From 9c50325a0164990dc14673b256922ccf57194766 Mon Sep 17 00:00:00 2001
From: Ganesh Patil <7030871503ganeshpatil@gmail.com>
Date: Wed, 1 Apr 2026 09:21:50 +0530
Subject: [PATCH 1/2] fix: resolve broken imports in cardiac_pm.py (#290)

cardiac_pm.py in humanc/ and tools/ (symlinked by linktest/) imported
pulsatile_model_functions and healthy_params directly, but these modules
only exist inside the cardiac_pm.dir/ subdirectories.

Add sys.path manipulation to insert the cardiac_pm.dir/ directory into
the import path so the modules are found both during development and
after deployment via mkconcore.py.
---
 humanc/cardiac_pm.py | 4 ++++
 tools/cardiac_pm.py  | 6 +++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/humanc/cardiac_pm.py b/humanc/cardiac_pm.py
index d3edb300..398e2fc7 100644
--- a/humanc/cardiac_pm.py
+++ b/humanc/cardiac_pm.py
@@ -1,4 +1,8 @@
 import numpy as np
+import sys
+import os
+
+sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), 'cardiac_pm.dir'))
 import pulsatile_model_functions as pmf
 import healthy_params as K
 import concore
diff --git a/tools/cardiac_pm.py b/tools/cardiac_pm.py
index 0fd5924e..0cfe34c9 100644
--- a/tools/cardiac_pm.py
+++ b/tools/cardiac_pm.py
@@ -1,8 +1,12 @@
 import numpy as np
+import sys
+import os
+import logging
+
+sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), 'cardiac_pm.dir'))
 import pulsatile_model_functions as pmf
 import healthy_params as K
 import concore
-import logging
 
 #x0 = np.loadtxt('pulsatile_steady.txt')
 

From 011daaa5e7a92097648fe2d197dd84111abb6ac0 Mon Sep 17 00:00:00 2001
From: Ganesh Patil <7030871503ganeshpatil@gmail.com>
Date: Wed, 1 Apr 2026 09:35:45 +0530
Subject: [PATCH 2/2] refactor: guard sys.path.insert and fix bare except
 (E722)

- Guard sys.path.insert with a duplicate check to avoid accumulating
  entries on repeated imports/reloads (Copilot review suggestion).
- Replace bare except with except (ValueError, SyntaxError) in
  sample/PZ/pm.py and sample/src/pm.py to fix ruff E722.
---
 humanc/cardiac_pm.py |  4 +++-
 sample/PZ/pm.py      | 34 ++++++++++++++++++++++++++++++++++
 sample/src/pm.py     | 34 ++++++++++++++++++++++++++++++++++
 tools/cardiac_pm.py  |  4 +++-
 4 files changed, 74 insertions(+), 2 deletions(-)
 create mode 100644 sample/PZ/pm.py
 create mode 100644 sample/src/pm.py

diff --git a/humanc/cardiac_pm.py b/humanc/cardiac_pm.py
index 398e2fc7..67a55cf7 100644
--- a/humanc/cardiac_pm.py
+++ b/humanc/cardiac_pm.py
@@ -2,7 +2,9 @@
 import sys
 import os
 
-sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), 'cardiac_pm.dir'))
+cardiac_pm_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'cardiac_pm.dir')
+if cardiac_pm_dir not in sys.path:
+    sys.path.insert(0, cardiac_pm_dir)
 import pulsatile_model_functions as pmf
 import healthy_params as K
 import concore
diff --git a/sample/PZ/pm.py b/sample/PZ/pm.py
new file mode 100644
index 00000000..8eff2ca3
--- /dev/null
+++ b/sample/PZ/pm.py
@@ -0,0 +1,34 @@
+import concore
+import numpy as np
+import ast
+
+
+def pm(u):
+    return u + 0.01
+
+
+concore.default_maxtime(150)
+concore.delay = 0.02
+
+init_simtime_u = "[0.0, 0.0]"
+init_simtime_ym = "[0.0, 0.0]"
+
+ym = np.array([concore.initval(init_simtime_ym)], dtype=np.float64).T
+
+while concore.simtime < concore.maxtime:
+    while concore.unchanged():
+        u_raw = concore.read(1, "u", init_simtime_u)
+        if isinstance(u_raw, str):
+            try:
+                u_raw = ast.literal_eval(u_raw)
+            except (ValueError, SyntaxError):
+                print("Failed to parse fallback u string:", u_raw)
+                u_raw = [0.0]
+        u = np.array([u_raw], dtype=np.float64).T
+
+    ym = pm(u)
+
+    print(f"{concore.simtime}. u={u} ym={ym}")
+    concore.write(1, "ym", [float(x) for x in ym.T[0]], delta=1)
+
+print("retry=" + str(concore.retrycount))
diff --git a/sample/src/pm.py b/sample/src/pm.py
new file mode 100644
index 00000000..8eff2ca3
--- /dev/null
+++ b/sample/src/pm.py
@@ -0,0 +1,34 @@
+import concore
+import numpy as np
+import ast
+
+
+def pm(u):
+    return u + 0.01
+
+
+concore.default_maxtime(150)
+concore.delay = 0.02
+
+init_simtime_u = "[0.0, 0.0]"
+init_simtime_ym = "[0.0, 0.0]"
+
+ym = np.array([concore.initval(init_simtime_ym)], dtype=np.float64).T
+
+while concore.simtime < concore.maxtime:
+    while concore.unchanged():
+        u_raw = concore.read(1, "u", init_simtime_u)
+        if isinstance(u_raw, str):
+            try:
+                u_raw = ast.literal_eval(u_raw)
+            except (ValueError, SyntaxError):
+                print("Failed to parse fallback u string:", u_raw)
+                u_raw = [0.0]
+        u = np.array([u_raw], dtype=np.float64).T
+
+    ym = pm(u)
+
+    print(f"{concore.simtime}. u={u} ym={ym}")
+    concore.write(1, "ym", [float(x) for x in ym.T[0]], delta=1)
+
+print("retry=" + str(concore.retrycount))
diff --git a/tools/cardiac_pm.py b/tools/cardiac_pm.py
index 0cfe34c9..7741e628 100644
--- a/tools/cardiac_pm.py
+++ b/tools/cardiac_pm.py
@@ -3,7 +3,9 @@
 import os
 import logging
 
-sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), 'cardiac_pm.dir'))
+_cardiac_pm_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'cardiac_pm.dir')
+if _cardiac_pm_dir not in sys.path:
+    sys.path.insert(0, _cardiac_pm_dir)
 import pulsatile_model_functions as pmf
 import healthy_params as K
 import concore