fix: resolve NO_FILE staging collision and module bin shadowing

edmundmiller · edmundmiller · commit 3c38d0bae833 · 2026-04-20T18:09:11.000-05:00
Two CI-breaking issues fixed:

1. NORMALIZE_BENCHMARK_JSONL crashed with 'input file name collision' when
   both optional inputs (CUR report + machines dir) were absent — both
   resolved to the same 'NO_FILE' sentinel. Use distinct sentinels:
   NO_FILE_CUR and NO_FILE_MACHINES.

2. Module-local bin/benchmark_report.py shims were shadowed by the root
   bin/benchmark_report.py (Typer CLI). Nextflow only adds projectDir/bin/
   to PATH, so the argparse shims were never found. Renamed module-local
   shims to stage-specific names (normalize_benchmark_jsonl.py, etc.)
   and moved them to root bin/. Worker modules (benchmark_report_normalize.py
   etc.) are symlinked from root bin/ to module-local bin/.

3. Fixed editorconfig-checker failures: 14 lines in
   benchmark_report_template.html had odd-number leading spaces.
diff --git a/bin/aggregate_benchmark_report_data.py b/bin/aggregate_benchmark_report_data.py
diff --git a/bin/benchmark_report_aggregate.py b/bin/benchmark_report_aggregate.py
@@ -0,0 +1 @@
+../modules/local/aggregate_benchmark_report_data/bin/benchmark_report_aggregate.py
diff --git a/bin/benchmark_report_normalize.py b/bin/benchmark_report_normalize.py
@@ -0,0 +1 @@
+../modules/local/normalize_benchmark_jsonl/bin/benchmark_report_normalize.py
diff --git a/bin/benchmark_report_render.py b/bin/benchmark_report_render.py
@@ -0,0 +1 @@
+../modules/local/render_benchmark_report/bin/benchmark_report_render.py
diff --git a/bin/benchmark_report_template.html b/bin/benchmark_report_template.html
@@ -0,0 +1 @@
+../modules/local/render_benchmark_report/bin/benchmark_report_template.html
diff --git a/bin/normalize_benchmark_jsonl.py b/bin/normalize_benchmark_jsonl.py
diff --git a/bin/render_benchmark_report.py b/bin/render_benchmark_report.py
diff --git a/modules/local/aggregate_benchmark_report_data/main.nf b/modules/local/aggregate_benchmark_report_data/main.nf
@@ -12,7 +12,7 @@ process AGGREGATE_BENCHMARK_REPORT_DATA {
 
     script:
     """
-    benchmark_report.py \\
+    aggregate_benchmark_report_data.py \\
         --jsonl-dir ${jsonl_bundle} \\
         --output report_data.json
 
diff --git a/modules/local/normalize_benchmark_jsonl/main.nf b/modules/local/normalize_benchmark_jsonl/main.nf
@@ -13,10 +13,10 @@ process NORMALIZE_BENCHMARK_JSONL {
     path "versions.yml",  emit: versions
 
     script:
-    def cost_flag = benchmark_aws_cur_report.name != 'NO_FILE' ? "--costs ${benchmark_aws_cur_report}" : ""
-    def machines_flag = machines_dir.name != 'NO_FILE' ? "--machines-dir ${machines_dir}" : ""
+    def cost_flag = benchmark_aws_cur_report.name != 'NO_FILE' && benchmark_aws_cur_report.name != 'NO_FILE_CUR' ? "--costs ${benchmark_aws_cur_report}" : ""
+    def machines_flag = machines_dir.name != 'NO_FILE' && machines_dir.name != 'NO_FILE_MACHINES' ? "--machines-dir ${machines_dir}" : ""
     """
-    benchmark_report.py \\
+    normalize_benchmark_jsonl.py \\
         --data-dir ${data_dir} \\
         ${cost_flag} \\
         ${machines_flag} \\
diff --git a/modules/local/render_benchmark_report/bin/benchmark_report_template.html b/modules/local/render_benchmark_report/bin/benchmark_report_template.html
@@ -11,7 +11,7 @@
 <style>
   * { box-sizing: border-box; margin: 0; padding: 0; }
   body { font-family: 'Inter', Helvetica, sans-serif;
-         background: {{ brand_white }}; color: {{ brand_heading }}; line-height: 1.6; font-size: 14px; }
+          background: {{ brand_white }}; color: {{ brand_heading }}; line-height: 1.6; font-size: 14px; }
   .container { max-width: 1200px; margin: 0 auto; padding: 0 15px; }
 
   .navbar { background: {{ brand_white }}; border-bottom: 1px solid {{ brand_border }}; padding: 12px 0; margin-bottom: 30px; }
@@ -22,9 +22,9 @@
 
   .section { margin-bottom: 40px; }
   .section h1 { font-size: 26px; font-weight: 600; color: {{ brand_heading }}; margin-bottom: 5px;
-                 padding-bottom: 8px; border-bottom: 1px solid {{ brand_border }}; }
+                  padding-bottom: 8px; border-bottom: 1px solid {{ brand_border }}; }
   .section h2 { font-size: 20px; font-weight: 500; color: {{ brand_heading }}; margin: 25px 0 8px;
-                 padding-bottom: 5px; border-bottom: 1px solid {{ brand_border }}; }
+                  padding-bottom: 5px; border-bottom: 1px solid {{ brand_border }}; }
   .section h3 { font-size: 17px; font-weight: 500; color: {{ brand_heading }}; margin: 20px 0 8px; }
   .section-desc { color: {{ brand_heading }}; font-size: 13px; margin-bottom: 15px; line-height: 1.5; }
   .section-desc strong { color: {{ brand_heading }}; font-weight: 600; }
@@ -49,7 +49,7 @@
 
   .callout { border: 1px solid {{ brand_border }}; border-radius: 4px; margin-bottom: 15px; }
   .callout-header { background: {{ brand_neutral }}; padding: 8px 12px; cursor: pointer; font-size: 13px;
-                     font-weight: 600; color: {{ brand_heading }}; border-bottom: 1px solid {{ brand_border }}; }
+                      font-weight: 600; color: {{ brand_heading }}; border-bottom: 1px solid {{ brand_border }}; }
   .callout-header:hover { background: {{ brand_accent_surface }}; }
   .callout-body { padding: 12px; display: none; }
   .callout-body.show { display: block; }
@@ -59,14 +59,14 @@
   .dl-row dd { color: {{ brand_heading }}; margin-right: 15px; }
 
   .status-badge { display: inline-block; padding: 1px 8px; border-radius: 9999px; font-size: 11px;
-                   font-weight: 600; line-height: 1.6; white-space: nowrap; }
+                    font-weight: 600; line-height: 1.6; white-space: nowrap; }
   .status-badge.success { background: rgba(25, 135, 84, 0.12); color: #146c43; }
   .status-badge.failed { background: rgba(220, 53, 69, 0.14); color: #b02a37; }
   .status-badge.cancelled { background: rgba(255, 193, 7, 0.18); color: #997404; }
   .status-badge.unknown { background: rgba(108, 117, 125, 0.14); color: #495057; }
 
   footer { border-top: 1px solid {{ brand_border }}; padding: 15px 0; margin-top: 40px;
-           font-size: 12px; color: {{ brand_border }}; text-align: center; }
+            font-size: 12px; color: {{ brand_border }}; text-align: center; }
   footer a { color: {{ brand_accent }}; text-decoration: none; }
 
   .side-nav { position: fixed; top: 53px; left: 0; width: 228px; padding: 12px 8px;
@@ -84,7 +84,7 @@
   .main-content { margin-left: 228px; }
 
   .csv-btn { float: right; font-size: 13px; color: {{ brand_accent }}; cursor: pointer; border: 1px solid {{ brand_border }};
-             background: {{ brand_white }}; padding: 2px 10px; border-radius: 3px; text-decoration: none; }
+              background: {{ brand_white }}; padding: 2px 10px; border-radius: 3px; text-decoration: none; }
   .csv-btn:hover { background: {{ brand_neutral }}; }
 
   .runtime-panels { display: flex; flex-direction: column; gap: 18px; }
@@ -168,7 +168,7 @@
   .group-colors span { display: inline-block; width: 12px; height: 12px; border-radius: 2px;
                         margin-right: 4px; vertical-align: middle; }
   .status-pill { display: inline-flex; align-items: center; border-radius: 999px; padding: 2px 8px;
-                 font-size: 11px; font-weight: 600; line-height: 1.3; }
+                  font-size: 11px; font-weight: 600; line-height: 1.3; }
   .status-success { background: #dcfce7; color: #166534; }
   .status-failed { background: #fee2e2; color: #991b1b; }
   .status-cancelled { background: #fef3c7; color: #92400e; }
@@ -896,8 +896,8 @@ <h2 id="pg-mem-savings"><svg class="h-icon sm"><use href="#ic-chart"/></svg> Sav
         grid: { top: 40, bottom: 40, containLabel: true },
         xAxis: { type: 'value', name: 'Run time (minutes)', nameLocation: 'center', nameGap: 25 },
         yAxis: { type: 'category', data: processes,
-                 axisLabel: { width: 280, overflow: 'truncate' },
-                 inverse: true },
+                  axisLabel: { width: 280, overflow: 'truncate' },
+                  inverse: true },
         series: [...series, ...errorSeries],
       });
 
@@ -908,8 +908,8 @@ <h2 id="pg-mem-savings"><svg class="h-icon sm"><use href="#ic-chart"/></svg> Sav
         grid: { top: 40, bottom: 40, containLabel: true },
         xAxis: { type: 'value', name: 'Cost ($)', nameLocation: 'center', nameGap: 25 },
         yAxis: { type: 'category', data: processes,
-                 axisLabel: { width: 280, overflow: 'truncate' },
-                 inverse: true },
+                  axisLabel: { width: 280, overflow: 'truncate' },
+                  inverse: true },
         series: costSeries,
       });
     }, 50);
@@ -1425,8 +1425,8 @@ <h2 id="pg-mem-savings"><svg class="h-icon sm"><use href="#ic-chart"/></svg> Sav
       tooltip: { trigger: 'item' },
       grid: { top: 40, bottom: 20, containLabel: true },
       yAxis: { type: 'category', data: processes,
-               axisLabel: { width: 220, overflow: 'truncate', interval: 0 },
-               inverse: true },
+                axisLabel: { width: 220, overflow: 'truncate', interval: 0 },
+                inverse: true },
       xAxis: { type: 'value', name: 'Cost ($)', nameLocation: 'center', nameGap: 25 },
       series: [{ type: 'boxplot', data: boxData }],
     });
diff --git a/modules/local/render_benchmark_report/main.nf b/modules/local/render_benchmark_report/main.nf
@@ -16,7 +16,7 @@ process RENDER_BENCHMARK_REPORT {
     def brand_flag = brand_yml.name != 'NO_FILE' ? "--brand ${brand_yml}" : ""
     def logo_flag = logo_svg.name != 'NO_FILE' ? "--logo ${logo_svg}" : ""
     """
-    benchmark_report.py \\
+    render_benchmark_report.py \\
         --data ${report_data_json} \\
         ${brand_flag} \\
         ${logo_flag} \\
diff --git a/workflows/nf_aggregate/main.nf b/workflows/nf_aggregate/main.nf
@@ -123,7 +123,7 @@ workflow NF_AGGREGATE {
 
         ch_cur = params.benchmark_aws_cur_report
             ? Channel.fromPath(params.benchmark_aws_cur_report)
-            : Channel.fromPath("${projectDir}/assets/NO_FILE", checkIfExists: false).ifEmpty(file("${projectDir}/assets/NO_FILE"))
+            : Channel.fromPath("${projectDir}/assets/NO_FILE_CUR", checkIfExists: false).ifEmpty(file("${projectDir}/assets/NO_FILE_CUR"))
 
         // Collect machine metrics CSVs from external runs (if present)
         ch_machines_dir = ch_split.external
@@ -134,18 +134,18 @@ workflow NF_AGGREGATE {
             }
             .collect()
             .map { files ->
-                if (!files) return file("${projectDir}/assets/NO_FILE")
+                if (!files) return file("${projectDir}/assets/NO_FILE_MACHINES")
                 def dir = file(benchmark_work_root.resolve("machines"))
                 if (dir.exists()) dir.deleteDir()
                 dir.mkdirs()
                 files.each { f -> f.copyTo(dir.resolve(f.name)) }
                 return dir
             }
-            .ifEmpty(file("${projectDir}/assets/NO_FILE"))
+            .ifEmpty(file("${projectDir}/assets/NO_FILE_MACHINES"))
 
         NORMALIZE_BENCHMARK_JSONL(
             ch_data_dir,
-            ch_cur.ifEmpty(file("${projectDir}/assets/NO_FILE")),
+            ch_cur.ifEmpty(file("${projectDir}/assets/NO_FILE_CUR")),
             ch_machines_dir,
         )
         ch_versions = ch_versions.mix(NORMALIZE_BENCHMARK_JSONL.out.versions)

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+../modules/local/aggregate_benchmark_report_data/bin/benchmark_report_aggregate.py`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+../modules/local/normalize_benchmark_jsonl/bin/benchmark_report_normalize.py`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+../modules/local/render_benchmark_report/bin/benchmark_report_render.py`