From ce0973a45a60e0aec022b5d59cb71acc530a2769 Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Fri, 29 Nov 2024 14:02:50 -0800
Subject: [PATCH 01/10] Filled out struct for mode capsule

---
 python/lib/modal_models/impl.c | 56 +++++++++++++++++++++++++++++++++-
 1 file changed, 55 insertions(+), 1 deletion(-)

diff --git a/python/lib/modal_models/impl.c b/python/lib/modal_models/impl.c
index c8cdff1f2..8a8487236 100644
--- a/python/lib/modal_models/impl.c
+++ b/python/lib/modal_models/impl.c
@@ -46,12 +46,14 @@ static PyObject* py_mode_set(PyObject* mode_capsule, PyObject* args) {
     lf_print_error("Null pointer received.");
     exit(1);
   }
+  Py_INCREF(m->mode);
 
   self_base_t* self = PyCapsule_GetPointer(m->lf_self, "lf_self");
   if (self == NULL) {
     lf_print_error("Null pointer received.");
     exit(1);
   }
+  Py_INCREF(m->lf_self);
 
   _LF_SET_MODE_WITH_TYPE(mode, m->change_type);
 
@@ -61,6 +63,24 @@ static PyObject* py_mode_set(PyObject* mode_capsule, PyObject* args) {
 
 //////////// Python Struct /////////////
 
+/**
+ * Called when an mode in Python is to be created. Note that this is not normally
+ * used because modes are not created in Python.
+ *
+ * To initialize the mode_capsule, this function first calls the tp_alloc
+ * method of type mode_capsule_struct_t and then assign default values of NULL, NULL, 0
+ * to the members of the generic_mode_capsule_struct.
+ */
+PyObject* py_mode_capsule_new(PyTypeObject* type, PyObject* args, PyObject* kwds) {
+  mode_capsule_struct_t* self = (mode_capsule_struct_t*)type->tp_alloc(type, 0);
+  if (self != NULL) {
+    self->mode = NULL;
+    self->lf_self = NULL;
+    self->change_type = 0;
+  }
+  return (PyObject*)self;
+}
+
 /*
  * The function members of mode_capsule.
  * The set function is used to set a new mode.
@@ -69,6 +89,37 @@ static PyMethodDef mode_capsule_methods[] = {
     {"set", (PyCFunction)py_mode_set, METH_NOARGS, "Set a new mode."}, {NULL} /* Sentinel */
 };
 
+/**
+ * Initialize the mode capsule "self" with NULL pointers and default change_type.
+ */
+static int py_mode_capsule_init(mode_capsule_struct_t* self, PyObject* args, PyObject* kwds) {
+  self->mode = NULL;
+  self->lf_self = NULL;
+  self->change_type = 0;
+  return 0;
+}
+
+/**
+ * Called when an mode capsule in Python is deallocated (generally
+ * called by the Python grabage collector).
+ * @param self
+ */
+void py_mode_capsule_dealloc(mode_capsule_struct_t* self) {
+  Py_XDECREF(self->mode);
+  Py_XDECREF(self->lf_self);
+  Py_TYPE(self)->tp_free((PyObject*)self);
+}
+
+/*
+ * The members of a mode_capsule that are accessible from a Python program, used to define
+ * a native Python type.
+ */
+PyMemberDef py_mode_capsule_members[] = {
+    {"mode", T_OBJECT, offsetof(mode_capsule_struct_t, mode), 0, "The pointer to the C mode struct"},
+    {"lf_self", T_OBJECT, offsetof(mode_capsule_struct_t, lf_self), 0, "Pointer to LF self"},
+    {NULL} /* Sentinel */
+};
+
 /*
  * The definition of mode_capsule type object, which is
  * used to describe how mode_capsule behaves.
@@ -79,7 +130,10 @@ static PyTypeObject mode_capsule_t = {
     .tp_basicsize = sizeof(mode_capsule_struct_t),
     .tp_itemsize = 0,
     .tp_flags = Py_TPFLAGS_DEFAULT,
-    .tp_new = PyType_GenericNew,
+    .tp_new = py_mode_capsule_new,
+    .tp_init = (initproc)py_mode_capsule_init,
+    .tp_dealloc = (destructor)py_mode_capsule_dealloc,
+    .tp_members = py_mode_capsule_members,
     .tp_methods = mode_capsule_methods,
 };
 

From 9a9e492ec1d63817b7a058de1d7c2ac4e47b08f0 Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Fri, 29 Nov 2024 15:15:16 -0800
Subject: [PATCH 02/10] Slightly more careful reference count decrementing

---
 python/include/python_port.h |  1 -
 python/lib/python_port.c     | 20 ++++++++++----------
 2 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/python/include/python_port.h b/python/include/python_port.h
index 7752b16c8..cc50524c6 100644
--- a/python/include/python_port.h
+++ b/python/include/python_port.h
@@ -97,5 +97,4 @@ typedef struct {
   FEDERATED_CAPSULE_EXTENSION
 } generic_port_capsule_struct;
 
-void python_count_decrement(void* py_object);
 #endif
diff --git a/python/lib/python_port.c b/python/lib/python_port.c
index 62f4b4732..571024946 100644
--- a/python/lib/python_port.c
+++ b/python/lib/python_port.c
@@ -47,7 +47,7 @@ PyTypeObject py_port_capsule_t;
  * Python can free its memory.
  * @param py_object A PyObject with count 1 or greater.
  */
-void python_count_decrement(void* py_object) { Py_XDECREF((PyObject*)py_object); }
+static void python_count_decrement(void* py_object) { Py_XDECREF((PyObject*)py_object); }
 
 //////////// set Function(s) /////////////
 /**
@@ -94,14 +94,13 @@ PyObject* py_port_set(PyObject* self, PyObject* args) {
   }
 
   if (val) {
-    LF_PRINT_DEBUG("Setting value %p with reference count %d.", val, (int)Py_REFCNT(val));
-    // Py_INCREF(val);
     // python_count_decrement(port->value);
 
     lf_token_t* token = lf_new_token((void*)port, val, 1);
     lf_set_destructor(port, python_count_decrement);
     lf_set_token(port, token);
     Py_INCREF(val);
+    LF_PRINT_DEBUG("Setting value %p with reference count %d.", val, (int)Py_REFCNT(val));
 
     // Also set the values for the port capsule.
     p->value = val;
@@ -117,9 +116,9 @@ PyObject* py_port_set(PyObject* self, PyObject* args) {
  * garbage collector).
  * @param self An instance of generic_port_instance_struct*
  */
-void py_port_capsule_dealloc(generic_port_capsule_struct* self) {
-  Py_XDECREF(self->port);
-  Py_XDECREF(self->value);
+static void py_port_capsule_dealloc(generic_port_capsule_struct* self) {
+  Py_CLEAR(self->port);
+  Py_CLEAR(self->value);
   Py_TYPE(self)->tp_free((PyObject*)self);
 }
 
@@ -147,7 +146,8 @@ PyObject* py_port_capsule_new(PyTypeObject* type, PyObject* args, PyObject* kwds
   generic_port_capsule_struct* self;
   self = (generic_port_capsule_struct*)type->tp_alloc(type, 0);
   if (self != NULL) {
-    self->port = NULL;
+    Py_INCREF(Py_None);
+    self->port = Py_None;
     Py_INCREF(Py_None);
     self->value = Py_None;
     self->is_present = false;
@@ -325,7 +325,7 @@ PyMappingMethods py_port_as_mapping = {(lenfunc)py_port_length, (binaryfunc)py_p
  */
 int py_port_capsule_init(generic_port_capsule_struct* self, PyObject* args, PyObject* kwds) {
   static char* kwlist[] = {"port", "value", "is_present", "width", "current_index", NULL};
-  PyObject *value = NULL, *tmp, *port = NULL;
+  PyObject *value = NULL, *port = NULL;
 
   if (!PyArg_ParseTupleAndKeywords(args, kwds, "|OOp", kwlist, &port, &value, &self->is_present, &self->width,
                                    &self->current_index)) {
@@ -333,14 +333,14 @@ int py_port_capsule_init(generic_port_capsule_struct* self, PyObject* args, PyOb
   }
 
   if (value) {
-    tmp = self->value;
+    PyObject *tmp = self->value;
     Py_INCREF(value);
     self->value = value;
     Py_XDECREF(tmp);
   }
 
   if (port) {
-    tmp = self->port;
+    PyObject *tmp = self->port;
     Py_INCREF(port);
     self->port = port;
     Py_XDECREF(tmp);

From 76bcf3282d4c8d58178da56a32720736379895f6 Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Fri, 29 Nov 2024 15:21:10 -0800
Subject: [PATCH 03/10] Replace deprecated function

---
 python/lib/pythontarget.c | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/python/lib/pythontarget.c b/python/lib/pythontarget.c
index 8e41f40f9..0847cac6e 100644
--- a/python/lib/pythontarget.c
+++ b/python/lib/pythontarget.c
@@ -603,7 +603,14 @@ PyObject* get_python_function(string module, string class, int instance_id, stri
 
     mbstowcs(wcwd, cwd, PATH_MAX);
 
-    Py_SetPath(wcwd);
+    // Deprecated: Py_SetPath(wcwd);
+    // Replace with the following more verbose version:
+    PyConfig config;
+    PyConfig_InitPythonConfig(&config);
+    // Add paths to the configuration
+    PyWideStringList_Append(&config.module_search_paths, wcwd);
+    // Initialize Python with the custom configuration
+    Py_InitializeFromConfig(&config);
 
     LF_PRINT_DEBUG("Loading module %s in %s.", module, cwd);
 

From eecb56c428f0d3e757c13ea4e34619f9be047dc7 Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Fri, 29 Nov 2024 17:59:04 -0800
Subject: [PATCH 04/10] Made function not static, apparently needed for Docker

---
 python/include/python_port.h | 1 +
 python/lib/python_port.c     | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/python/include/python_port.h b/python/include/python_port.h
index cc50524c6..7752b16c8 100644
--- a/python/include/python_port.h
+++ b/python/include/python_port.h
@@ -97,4 +97,5 @@ typedef struct {
   FEDERATED_CAPSULE_EXTENSION
 } generic_port_capsule_struct;
 
+void python_count_decrement(void* py_object);
 #endif
diff --git a/python/lib/python_port.c b/python/lib/python_port.c
index 571024946..aceff28a7 100644
--- a/python/lib/python_port.c
+++ b/python/lib/python_port.c
@@ -47,7 +47,7 @@ PyTypeObject py_port_capsule_t;
  * Python can free its memory.
  * @param py_object A PyObject with count 1 or greater.
  */
-static void python_count_decrement(void* py_object) { Py_XDECREF((PyObject*)py_object); }
+void python_count_decrement(void* py_object) { Py_XDECREF((PyObject*)py_object); }
 
 //////////// set Function(s) /////////////
 /**

From 441e3ad6e31f70467651a070829d4fe5c1759445 Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Mon, 2 Dec 2024 10:25:47 -0800
Subject: [PATCH 05/10] Issue error message on failure

---
 python/lib/modal_models/impl.c | 1 +
 1 file changed, 1 insertion(+)

diff --git a/python/lib/modal_models/impl.c b/python/lib/modal_models/impl.c
index 8a8487236..e212436e5 100644
--- a/python/lib/modal_models/impl.c
+++ b/python/lib/modal_models/impl.c
@@ -154,6 +154,7 @@ void initialize_mode_capsule_t(PyObject* current_module) {
   if (PyModule_AddObject(current_module, "mode_capsule", (PyObject*)&mode_capsule_t) < 0) {
     Py_DECREF(&mode_capsule_t);
     Py_DECREF(current_module);
+    lf_print_error_and_exit("Failed to initialize mode_capsule.");
     return;
   }
 }

From 601e633beddc51e6f5ca492319b1ec4caf05c278 Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Thu, 5 Dec 2024 15:12:31 -0800
Subject: [PATCH 06/10] Point reactor-c to lingua-franca master

---
 lingua-franca-ref.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lingua-franca-ref.txt b/lingua-franca-ref.txt
index edf165c42..8b25206ff 100644
--- a/lingua-franca-ref.txt
+++ b/lingua-franca-ref.txt
@@ -1 +1 @@
-fix-concurrency
\ No newline at end of file
+master
\ No newline at end of file

From fe1ee790b313c4ee0ced0e80e7b58319d5a8090a Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Sat, 7 Dec 2024 10:53:09 -0800
Subject: [PATCH 07/10] Use Python_New not Python_GC_New

---
 python/lib/modal_models/impl.c | 6 +++++-
 python/lib/python_tag.c        | 3 ++-
 python/lib/pythontarget.c      | 8 ++++++--
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/python/lib/modal_models/impl.c b/python/lib/modal_models/impl.c
index e212436e5..f47c7135f 100644
--- a/python/lib/modal_models/impl.c
+++ b/python/lib/modal_models/impl.c
@@ -164,16 +164,19 @@ void initialize_mode_capsule_t(PyObject* current_module) {
  */
 PyObject* convert_C_mode_to_py(reactor_mode_t* mode, self_base_t* lf_self, lf_mode_change_type_t change_type) {
   // Create the mode struct in Python
-  mode_capsule_struct_t* cap = (mode_capsule_struct_t*)PyObject_GC_New(mode_capsule_struct_t, &mode_capsule_t);
+  mode_capsule_struct_t* cap = (mode_capsule_struct_t*)PyObject_New(mode_capsule_struct_t, &mode_capsule_t);
+
   if (cap == NULL) {
     lf_print_error_and_exit("Failed to convert mode.");
   }
+  Py_INCREF(cap);
 
   // Create the capsule to hold the reactor_mode_t* mode
   PyObject* capsule = PyCapsule_New(mode, "mode", NULL);
   if (capsule == NULL) {
     lf_print_error_and_exit("Failed to convert mode.");
   }
+  Py_INCREF(capsule);
   // Fill in the Python mode struct.
   cap->mode = capsule;
 
@@ -182,6 +185,7 @@ PyObject* convert_C_mode_to_py(reactor_mode_t* mode, self_base_t* lf_self, lf_mo
   if (self_capsule == NULL) {
     lf_print_error_and_exit("Failed to convert self.");
   }
+  Py_INCREF(self_capsule);
   cap->lf_self = self_capsule;
 
   cap->change_type = change_type;
diff --git a/python/lib/python_tag.c b/python/lib/python_tag.c
index 991f94f64..f32eb0e9d 100644
--- a/python/lib/python_tag.c
+++ b/python/lib/python_tag.c
@@ -191,10 +191,11 @@ PyTypeObject PyTagType = {
  * @return PyObject* The tag in Python.
  */
 py_tag_t* convert_C_tag_to_py(tag_t c_tag) {
-  py_tag_t* py_tag = PyObject_GC_New(py_tag_t, &PyTagType);
+  py_tag_t* py_tag = PyObject_New(py_tag_t, &PyTagType);
   if (py_tag == NULL) {
     lf_print_error_and_exit("Failed to convert tag from C to Python.");
   }
+  Py_INCREF(py_tag);
   py_tag->tag = c_tag;
   return py_tag;
 }
diff --git a/python/lib/pythontarget.c b/python/lib/pythontarget.c
index 0847cac6e..cc5c51c24 100644
--- a/python/lib/pythontarget.c
+++ b/python/lib/pythontarget.c
@@ -445,16 +445,18 @@ void destroy_action_capsule(PyObject* capsule) { free(PyCapsule_GetPointer(capsu
  */
 PyObject* convert_C_port_to_py(void* port, int width) {
   // Create the port struct in Python
-  PyObject* cap = (PyObject*)PyObject_GC_New(generic_port_capsule_struct, &py_port_capsule_t);
+  PyObject* cap = (PyObject*)PyObject_New(generic_port_capsule_struct, &py_port_capsule_t);
   if (cap == NULL) {
     lf_print_error_and_exit("Failed to convert port.");
   }
+  Py_INCREF(cap);
 
   // Create the capsule to hold the void* port
   PyObject* capsule = PyCapsule_New(port, "port", NULL);
   if (capsule == NULL) {
     lf_print_error_and_exit("Failed to convert port.");
   }
+  Py_INCREF(capsule);
 
   // Fill in the Python port struct
   ((generic_port_capsule_struct*)cap)->port = capsule;
@@ -512,16 +514,18 @@ PyObject* convert_C_action_to_py(void* action) {
   trigger_t* trigger = ((lf_action_base_t*)action)->trigger;
 
   // Create the action struct in Python
-  PyObject* cap = (PyObject*)PyObject_GC_New(generic_action_capsule_struct, &py_action_capsule_t);
+  PyObject* cap = (PyObject*)PyObject_New(generic_action_capsule_struct, &py_action_capsule_t);
   if (cap == NULL) {
     lf_print_error_and_exit("Failed to convert action.");
   }
+  Py_INCREF(cap);
 
   // Create the capsule to hold the void* action
   PyObject* capsule = PyCapsule_New(action, "action", NULL);
   if (capsule == NULL) {
     lf_print_error_and_exit("Failed to convert action.");
   }
+  Py_INCREF(capsule);
 
   // Fill in the Python action struct
   ((generic_action_capsule_struct*)cap)->action = capsule;

From 3152ea31eb24980d7fe5c0baaec9c0e403d77db4 Mon Sep 17 00:00:00 2001
From: erlingrj <erling.jellum@gmail.com>
Date: Mon, 9 Dec 2024 18:18:53 -0800
Subject: [PATCH 08/10] Run clang-format

---
 python/lib/python_port.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/lib/python_port.c b/python/lib/python_port.c
index aceff28a7..be12861d5 100644
--- a/python/lib/python_port.c
+++ b/python/lib/python_port.c
@@ -333,14 +333,14 @@ int py_port_capsule_init(generic_port_capsule_struct* self, PyObject* args, PyOb
   }
 
   if (value) {
-    PyObject *tmp = self->value;
+    PyObject* tmp = self->value;
     Py_INCREF(value);
     self->value = value;
     Py_XDECREF(tmp);
   }
 
   if (port) {
-    PyObject *tmp = self->port;
+    PyObject* tmp = self->port;
     Py_INCREF(port);
     self->port = port;
     Py_XDECREF(tmp);

From 6c7379e658aed9aa22d53163cb004e77a82d31eb Mon Sep 17 00:00:00 2001
From: erlingrj <erling.jellum@gmail.com>
Date: Mon, 9 Dec 2024 18:57:02 -0800
Subject: [PATCH 09/10] Update to clang-format v19.1.5

---
 .github/workflows/clang-format.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/clang-format.yml b/.github/workflows/clang-format.yml
index 11028dd38..2f099df81 100644
--- a/.github/workflows/clang-format.yml
+++ b/.github/workflows/clang-format.yml
@@ -5,12 +5,15 @@ on: [pull_request]
 
 jobs:
   clang-format:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v2
-      - name: Install clang-tidy
+      - name: Install clang-tidy and clang-format
         run: |
           sudo apt-get update
           sudo apt-get install -y clang-tidy
+          sudo apt-get install -y pipx
+          pipx install clang-format
+          clang-format --version
       - name: Analyze
         run: make format-check

From 8cd66aa792954589d4125ddd17800c1ea5816739 Mon Sep 17 00:00:00 2001
From: erlingrj <erling.jellum@gmail.com>
Date: Mon, 9 Dec 2024 18:57:45 -0800
Subject: [PATCH 10/10] Run clang-format 19.1.5

---
 core/federated/federate.c                 | 6 +++---
 include/core/utils/impl/hashmap.h         | 2 +-
 include/core/utils/impl/pointer_hashmap.h | 2 +-
 tag/api/tag.h                             | 9 +++------
 4 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/core/federated/federate.c b/core/federated/federate.c
index 9be45fdd7..2bfc3656a 100644
--- a/core/federated/federate.c
+++ b/core/federated/federate.c
@@ -1951,9 +1951,9 @@ void lf_connect_to_rti(const char* hostname, int port) {
     if (result < 0)
       continue; // Connect failed.
 
-      // Have connected to an RTI, but not sure it's the right RTI.
-      // Send a MSG_TYPE_FED_IDS message and wait for a reply.
-      // Notify the RTI of the ID of this federate and its federation.
+    // Have connected to an RTI, but not sure it's the right RTI.
+    // Send a MSG_TYPE_FED_IDS message and wait for a reply.
+    // Notify the RTI of the ID of this federate and its federation.
 
 #ifdef FEDERATED_AUTHENTICATED
     LF_PRINT_LOG("Connected to an RTI. Performing HMAC-based authentication using federation ID.");
diff --git a/include/core/utils/impl/hashmap.h b/include/core/utils/impl/hashmap.h
index e64774887..94d5969a7 100644
--- a/include/core/utils/impl/hashmap.h
+++ b/include/core/utils/impl/hashmap.h
@@ -19,7 +19,7 @@
 #define V void*
 #endif
 #ifndef HASH_OF
-#define HASH_OF(key) (size_t) key
+#define HASH_OF(key) (size_t)key
 #endif
 #ifndef HASHMAP
 #define HASHMAP(token) hashmap##_##token
diff --git a/include/core/utils/impl/pointer_hashmap.h b/include/core/utils/impl/pointer_hashmap.h
index 2184518b3..c2a60aef1 100644
--- a/include/core/utils/impl/pointer_hashmap.h
+++ b/include/core/utils/impl/pointer_hashmap.h
@@ -30,7 +30,7 @@
 #define HASHMAP(token) hashmap_object2int##_##token
 #define K void*
 #define V int
-#define HASH_OF(key) (size_t) key
+#define HASH_OF(key) (size_t)key
 #include "hashmap.h"
 #undef HASHMAP
 #undef K
diff --git a/tag/api/tag.h b/tag/api/tag.h
index c40e490f8..ab6b9ccbc 100644
--- a/tag/api/tag.h
+++ b/tag/api/tag.h
@@ -37,15 +37,12 @@
 #define NEVER_TAG                                                                                                      \
   (tag_t) { .time = NEVER, .microstep = NEVER_MICROSTEP }
 // Need a separate initializer expression to comply with some C compilers
-#define NEVER_TAG_INITIALIZER                                                                                          \
-  { NEVER, NEVER_MICROSTEP }
+#define NEVER_TAG_INITIALIZER {NEVER, NEVER_MICROSTEP}
 #define FOREVER_TAG                                                                                                    \
   (tag_t) { .time = FOREVER, .microstep = FOREVER_MICROSTEP }
 // Need a separate initializer expression to comply with some C compilers
-#define FOREVER_TAG_INITIALIZER                                                                                        \
-  { FOREVER, FOREVER_MICROSTEP }
-#define ZERO_TAG                                                                                                       \
-  (tag_t) { .time = 0LL, .microstep = 0u }
+#define FOREVER_TAG_INITIALIZER {FOREVER, FOREVER_MICROSTEP}
+#define ZERO_TAG (tag_t){.time = 0LL, .microstep = 0u}
 
 // Returns true if timeout has elapsed.
 #define CHECK_TIMEOUT(start, duration) (lf_time_physical() > ((start) + (duration)))