From 8d4f20c6763a23a60028a5dc64f2abe9e7881056 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Thu, 9 Apr 2026 17:46:53 +0000
Subject: [PATCH 1/2] Properly route standard output and standard error from
 nbopen subprocess call.

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
---
 bionetgen/core/main.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/bionetgen/core/main.py b/bionetgen/core/main.py
index 32de2a9d..208a8980 100644
--- a/bionetgen/core/main.py
+++ b/bionetgen/core/main.py
@@ -233,7 +233,6 @@ def generate_notebook(app):
     app.log.debug(f"Writing notebook to file: {fname}", f"{__file__} : notebook()")
     notebook.write(fname)
     # open the notebook with nbopen
-    # TODO: deal with stdout/err
     app.log.debug(
         f"Attempting to open notebook {fname} with nbopen",
         f"{__file__} : notebook()",
@@ -242,4 +241,9 @@ def generate_notebook(app):
     stderr = getattr(subprocess, app.config["bionetgen"]["stderr"])
     if args.open:
         command = ["nbopen", fname]
-        rc, _ = run_command(command)
+        process = subprocess.Popen(command, stdout=stdout, stderr=stderr)
+        p_out, p_err = process.communicate()
+        if p_out:
+            app.log.info(p_out.decode("utf-8") if isinstance(p_out, bytes) else p_out)
+        if p_err:
+            app.log.error(p_err.decode("utf-8") if isinstance(p_err, bytes) else p_err)

From 10605966084d2272ad001b9fcf4b2f988951ae9d Mon Sep 17 00:00:00 2001
From: akutuva21 <akutuva22@gmail.com>
Date: Mon, 13 Apr 2026 10:11:00 -0400
Subject: [PATCH 2/2] chore: PR #40 remove forbidden artifacts and run black

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index 39aa9026..f9bf9c80 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/