,7 @@ def run_meta_analyses_from_files(
                 corrector_name,
                 corrector_args,
                 include_ids=include_ids_set,
+                generate_reports=generate_reports,
             )
             if meta_results is not None:
                 results[column] = meta_results
@@ -383,6 +389,7 @@ def run_meta_analyses(
     columns=None,
     fail_fast=False,
     debug=False,
+    generate_reports=False,
 ):
     """Run meta-analyses on all boolean annotation columns in the NiMADS files."""
     output_folder = Path(output_folder) / "outputs"
@@ -404,6 +411,7 @@ def run_meta_analyses(
         columns=columns,
         fail_fast=fail_fast,
         debug=debug,
+        generate_reports=generate_reports,
     )
 
 
@@ -459,6 +467,11 @@ def main():
         action="store_true",
         help="Enable post-mortem debugging (prefers ipdb) when used with --fail-fast",
     )
+    parser.add_argument(
+        "--run-reports",
+        action="store_true",
+        help="Generate NiMARE HTML reports (disabled by default to reduce memory use)",
+    )
 
     args = parser.parse_args()
 
@@ -482,6 +495,7 @@ def main():
         include_ids=args.include_ids,
         fail_fast=args.fail_fast,
         debug=args.debug,
+        generate_reports=args.run_reports,
     )
     print(f"Completed meta-analyses for {len(results)} columns")
 

docs/guides/cli.md

@@ -80,6 +80,7 @@ autonima meta projects/cue_reactivity/default/outputs
 ```
 
 Optional parameters let you change the estimator, corrector, and include-ID filtering.
+Report generation is now opt-in via `--run-reports`.
 For large jobs, use `--fail-fast` (or `--debug`, which implies fail-fast) to stop on the
 first failing column instead of continuing.
 

docs/guides/meta-analysis.md

@@ -39,6 +39,8 @@ autonima meta projects/cue_reactivity/default/outputs
   JSON string of corrector arguments
 - `--include-ids`
   Newline-delimited study IDs or PMIDs to include
+- `--run-reports`
+  Generate NiMARE HTML reports (default: disabled to reduce memory use)
 - `--fail-fast`
   Stop on the first failing annotation column
 - `--debug`
@@ -63,7 +65,8 @@ Meta-analysis results are written under:
 This directory contains:
 
 - one folder per boolean annotation column
-- NiMARE reports and statistical images
+- statistical images and result artifacts
+- NiMARE reports only when `--run-reports` is enabled
 - summary artifacts for each analysis set
 
 ## Common Failure Modes