From 0a606a15e0eb82d01a45eb60a8722e3628c79f74 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Mon, 13 Apr 2026 13:42:51 +0000
Subject: [PATCH 1/2] Fix nbopen standard output and error handling in notebook
 generation

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
---
 bionetgen/core/main.py | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/bionetgen/core/main.py b/bionetgen/core/main.py
index 32de2a9d..d97b05a5 100644
--- a/bionetgen/core/main.py
+++ b/bionetgen/core/main.py
@@ -233,13 +233,24 @@ 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()",
     )
-    stdout = getattr(subprocess, app.config["bionetgen"]["stdout"])
-    stderr = getattr(subprocess, app.config["bionetgen"]["stderr"])
+    try:
+        stdout_loc = getattr(subprocess, app.config["bionetgen"]["stdout"])
+    except (AttributeError, KeyError):
+        stdout_loc = subprocess.PIPE
+    try:
+        stderr_loc = getattr(subprocess, app.config["bionetgen"]["stderr"])
+    except (AttributeError, KeyError):
+        stderr_loc = subprocess.STDOUT
+
     if args.open:
         command = ["nbopen", fname]
-        rc, _ = run_command(command)
+        process = subprocess.Popen(
+            command,
+            stdout=stdout_loc,
+            stderr=stderr_loc,
+        )
+        rc = process.wait()

From 52bd0f6ac4bbc20bb65e92aefa9572230eef5892 Mon Sep 17 00:00:00 2001
From: akutuva21 <akutuva22@gmail.com>
Date: Mon, 13 Apr 2026 10:20:44 -0400
Subject: [PATCH 2/2] chore: PR #89 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__/