From 53a0e98227551f15207565ba2c6bc8f8208c03af Mon Sep 17 00:00:00 2001
From: RunasSudo <runassudo@yingtongli.me>
Date: Fri, 21 Apr 2023 18:10:40 +1000
Subject: [PATCH] Pass through interval-censored Cox fitting progress to stderr

---
 yli/regress.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/yli/regress.py b/yli/regress.py
index cd17a89..a84f673 100644
--- a/yli/regress.py
+++ b/yli/regress.py
@@ -697,9 +697,12 @@ class IntervalCensoredCox(RegressionModel):
 		csv_str = csv_buf.getvalue()
 		
 		# Run intcens binary
-		proc = subprocess.run([config.hpstat_path, 'intcox', '-', '--output', 'json'], input=csv_str, capture_output=True, encoding='utf-8', check=True)
+		proc = subprocess.run([config.hpstat_path, 'intcox', '-', '--output', 'json'], input=csv_str, stdout=subprocess.PIPE, stderr=None, encoding='utf-8', check=True)
 		raw_result = json.loads(proc.stdout)
 		
+		from IPython.display import clear_output
+		clear_output(wait=True)
+		
 		z_critical = -stats.norm.ppf(config.alpha / 2)
 		result.terms = {raw_name: SingleTerm(
 			raw_name=raw_name,