From ccc8ce17bad4bb9339fe4a5120f9fed9974191be Mon Sep 17 00:00:00 2001
From: Chad Baker <chad.baker@nrel.gov>
Date: Tue, 14 Jan 2025 17:00:13 -0700
Subject: [PATCH 01/11] changed order to see if that helps

---
 rust/altrios-core/src/consist/consist_model.rs                | 2 +-
 rust/altrios-core/src/consist/locomotive/locomotive_model.rs  | 2 +-
 .../src/consist/locomotive/powertrain/electric_drivetrain.rs  | 4 ++--
 .../src/consist/locomotive/powertrain/fuel_converter.rs       | 4 ++--
 .../src/consist/locomotive/powertrain/generator.rs            | 2 +-
 .../locomotive/powertrain/reversible_energy_storage.rs        | 4 ++--
 rust/altrios-core/src/train/friction_brakes.rs                | 2 +-
 rust/altrios-core/src/train/set_speed_train_sim.rs            | 2 +-
 rust/altrios-core/src/train/speed_limit_train_sim.rs          | 2 +-
 9 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/rust/altrios-core/src/consist/consist_model.rs b/rust/altrios-core/src/consist/consist_model.rs
index 2a217fc..bbfa809 100644
--- a/rust/altrios-core/src/consist/consist_model.rs
+++ b/rust/altrios-core/src/consist/consist_model.rs
@@ -115,7 +115,7 @@ pub struct Consist {
     #[serde(default)]
     #[serde(skip_serializing_if = "EqDefault::eq_default")]
     pub state: ConsistState,
-    #[serde(skip_serializing_if = "ConsistStateHistoryVec::is_empty", default)]
+    #[serde(default, skip_serializing_if = "ConsistStateHistoryVec::is_empty")]
     /// Custom vector of [Self::state]
     pub history: ConsistStateHistoryVec,
     #[api(skip_set, skip_get)] // custom needed for this
diff --git a/rust/altrios-core/src/consist/locomotive/locomotive_model.rs b/rust/altrios-core/src/consist/locomotive/locomotive_model.rs
index 1375158..453996c 100644
--- a/rust/altrios-core/src/consist/locomotive/locomotive_model.rs
+++ b/rust/altrios-core/src/consist/locomotive/locomotive_model.rs
@@ -617,7 +617,7 @@ pub struct Locomotive {
     #[api(skip_set, skip_get)]
     save_interval: Option<usize>,
     /// Custom vector of [Self::state]
-    #[serde(skip_serializing_if = "LocomotiveStateHistoryVec::is_empty", default)]
+    #[serde(default, skip_serializing_if = "LocomotiveStateHistoryVec::is_empty")]
     pub history: LocomotiveStateHistoryVec,
     #[serde(default = "utils::return_true")]
     /// If true, requires power demand to not exceed consist
diff --git a/rust/altrios-core/src/consist/locomotive/powertrain/electric_drivetrain.rs b/rust/altrios-core/src/consist/locomotive/powertrain/electric_drivetrain.rs
index 244af0d..15665c3 100644
--- a/rust/altrios-core/src/consist/locomotive/powertrain/electric_drivetrain.rs
+++ b/rust/altrios-core/src/consist/locomotive/powertrain/electric_drivetrain.rs
@@ -77,8 +77,8 @@ pub struct ElectricDrivetrain {
     pub save_interval: Option<usize>,
     /// Custom vector of [Self::state]
     #[serde(
-        skip_serializing_if = "ElectricDrivetrainStateHistoryVec::is_empty",
-        default
+        default,
+        skip_serializing_if = "ElectricDrivetrainStateHistoryVec::is_empty"
     )]
     pub history: ElectricDrivetrainStateHistoryVec,
 }
diff --git a/rust/altrios-core/src/consist/locomotive/powertrain/fuel_converter.rs b/rust/altrios-core/src/consist/locomotive/powertrain/fuel_converter.rs
index 11d06b2..cdff62a 100644
--- a/rust/altrios-core/src/consist/locomotive/powertrain/fuel_converter.rs
+++ b/rust/altrios-core/src/consist/locomotive/powertrain/fuel_converter.rs
@@ -75,8 +75,8 @@ pub struct FuelConverter {
     pub save_interval: Option<usize>,
     /// Custom vector of [Self::state]
     #[serde(
-        skip_serializing_if = "FuelConverterStateHistoryVec::is_empty",
-        default
+        default,
+        skip_serializing_if = "FuelConverterStateHistoryVec::is_empty"
     )]
     pub history: FuelConverterStateHistoryVec, // TODO: spec out fuel tank size and track kg of fuel
 }
diff --git a/rust/altrios-core/src/consist/locomotive/powertrain/generator.rs b/rust/altrios-core/src/consist/locomotive/powertrain/generator.rs
index 10fe88b..ed10c4e 100644
--- a/rust/altrios-core/src/consist/locomotive/powertrain/generator.rs
+++ b/rust/altrios-core/src/consist/locomotive/powertrain/generator.rs
@@ -102,7 +102,7 @@ pub struct Generator {
     /// Time step interval between saves. 1 is a good option. If None, no saving occurs.
     pub save_interval: Option<usize>,
     /// Custom vector of [Self::state]
-    #[serde(skip_serializing_if = "GeneratorStateHistoryVec::is_empty", default)]
+    #[serde(default, skip_serializing_if = "GeneratorStateHistoryVec::is_empty")]
     pub history: GeneratorStateHistoryVec,
 }
 
diff --git a/rust/altrios-core/src/consist/locomotive/powertrain/reversible_energy_storage.rs b/rust/altrios-core/src/consist/locomotive/powertrain/reversible_energy_storage.rs
index 119464f..18f28db 100644
--- a/rust/altrios-core/src/consist/locomotive/powertrain/reversible_energy_storage.rs
+++ b/rust/altrios-core/src/consist/locomotive/powertrain/reversible_energy_storage.rs
@@ -187,8 +187,8 @@ pub struct ReversibleEnergyStorage {
     /// Time step interval at which history is saved
     pub save_interval: Option<usize>,
     #[serde(
-        skip_serializing_if = "ReversibleEnergyStorageStateHistoryVec::is_empty",
-        default
+        default,
+        skip_serializing_if = "ReversibleEnergyStorageStateHistoryVec::is_empty"
     )]
     /// Custom vector of [Self::state]
     pub history: ReversibleEnergyStorageStateHistoryVec,
diff --git a/rust/altrios-core/src/train/friction_brakes.rs b/rust/altrios-core/src/train/friction_brakes.rs
index c982238..b86aa6f 100644
--- a/rust/altrios-core/src/train/friction_brakes.rs
+++ b/rust/altrios-core/src/train/friction_brakes.rs
@@ -43,7 +43,7 @@ pub struct FricBrake {
     #[serde(default)]
     #[serde(skip_serializing_if = "EqDefault::eq_default")]
     pub state: FricBrakeState,
-    #[serde(skip_serializing_if = "FricBrakeStateHistoryVec::is_empty", default)]
+    #[serde(default, skip_serializing_if = "FricBrakeStateHistoryVec::is_empty")]
     /// Custom vector of [Self::state]
     pub history: FricBrakeStateHistoryVec,
     pub save_interval: Option<usize>,
diff --git a/rust/altrios-core/src/train/set_speed_train_sim.rs b/rust/altrios-core/src/train/set_speed_train_sim.rs
index 75ec44e..3e063ef 100644
--- a/rust/altrios-core/src/train/set_speed_train_sim.rs
+++ b/rust/altrios-core/src/train/set_speed_train_sim.rs
@@ -290,7 +290,7 @@ pub struct SetSpeedTrainSim {
     #[api(skip_set)]
     path_tpc: PathTpc,
     /// Custom vector of [Self::state]
-    #[serde(skip_serializing_if = "TrainStateHistoryVec::is_empty", default)]
+    #[serde(default, skip_serializing_if = "TrainStateHistoryVec::is_empty")]
     pub history: TrainStateHistoryVec,
     #[api(skip_set, skip_get)]
     save_interval: Option<usize>,
diff --git a/rust/altrios-core/src/train/speed_limit_train_sim.rs b/rust/altrios-core/src/train/speed_limit_train_sim.rs
index 0b81c7f..9e4e70a 100644
--- a/rust/altrios-core/src/train/speed_limit_train_sim.rs
+++ b/rust/altrios-core/src/train/speed_limit_train_sim.rs
@@ -153,7 +153,7 @@ pub struct SpeedLimitTrainSim {
     pub braking_points: BrakingPoints,
     pub fric_brake: FricBrake,
     /// Custom vector of [Self::state]
-    #[serde(skip_serializing_if = "TrainStateHistoryVec::is_empty", default)]
+    #[serde(default, skip_serializing_if = "TrainStateHistoryVec::is_empty")]
     pub history: TrainStateHistoryVec,
     #[api(skip_set, skip_get)]
     save_interval: Option<usize>,

From 0c52033770c142ab90150d668e8bb8ee0f98399a Mon Sep 17 00:00:00 2001
From: Chad Baker <chad.baker@nrel.gov>
Date: Tue, 14 Jan 2025 17:01:45 -0700
Subject: [PATCH 02/11] some tests are failing with `msg_pack`

---
 pyproject.toml                                |  1 +
 python/altrios/__init__.py                    | 67 ++++++++++++++++---
 python/altrios/altrios_pyo3.pyi               |  3 +
 rust/Cargo.lock                               | 23 +++++++
 rust/altrios-core/Cargo.toml                  |  7 +-
 .../src/altrios_api/mod.rs                    | 24 +++++++
 rust/altrios-core/src/traits.rs               | 21 ++++++
 7 files changed, 134 insertions(+), 12 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c608316..28d3299 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,6 +47,7 @@ dependencies = [
     "pyarrow",
     "requests",
     "PyYAML==6.0.2",
+    "msgpack==1.1.0",
 ]
 
 [project.urls]
diff --git a/python/altrios/__init__.py b/python/altrios/__init__.py
index 6c8c4fb..3008811 100644
--- a/python/altrios/__init__.py
+++ b/python/altrios/__init__.py
@@ -121,25 +121,70 @@ def history_path_list(self, element_as_list:bool=False) -> List[str]:
     ]
     return history_path_list
             
-def to_pydict(self) -> Dict:
+# TODO connect to crate features
+data_formats = [
+    'yaml',
+    'msg_pack',
+    # 'toml',
+    'json',
+]
+
+def to_pydict(self, data_fmt: str = "msg_pack", flatten: bool = False) -> Dict:
     """
     Returns self converted to pure python dictionary with no nested Rust objects
+    # Arguments
+    - `flatten`: if True, returns dict without any hierarchy
+    - `data_fmt`: data format for intermediate conversion step
     """
-    from yaml import load
-    try:
-        from yaml import CLoader as Loader
-    except ImportError:
-        from yaml import Loader
-    pydict = load(self.to_yaml(), Loader = Loader)
-    return pydict
+    data_fmt = data_fmt.lower()
+    assert data_fmt in data_formats, f"`data_fmt` must be one of {data_formats}"
+    match data_fmt:
+        case "msg_pack":
+            import msgpack
+            pydict = msgpack.loads(self.to_msg_pack())
+        case "yaml":
+            from yaml import load
+            try:
+                from yaml import CLoader as Loader
+            except ImportError:
+                from yaml import Loader
+            pydict = load(self.to_yaml(), Loader=Loader)
+        case "json":
+            from json import loads
+            pydict = loads(self.to_json())
+
+    if not flatten:
+        return pydict
+    else:
+        return next(iter(pd.json_normalize(pydict, sep=".").to_dict(orient='records')))
 
 @classmethod
-def from_pydict(cls, pydict: Dict) -> Self:
+def from_pydict(cls, pydict: Dict, data_fmt: str = "msg_pack") -> Self:
     """
     Instantiates Self from pure python dictionary 
+    # Arguments
+    - `pydict`: dictionary to be converted to ALTRIOS object
+    - `data_fmt`: data format for intermediate conversion step
     """
-    import yaml
-    return cls.from_yaml(yaml.dump(pydict),skip_init=False)
+    data_fmt = data_fmt.lower()
+    assert data_fmt in data_formats, f"`data_fmt` must be one of {data_formats}"
+    match data_fmt.lower():
+        case "yaml":
+            import yaml
+            obj = cls.from_yaml(yaml.dump(pydict), skip_init=False)
+        case "msg_pack":
+            import msgpack
+            try:
+                obj = cls.from_msg_pack(msgpack.packb(pydict))
+            except Exception as err:
+                print(
+                    f"{err}\nFalling back to YAML.")
+                obj = cls.from_pydict(pydict, data_fmt="yaml")
+        case "json":
+            from json import dumps
+            obj = cls.from_json(dumps(pydict))
+
+    return obj
 
 def to_dataframe(self, pandas:bool=False) -> [pd.DataFrame, pl.DataFrame, pl.LazyFrame]:
     """
diff --git a/python/altrios/altrios_pyo3.pyi b/python/altrios/altrios_pyo3.pyi
index d16a794..a41835a 100644
--- a/python/altrios/altrios_pyo3.pyi
+++ b/python/altrios/altrios_pyo3.pyi
@@ -21,6 +21,9 @@ class SerdeAPI(object):
     def to_bincode(self) -> bytes: ...
     def to_json(self) -> str: ...
     def to_yaml(self) -> str: ...
+    def to_pydict(self, data_fmt: str = "msg_pack", flatten: bool = False) -> Dict: ...
+    @classmethod
+    def from_pydict(cls, pydict: Dict, data_fmt: str = "msg_pack") -> Self:
 
 
 class Consist(SerdeAPI):
diff --git a/rust/Cargo.lock b/rust/Cargo.lock
index 93cf303..d39ac94 100644
--- a/rust/Cargo.lock
+++ b/rust/Cargo.lock
@@ -70,6 +70,7 @@ dependencies = [
  "pyo3-polars",
  "rayon",
  "readonly",
+ "rmp-serde",
  "serde",
  "serde-this-or-that",
  "serde_json",
@@ -2173,6 +2174,28 @@ version = "0.8.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2b15c43186be67a4fd63bee50d0303afffcef381492ebe2c5d87f324e1b8815c"
 
+[[package]]
+name = "rmp"
+version = "0.8.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "228ed7c16fa39782c3b3468e974aec2795e9089153cd08ee2e9aefb3613334c4"
+dependencies = [
+ "byteorder",
+ "num-traits",
+ "paste",
+]
+
+[[package]]
+name = "rmp-serde"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "52e599a477cf9840e92f2cde9a7189e67b42c57532749bf90aea6ec10facd4db"
+dependencies = [
+ "byteorder",
+ "rmp",
+ "serde",
+]
+
 [[package]]
 name = "rustc-demangle"
 version = "0.1.24"
diff --git a/rust/altrios-core/Cargo.toml b/rust/altrios-core/Cargo.toml
index 7d46e12..9dfff66 100644
--- a/rust/altrios-core/Cargo.toml
+++ b/rust/altrios-core/Cargo.toml
@@ -54,11 +54,16 @@ eng_fmt = { workspace = true }
 directories = "5.0.1"
 tempfile = "3.10.1"
 derive_more = { version = "1.0.0", features = ["from_str", "from", "is_variant", "try_into"] }
+rmp-serde = { version = "1.3.0", optional = true }
 
 [features]
-default = []
+default = ["serde-default"]
+## Enables several text file formats for serialization and deserialization
+serde-default = ["msgpack"]
 ## Exposes ALTRIOS structs, methods, and functions to Python.
 pyo3 = ["dep:pyo3"]
+## Enables message pack serialization and deserialization via `rmp-serde`
+msgpack = ["dep:rmp-serde"]
 
 [lints.rust]
 # `'cfg(debug_advance_rewind)'` is expected for debugging in `advance_rewind.rs`
diff --git a/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs b/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
index 9038724..575b9da 100644
--- a/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
+++ b/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
@@ -71,6 +71,30 @@ pub(crate) fn altrios_api(attr: TokenStream, item: TokenStream) -> TokenStream {
             Self::from_yaml(yaml_str)
         }
 
+        /// Write (serialize) an object to a message pack
+        #[cfg(feature = "msgpack")]
+        #[pyo3(name = "to_msg_pack")]
+        // TODO: figure from Kyle out how to use `PyIOError`
+        pub fn to_msg_pack_py(&self) -> anyhow::Result<Vec<u8>> {
+            self.to_msg_pack()
+        }
+
+        /// Read (deserialize) an object from a message pack
+        ///
+        /// # Arguments
+        /// * `msg_pack`: message pack
+        #[cfg(feature = "msgpack")]
+        #[staticmethod]
+        #[pyo3(name = "from_msg_pack")]
+        #[pyo3(signature = (msg_pack, skip_init=None))]
+        // TODO: figure from Kyle out how to use `PyIOError`
+        pub fn from_msg_pack_py(msg_pack: &Bound<PyBytes>, skip_init: Option<bool>) -> anyhow::Result<Self> {
+            Self::from_msg_pack(
+                msg_pack.as_bytes(), 
+                skip_init.unwrap_or_default()
+            )
+        }
+
         /// See [SerdeAPI::to_bincode]
         #[pyo3(name = "to_bincode")]
         fn to_bincode_py<'py>(&self, py: Python<'py>) -> PyResult<Vec<u8>> {
diff --git a/rust/altrios-core/src/traits.rs b/rust/altrios-core/src/traits.rs
index 51225a7..be167ed 100644
--- a/rust/altrios-core/src/traits.rs
+++ b/rust/altrios-core/src/traits.rs
@@ -249,6 +249,27 @@ pub trait SerdeAPI: Serialize + for<'a> Deserialize<'a> {
         Ok(serde_yaml::to_string(&self)?)
     }
 
+    /// Write (serialize) an object to a message pack
+    #[cfg(feature = "msgpack")]
+    fn to_msg_pack(&self) -> anyhow::Result<Vec<u8>> {
+        Ok(rmp_serde::encode::to_vec_named(&self)?)
+    }
+
+    /// Read (deserialize) an object from a message pack
+    ///
+    /// # Arguments
+    ///
+    /// * `msg_pack` - message pack object
+    ///
+    #[cfg(feature = "msgpack")]
+    fn from_msg_pack(msg_pack: &[u8], skip_init: bool) -> anyhow::Result<Self> {
+        let mut msg_pack_de: Self = rmp_serde::decode::from_slice(msg_pack)?;
+        if !skip_init {
+            msg_pack_de.init()?;
+        }
+        Ok(msg_pack_de)
+    }
+
     /// Read (deserialize) an object from a YAML string
     ///
     /// # Arguments

From dc759760577da115b7ac9cc144d6f02ca348fbea Mon Sep 17 00:00:00 2001
From: Chad Baker <chad.baker@nrel.gov>
Date: Tue, 14 Jan 2025 17:13:13 -0700
Subject: [PATCH 03/11] msg_pack is doing weird things with lists. need to try
 `PyBytes`

---
 python/altrios/__init__.py         | 50 +++++++++++++++++++-----------
 python/altrios/tests/test_serde.py |  1 +
 2 files changed, 33 insertions(+), 18 deletions(-)
 create mode 100644 python/altrios/tests/test_serde.py

diff --git a/python/altrios/__init__.py b/python/altrios/__init__.py
index 3008811..950a324 100644
--- a/python/altrios/__init__.py
+++ b/python/altrios/__init__.py
@@ -105,20 +105,21 @@ def variable_path_list_from_py_objs(
     
     return key_paths
 
-def history_path_list(self, element_as_list:bool=False) -> List[str]:
+def history_path_list(self, element_as_list: bool = False) -> List[str]:
     """
     Returns a list of relative paths to all history variables (all variables
     that contain history as a subpath). 
-    See example usage in `altrios/demo_data/demo_variable_paths.py`.
+    See example usage in `fastsim/demos/demo_variable_paths.py`.
 
     # Arguments
     - `element_as_list`: if True, each element is itself a list of the path elements
     """
-    item_str = lambda item: item if not element_as_list else ".".join(item)
-    history_path_list = [
-        item for item in self.variable_path_list(
-            element_as_list=element_as_list) if "history" in item_str(item)
-    ]
+    var_paths = self.variable_path_list(element_as_list=element_as_list)
+    history_path_list = []
+    for key in var_paths:
+        if (("history" in key_as_str(key)) or is_cyc_key(key)):
+            history_path_list.append(key)
+
     return history_path_list
             
 # TODO connect to crate features
@@ -186,29 +187,42 @@ def from_pydict(cls, pydict: Dict, data_fmt: str = "msg_pack") -> Self:
 
     return obj
 
-def to_dataframe(self, pandas:bool=False) -> [pd.DataFrame, pl.DataFrame, pl.LazyFrame]:
+def to_dataframe(self, pandas: bool = False, allow_partial: bool = False) -> Union[pd.DataFrame, pl.DataFrame]:
     """
-    Returns time series results from altrios object as a Polars or Pandas dataframe.
+    Returns time series results from fastsim object as a Polars or Pandas dataframe.
 
     # Arguments
     - `pandas`: returns pandas dataframe if True; otherwise, returns polars dataframe by default
+    - `allow_partial`: returns dataframe of length equal to solved time steps if simulation fails early
     """
-    obj_dict = self.to_pydict()
-    history_paths = self.history_path_list(element_as_list=True)   
+    obj_dict = self.to_pydict(flatten=False)
+    history_paths = self.history_path_list(element_as_list=True)
     cols = [".".join(hp) for hp in history_paths]
     vals = []
     for hp in history_paths:
-        obj:Union[dict|list] = obj_dict
+        obj: Union[dict | list] = obj_dict
         for elem in hp:
-            try: 
+            try:
                 obj = obj[elem]
-            except:
-                obj = obj[int(elem)]
+            except Exception:
+                try:
+                    obj = obj[int(elem)]
+                except Exception as err:
+                    raise err
         vals.append(obj)
-    if not pandas:
-        df = pl.DataFrame({col: val for col, val in zip(cols, vals)})
+    if allow_partial:
+        cutoff = min([len(val) for val in vals])
+        if not pandas:
+            df = pl.DataFrame({col: val[:cutoff]
+                              for col, val in zip(cols, vals)})
+        else:
+            df = pd.DataFrame({col: val[:cutoff]
+                              for col, val in zip(cols, vals)})
     else:
-        df = pd.DataFrame({col: val for col, val in zip(cols, vals)})
+        if not pandas:
+            df = pl.DataFrame({col: val for col, val in zip(cols, vals)})
+        else:
+            df = pd.DataFrame({col: val for col, val in zip(cols, vals)})
     return df
 
 # adds variable_path_list() and history_path_list() as methods to all classes in
diff --git a/python/altrios/tests/test_serde.py b/python/altrios/tests/test_serde.py
new file mode 100644
index 0000000..761750c
--- /dev/null
+++ b/python/altrios/tests/test_serde.py
@@ -0,0 +1 @@
+# TODO: populate this, e.g. with equivalent from fastsim-3

From 7ef3d7c7166a1ef86a7562eed7a1a103ffe5634c Mon Sep 17 00:00:00 2001
From: Chad Baker <chad.baker@nrel.gov>
Date: Wed, 15 Jan 2025 14:02:07 -0700
Subject: [PATCH 04/11] PyBytes fixed `to_msg_pack_py`

---
 rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs b/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
index 575b9da..3753259 100644
--- a/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
+++ b/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
@@ -75,8 +75,8 @@ pub(crate) fn altrios_api(attr: TokenStream, item: TokenStream) -> TokenStream {
         #[cfg(feature = "msgpack")]
         #[pyo3(name = "to_msg_pack")]
         // TODO: figure from Kyle out how to use `PyIOError`
-        pub fn to_msg_pack_py(&self) -> anyhow::Result<Vec<u8>> {
-            self.to_msg_pack()
+        pub fn to_msg_pack_py<'py>(&self, py: Python<'py>) -> anyhow::Result<Bound<'py, PyBytes>> {
+            Ok(PyBytes::new_bound(py, &self.to_msg_pack()?))
         }
 
         /// Read (deserialize) an object from a message pack

From cb47708f38cf4e534745d90aef1385dd12594c7f Mon Sep 17 00:00:00 2001
From: Chad Baker <chad.baker@nrel.gov>
Date: Wed, 15 Jan 2025 14:02:36 -0700
Subject: [PATCH 05/11] tidying up

---
 rust/altrios-core/Cargo.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rust/altrios-core/Cargo.toml b/rust/altrios-core/Cargo.toml
index 9dfff66..7dd3f70 100644
--- a/rust/altrios-core/Cargo.toml
+++ b/rust/altrios-core/Cargo.toml
@@ -13,6 +13,7 @@ rust-version = { workspace = true }
 [dependencies]
 csv = "1.1.6"
 serde = { version = "1.0.136", features = ["derive"] }
+rmp-serde = { version = "1.3.0", optional = true }
 serde_yaml = "0.8.23"
 serde_json = "1.0"
 uom = { workspace = true, features = ["use_serde"] }
@@ -54,7 +55,6 @@ eng_fmt = { workspace = true }
 directories = "5.0.1"
 tempfile = "3.10.1"
 derive_more = { version = "1.0.0", features = ["from_str", "from", "is_variant", "try_into"] }
-rmp-serde = { version = "1.3.0", optional = true }
 
 [features]
 default = ["serde-default"]

From 93d067c1044fc6f3497e9aeb84f6148b44d3c235 Mon Sep 17 00:00:00 2001
From: Chad Baker <chad.baker@nrel.gov>
Date: Wed, 15 Jan 2025 14:07:30 -0700
Subject: [PATCH 06/11] all tests pass

---
 python/altrios/__init__.py | 70 ++++++++++++++++----------------------
 1 file changed, 30 insertions(+), 40 deletions(-)

diff --git a/python/altrios/__init__.py b/python/altrios/__init__.py
index 950a324..fe855bb 100644
--- a/python/altrios/__init__.py
+++ b/python/altrios/__init__.py
@@ -105,23 +105,22 @@ def variable_path_list_from_py_objs(
     
     return key_paths
 
-def history_path_list(self, element_as_list: bool = False) -> List[str]:
+def history_path_list(self, element_as_list:bool=False) -> List[str]:
     """
     Returns a list of relative paths to all history variables (all variables
     that contain history as a subpath). 
-    See example usage in `fastsim/demos/demo_variable_paths.py`.
+    See example usage in `altrios/demo_data/demo_variable_paths.py`.
 
     # Arguments
     - `element_as_list`: if True, each element is itself a list of the path elements
     """
-    var_paths = self.variable_path_list(element_as_list=element_as_list)
-    history_path_list = []
-    for key in var_paths:
-        if (("history" in key_as_str(key)) or is_cyc_key(key)):
-            history_path_list.append(key)
-
-    return history_path_list
-            
+    item_str = lambda item: item if not element_as_list else ".".join(item)
+    history_path_list = [
+        item for item in self.variable_path_list(
+            element_as_list=element_as_list) if "history" in item_str(item)
+    ]
+    return history_path_list            
+
 # TODO connect to crate features
 data_formats = [
     'yaml',
@@ -160,69 +159,60 @@ def to_pydict(self, data_fmt: str = "msg_pack", flatten: bool = False) -> Dict:
         return next(iter(pd.json_normalize(pydict, sep=".").to_dict(orient='records')))
 
 @classmethod
-def from_pydict(cls, pydict: Dict, data_fmt: str = "msg_pack") -> Self:
+def from_pydict(cls, pydict: Dict, data_fmt: str = "msg_pack", skip_init: bool = True) -> Self:
     """
     Instantiates Self from pure python dictionary 
     # Arguments
     - `pydict`: dictionary to be converted to ALTRIOS object
-    - `data_fmt`: data format for intermediate conversion step
+    - `data_fmt`: data format for intermediate conversion step  
+    - `skip_init`: passed to `SerdeAPI` methods to control whether initialization
+      is skipped
     """
     data_fmt = data_fmt.lower()
     assert data_fmt in data_formats, f"`data_fmt` must be one of {data_formats}"
     match data_fmt.lower():
         case "yaml":
             import yaml
-            obj = cls.from_yaml(yaml.dump(pydict), skip_init=False)
+            obj = cls.from_yaml(yaml.dump(pydict), skip_init=skip_init)
         case "msg_pack":
             import msgpack
             try:
-                obj = cls.from_msg_pack(msgpack.packb(pydict))
+                obj = cls.from_msg_pack(
+                    msgpack.packb(pydict), skip_init=skip_init)
             except Exception as err:
                 print(
                     f"{err}\nFalling back to YAML.")
-                obj = cls.from_pydict(pydict, data_fmt="yaml")
+                obj = cls.from_pydict(
+                    pydict, data_fmt="yaml", skip_init=skip_init)
         case "json":
             from json import dumps
-            obj = cls.from_json(dumps(pydict))
+            obj = cls.from_json(dumps(pydict), skip_init=skip_init)
 
     return obj
 
-def to_dataframe(self, pandas: bool = False, allow_partial: bool = False) -> Union[pd.DataFrame, pl.DataFrame]:
+def to_dataframe(self, pandas:bool=False) -> [pd.DataFrame, pl.DataFrame, pl.LazyFrame]:
     """
-    Returns time series results from fastsim object as a Polars or Pandas dataframe.
+    Returns time series results from altrios object as a Polars or Pandas dataframe.
 
     # Arguments
     - `pandas`: returns pandas dataframe if True; otherwise, returns polars dataframe by default
-    - `allow_partial`: returns dataframe of length equal to solved time steps if simulation fails early
     """
-    obj_dict = self.to_pydict(flatten=False)
-    history_paths = self.history_path_list(element_as_list=True)
+    obj_dict = self.to_pydict()
+    history_paths = self.history_path_list(element_as_list=True)   
     cols = [".".join(hp) for hp in history_paths]
     vals = []
     for hp in history_paths:
-        obj: Union[dict | list] = obj_dict
+        obj:Union[dict|list] = obj_dict
         for elem in hp:
-            try:
+            try: 
                 obj = obj[elem]
-            except Exception:
-                try:
-                    obj = obj[int(elem)]
-                except Exception as err:
-                    raise err
+            except:
+                obj = obj[int(elem)]
         vals.append(obj)
-    if allow_partial:
-        cutoff = min([len(val) for val in vals])
-        if not pandas:
-            df = pl.DataFrame({col: val[:cutoff]
-                              for col, val in zip(cols, vals)})
-        else:
-            df = pd.DataFrame({col: val[:cutoff]
-                              for col, val in zip(cols, vals)})
+    if not pandas:
+        df = pl.DataFrame({col: val for col, val in zip(cols, vals)})
     else:
-        if not pandas:
-            df = pl.DataFrame({col: val for col, val in zip(cols, vals)})
-        else:
-            df = pd.DataFrame({col: val for col, val in zip(cols, vals)})
+        df = pd.DataFrame({col: val for col, val in zip(cols, vals)})
     return df
 
 # adds variable_path_list() and history_path_list() as methods to all classes in

From 65d857ab7ca5b74d140e9996cc88385947d40b7e Mon Sep 17 00:00:00 2001
From: Chad Baker <chad.baker@nrel.gov>
Date: Wed, 15 Jan 2025 14:54:37 -0700
Subject: [PATCH 07/11] borrowed lot of code from fastsim-3

---
 python/altrios/altrios_pyo3.pyi               |   2 +-
 python/altrios/demos/sim_manager_demo.py      |   2 +-
 .../altrios/demos/version_migration_demo.py   |   4 +-
 python/altrios/rollout.py                     |   4 +-
 python/altrios/tests/test_serde.py            | 123 +++++++++++++++++-
 python/altrios/train_planner.py               |   2 +-
 .../src/altrios_api/mod.rs                    |  44 +++++--
 .../powertrain/electric_drivetrain.rs         |   2 +-
 .../locomotive/powertrain/fuel_converter.rs   |   2 +-
 .../locomotive/powertrain/generator.rs        |   2 +-
 .../powertrain/reversible_energy_storage.rs   |   2 +-
 rust/altrios-core/src/meet_pass/dispatch.rs   |   2 +-
 .../src/meet_pass/train_disp/mod.rs           |   4 +-
 rust/altrios-core/src/track/link/link_impl.rs |  15 ++-
 .../src/train/set_speed_train_sim.rs          |   4 +-
 .../src/train/speed_limit_train_sim.rs        |   2 +-
 rust/altrios-core/src/traits.rs               |  42 +++---
 17 files changed, 205 insertions(+), 53 deletions(-)

diff --git a/python/altrios/altrios_pyo3.pyi b/python/altrios/altrios_pyo3.pyi
index a41835a..45f6948 100644
--- a/python/altrios/altrios_pyo3.pyi
+++ b/python/altrios/altrios_pyo3.pyi
@@ -16,7 +16,7 @@ class SerdeAPI(object):
     @classmethod
     def from_yaml(cls) -> Self: ...
     @classmethod
-    def from_file(cls) -> Self: ...
+    def from_file(cls, skip_init=false) -> Self: ...
     def to_file(self): ...
     def to_bincode(self) -> bytes: ...
     def to_json(self) -> str: ...
diff --git a/python/altrios/demos/sim_manager_demo.py b/python/altrios/demos/sim_manager_demo.py
index 65d99b3..48327a2 100644
--- a/python/altrios/demos/sim_manager_demo.py
+++ b/python/altrios/demos/sim_manager_demo.py
@@ -23,7 +23,7 @@
 t0_import = time.perf_counter()
 t0_total = time.perf_counter()
 
-rail_vehicles=[alt.RailVehicle.from_file(vehicle_file) 
+rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=false) 
                for vehicle_file in Path(alt.resources_root() / "rolling_stock/").glob('*.yaml')]
 
 location_map = alt.import_locations(alt.resources_root() / "networks/default_locations.csv")
diff --git a/python/altrios/demos/version_migration_demo.py b/python/altrios/demos/version_migration_demo.py
index 8f83e47..8170548 100644
--- a/python/altrios/demos/version_migration_demo.py
+++ b/python/altrios/demos/version_migration_demo.py
@@ -13,8 +13,8 @@ def migrate_network() -> Tuple[alt.Network, alt.Network]:
     old_network_path = alt.resources_root() / "networks/Taconite_v0.1.6.yaml"
     new_network_path = alt.resources_root() / "networks/Taconite.yaml"
 
-    network_from_old = alt.Network.from_file(old_network_path)
-    network_from_new = alt.Network.from_file(new_network_path)
+    network_from_old = alt.Network.from_file(old_network_path, skip_init=false)
+    network_from_new = alt.Network.from_file(new_network_path, skip_init=false)
 
     # `network_from_old` could be used to overwrite the file in the new format with 
     # ```
diff --git a/python/altrios/rollout.py b/python/altrios/rollout.py
index 6e8b430..edcd8fe 100644
--- a/python/altrios/rollout.py
+++ b/python/altrios/rollout.py
@@ -59,13 +59,13 @@ def simulate_prescribed_rollout(
         else:
             demand_paths.append(demand_file)
 
-    rail_vehicles=[alt.RailVehicle.from_file(vehicle_file) 
+    rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=false) 
                 for vehicle_file in Path(alt.resources_root() / "rolling_stock/").glob('*.yaml')]
 
     location_map = alt.import_locations(
         str(alt.resources_root() / "networks/default_locations.csv")
     )
-    network = alt.Network.from_file(network_filename_path)
+    network = alt.Network.from_file(network_filename_path, skip_init=false)
     sim_days = defaults.SIMULATION_DAYS
     scenarios = []
     for idx, scenario_year in enumerate(years):
diff --git a/python/altrios/tests/test_serde.py b/python/altrios/tests/test_serde.py
index 761750c..768aae0 100644
--- a/python/altrios/tests/test_serde.py
+++ b/python/altrios/tests/test_serde.py
@@ -1 +1,122 @@
-# TODO: populate this, e.g. with equivalent from fastsim-3
+import time
+import altrios as alt
+
+SAVE_INTERVAL = 100
+def get_solved_speed_limit_train_sim():
+    # Build the train config
+    rail_vehicle_loaded = alt.RailVehicle.from_file(
+        alt.resources_root() / "rolling_stock/Manifest_Loaded.yaml")
+    rail_vehicle_empty = alt.RailVehicle.from_file(
+        alt.resources_root() / "rolling_stock/Manifest_Empty.yaml")
+
+    # https://docs.rs/altrios-core/latest/altrios_core/train/struct.TrainConfig.html
+    train_config = alt.TrainConfig(
+        rail_vehicles=[rail_vehicle_loaded, rail_vehicle_empty],
+        n_cars_by_type={
+            "Manifest_Loaded": 50,
+            "Manifest_Empty": 50,
+        },
+        train_length_meters=None,
+        train_mass_kilograms=None,
+    )
+
+    # Build the locomotive consist model
+    # instantiate battery model
+    # https://docs.rs/altrios-core/latest/altrios_core/consist/locomotive/powertrain/reversible_energy_storage/struct.ReversibleEnergyStorage.html#
+    res = alt.ReversibleEnergyStorage.from_file(
+        alt.resources_root() / "powertrains/reversible_energy_storages/Kokam_NMC_75Ah_flx_drive.yaml"
+    )
+
+    edrv = alt.ElectricDrivetrain(
+        pwr_out_frac_interp=[0., 1.],
+        eta_interp=[0.98, 0.98],
+        pwr_out_max_watts=5e9,
+        save_interval=SAVE_INTERVAL,
+    )
+
+    bel: alt.Locomotive = alt.Locomotive.build_battery_electric_loco(
+        reversible_energy_storage=res,
+        drivetrain=edrv,
+        loco_params=alt.LocoParams.from_dict(dict(
+            pwr_aux_offset_watts=8.55e3,
+            pwr_aux_traction_coeff_ratio=540.e-6,
+            force_max_newtons=667.2e3,
+        )))
+
+    # construct a vector of one BEL and several conventional locomotives
+    loco_vec = [bel.clone()] + [alt.Locomotive.default()] * 7
+    # instantiate consist
+    loco_con = alt.Consist(
+        loco_vec
+    )
+
+    # Instantiate the intermediate `TrainSimBuilder`
+    tsb = alt.TrainSimBuilder(
+        train_id="0",
+        origin_id="A",
+        destination_id="B",
+        train_config=train_config,
+        loco_con=loco_con,
+    )
+
+    # Load the network and construct the timed link path through the network.
+    network = alt.Network.from_file(
+        alt.resources_root() / 'networks/simple_corridor_network.yaml')
+
+    location_map = alt.import_locations(
+        alt.resources_root() / "networks/simple_corridor_locations.csv")
+    train_sim: alt.SetSpeedTrainSim = tsb.make_speed_limit_train_sim(
+        location_map=location_map,
+        save_interval=1,
+    )
+    train_sim.set_save_interval(SAVE_INTERVAL)
+    est_time_net, _consist = alt.make_est_times(train_sim, network)
+
+    timed_link_path = alt.run_dispatch(
+        network,
+        alt.SpeedLimitTrainSimVec([train_sim]),
+        [est_time_net],
+        False,
+        False,
+    )[0]
+
+    train_sim.walk_timed_path(
+        network=network,
+        timed_path=timed_link_path,
+    )
+    assert len(train_sim.history) > 1
+
+    return train_sim
+
+
+def test_pydict():
+    ts = get_solved_speed_limit_train_sim()
+
+    t0 = time.perf_counter_ns()
+    ts_dict_msg = ts.to_pydict(flatten=False, data_fmt="msg_pack")
+    ts_msg = alt.SpeedLimitTrainSim.from_pydict(
+        ts_dict_msg, data_fmt="msg_pack")
+    t1 = time.perf_counter_ns()
+    t_msg = t1 - t0
+    print(f"\nElapsed time for MessagePack: {t_msg:.3e} ns ")
+
+    t0 = time.perf_counter_ns()
+    ts_dict_yaml = ts.to_pydict(flatten=False, data_fmt="yaml")
+    ts_yaml = alt.SpeedLimitTrainSim.from_pydict(ts_dict_yaml, data_fmt="yaml")
+    t1 = time.perf_counter_ns()
+    t_yaml = t1 - t0
+    print(f"Elapsed time for YAML: {t_yaml:.3e} ns ")
+    print(f"YAML time per MessagePack time: {(t_yaml / t_msg):.3e} ")
+
+    t0 = time.perf_counter_ns()
+    ts_dict_json = ts.to_pydict(flatten=False, data_fmt="json")
+    _ts_json = alt.SpeedLimitTrainSim.from_pydict(
+        ts_dict_json, data_fmt="json")
+    t1 = time.perf_counter_ns()
+    t_json = t1 - t0
+    print(f"Elapsed time for json: {t_json:.3e} ns ")
+    print(f"JSON time per MessagePack time: {(t_json / t_msg):.3e} ")
+
+    # `to_yaml` is probably needed because of NAN variables
+    assert ts_msg == ts
+    assert ts_yaml == ts
diff --git a/python/altrios/train_planner.py b/python/altrios/train_planner.py
index e8165e6..7279d89 100644
--- a/python/altrios/train_planner.py
+++ b/python/altrios/train_planner.py
@@ -1129,7 +1129,7 @@ def run_train_planner(
 
 if __name__ == "__main__":
 
-    rail_vehicles=[alt.RailVehicle.from_file(vehicle_file) 
+    rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=false) 
                 for vehicle_file in Path(alt.resources_root() / "rolling_stock/").glob('*.yaml')]
 
     location_map = alt.import_locations(
diff --git a/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs b/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
index 3753259..521d6bc 100644
--- a/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
+++ b/rust/altrios-core/altrios-proc-macros/src/altrios_api/mod.rs
@@ -38,11 +38,18 @@ pub(crate) fn altrios_api(attr: TokenStream, item: TokenStream) -> TokenStream {
             self.to_str(format)
         }
 
-        /// See [SerdeAPI::from_str]
+        /// Read (deserialize) an object from a string
+        ///
+        /// # Arguments:
+        ///
+        /// * `contents`: `str` - The string containing the object data
+        /// * `format`: `str` - The source format, any of those listed in [`ACCEPTED_STR_FORMATS`](`SerdeAPI::ACCEPTED_STR_FORMATS`)
+        ///
         #[staticmethod]
         #[pyo3(name = "from_str")]
-        pub fn from_str_py(contents: &str, format: &str) -> anyhow::Result<Self> {
-            Self::from_str(contents, format)
+        #[pyo3(signature = (contents, format, skip_init=None))]
+        pub fn from_str_py(contents: &str, format: &str, skip_init: Option<bool>) -> PyResult<Self> {
+            Ok(SerdeAPI::from_str(contents, format, skip_init.unwrap_or_default())?)
         }
 
         /// See [SerdeAPI::to_json]
@@ -51,11 +58,17 @@ pub(crate) fn altrios_api(attr: TokenStream, item: TokenStream) -> TokenStream {
             self.to_json()
         }
 
-        /// See [SerdeAPI::from_json]
+        /// Read (deserialize) an object from a JSON string
+        ///
+        /// # Arguments
+        ///
+        /// * `json_str`: `str` - JSON-formatted string to deserialize from
+        ///
         #[staticmethod]
         #[pyo3(name = "from_json")]
-        fn from_json_py(json_str: &str) -> anyhow::Result<Self> {
-            Self::from_json(json_str)
+        #[pyo3(signature = (json_str, skip_init=None))]
+        pub fn from_json_py(json_str: &str, skip_init: Option<bool>) -> PyResult<Self> {
+            Ok(Self::from_json(json_str, skip_init.unwrap_or_default())?)
         }
 
         /// See [SerdeAPI::to_yaml]
@@ -64,11 +77,17 @@ pub(crate) fn altrios_api(attr: TokenStream, item: TokenStream) -> TokenStream {
             self.to_yaml()
         }
 
-        /// See [SerdeAPI::from_yaml]
+        /// Read (deserialize) an object from a YAML string
+        ///
+        /// # Arguments
+        ///
+        /// * `yaml_str`: `str` - YAML-formatted string to deserialize from
+        ///
         #[staticmethod]
         #[pyo3(name = "from_yaml")]
-        fn from_yaml_py(yaml_str: &str) -> anyhow::Result<Self> {
-            Self::from_yaml(yaml_str)
+        #[pyo3(signature = (yaml_str, skip_init=None))]
+        pub fn from_yaml_py(yaml_str: &str, skip_init: Option<bool>) -> PyResult<Self> {
+            Ok(Self::from_yaml(yaml_str, skip_init.unwrap_or_default())?)
         }
 
         /// Write (serialize) an object to a message pack
@@ -160,14 +179,15 @@ pub(crate) fn altrios_api(attr: TokenStream, item: TokenStream) -> TokenStream {
             ///
             #[staticmethod]
             #[pyo3(name = "from_file")]
-            pub fn from_file_py(filepath: &Bound<PyAny>) -> anyhow::Result<Self> {
-                Self::from_file(PathBuf::extract_bound(filepath)?)
+            #[pyo3(signature = (filepath, skip_init=None))]
+            pub fn from_file_py(filepath: &Bound<PyAny>, skip_init: Option<bool>) -> PyResult<Self> {
+                Ok(Self::from_file(PathBuf::extract_bound(filepath)?, skip_init.unwrap_or_default())?)
             }
         }
     };
     let mut final_output = TokenStream2::default();
     final_output.extend::<TokenStream2>(quote! {
-        #[cfg_attr(feature="pyo3", pyclass(module="altrios_pyo3", subclass))]
+        #[cfg_attr(feature="pyo3", pyclass(module="altrios_pyo3", subclass, eq))]
     });
     let mut output: TokenStream2 = ast.to_token_stream();
     output.extend(impl_block);
diff --git a/rust/altrios-core/src/consist/locomotive/powertrain/electric_drivetrain.rs b/rust/altrios-core/src/consist/locomotive/powertrain/electric_drivetrain.rs
index 15665c3..a38dddb 100644
--- a/rust/altrios-core/src/consist/locomotive/powertrain/electric_drivetrain.rs
+++ b/rust/altrios-core/src/consist/locomotive/powertrain/electric_drivetrain.rs
@@ -250,7 +250,7 @@ impl Default for ElectricDrivetrain {
     fn default() -> Self {
         // let file_contents = include_str!(EDRV_DEFAULT_PATH_STR);
         let file_contents = include_str!("electric_drivetrain.default.yaml");
-        Self::from_yaml(file_contents).unwrap()
+        Self::from_yaml(file_contents, false).unwrap()
     }
 }
 
diff --git a/rust/altrios-core/src/consist/locomotive/powertrain/fuel_converter.rs b/rust/altrios-core/src/consist/locomotive/powertrain/fuel_converter.rs
index cdff62a..c611db6 100644
--- a/rust/altrios-core/src/consist/locomotive/powertrain/fuel_converter.rs
+++ b/rust/altrios-core/src/consist/locomotive/powertrain/fuel_converter.rs
@@ -84,7 +84,7 @@ pub struct FuelConverter {
 impl Default for FuelConverter {
     fn default() -> Self {
         let file_contents = include_str!("fuel_converter.default.yaml");
-        Self::from_yaml(file_contents).unwrap()
+        Self::from_yaml(file_contents, false).unwrap()
     }
 }
 
diff --git a/rust/altrios-core/src/consist/locomotive/powertrain/generator.rs b/rust/altrios-core/src/consist/locomotive/powertrain/generator.rs
index ed10c4e..356f825 100644
--- a/rust/altrios-core/src/consist/locomotive/powertrain/generator.rs
+++ b/rust/altrios-core/src/consist/locomotive/powertrain/generator.rs
@@ -306,7 +306,7 @@ impl Generator {
 impl Default for Generator {
     fn default() -> Self {
         let file_contents = include_str!("generator.default.yaml");
-        Self::from_yaml(file_contents).unwrap()
+        Self::from_yaml(file_contents, false).unwrap()
     }
 }
 
diff --git a/rust/altrios-core/src/consist/locomotive/powertrain/reversible_energy_storage.rs b/rust/altrios-core/src/consist/locomotive/powertrain/reversible_energy_storage.rs
index 18f28db..0e1c843 100644
--- a/rust/altrios-core/src/consist/locomotive/powertrain/reversible_energy_storage.rs
+++ b/rust/altrios-core/src/consist/locomotive/powertrain/reversible_energy_storage.rs
@@ -197,7 +197,7 @@ pub struct ReversibleEnergyStorage {
 impl Default for ReversibleEnergyStorage {
     fn default() -> Self {
         let file_contents = include_str!("reversible_energy_storage.default.yaml");
-        let mut res = Self::from_yaml(file_contents).unwrap();
+        let mut res = Self::from_yaml(file_contents, false).unwrap();
         res.state.soc = res.max_soc;
         res
     }
diff --git a/rust/altrios-core/src/meet_pass/dispatch.rs b/rust/altrios-core/src/meet_pass/dispatch.rs
index e7a9f5b..7b3573d 100644
--- a/rust/altrios-core/src/meet_pass/dispatch.rs
+++ b/rust/altrios-core/src/meet_pass/dispatch.rs
@@ -304,7 +304,7 @@ mod test_dispatch {
         let network_file_path = project_root::get_project_root()
             .unwrap()
             .join("../python/altrios/resources/networks/Taconite.yaml");
-        let network = Network::from_file(network_file_path).unwrap();
+        let network = Network::from_file(network_file_path, false).unwrap();
 
         let train_sims = vec![
             crate::train::speed_limit_train_sim_fwd(),
diff --git a/rust/altrios-core/src/meet_pass/train_disp/mod.rs b/rust/altrios-core/src/meet_pass/train_disp/mod.rs
index 0263992..4ebe48d 100644
--- a/rust/altrios-core/src/meet_pass/train_disp/mod.rs
+++ b/rust/altrios-core/src/meet_pass/train_disp/mod.rs
@@ -223,7 +223,7 @@ mod test_train_disp {
         let network_file_path = project_root::get_project_root()
             .unwrap()
             .join("../python/altrios/resources/networks/Taconite.yaml");
-        let network = Network::from_file(network_file_path).unwrap();
+        let network = Network::from_file(network_file_path, false).unwrap();
 
         let speed_limit_train_sim = crate::train::speed_limit_train_sim_fwd();
         let est_times = make_est_times(speed_limit_train_sim.clone(), network)
@@ -248,7 +248,7 @@ mod test_train_disp {
         let network_file_path = project_root::get_project_root()
             .unwrap()
             .join("../python/altrios/resources/networks/Taconite.yaml");
-        let network = Network::from_file(network_file_path).unwrap();
+        let network = Network::from_file(network_file_path, false).unwrap();
 
         let speed_limit_train_sim = crate::train::speed_limit_train_sim_rev();
         let est_times = make_est_times(speed_limit_train_sim.clone(), network)
diff --git a/rust/altrios-core/src/track/link/link_impl.rs b/rust/altrios-core/src/track/link/link_impl.rs
index 11a2f75..d822561 100644
--- a/rust/altrios-core/src/track/link/link_impl.rs
+++ b/rust/altrios-core/src/track/link/link_impl.rs
@@ -310,22 +310,22 @@ impl ObjState for Network {
 }
 
 impl SerdeAPI for Network {
-    fn from_file<P: AsRef<Path>>(filepath: P) -> anyhow::Result<Self> {
+    fn from_file<P: AsRef<Path>>(filepath: P, skip_init: bool) -> anyhow::Result<Self> {
         let filepath = filepath.as_ref();
         let extension = filepath
             .extension()
             .and_then(OsStr::to_str)
             .with_context(|| format!("File extension could not be parsed: {filepath:?}"))?;
-        let file = File::open(filepath).with_context(|| {
+        let mut file = File::open(filepath).with_context(|| {
             if !filepath.exists() {
                 format!("File not found: {filepath:?}")
             } else {
                 format!("Could not open file: {filepath:?}")
             }
         })?;
-        let mut network = match Self::from_reader(file, extension) {
+        let mut network = match Self::from_reader(&mut file, extension, skip_init) {
             Ok(network) => network,
-            Err(err) => NetworkOld::from_file(filepath)
+            Err(err) => NetworkOld::from_file(filepath, false)
                 .map_err(|old_err| {
                     anyhow!("\nattempting to load as `Network`:\n{}\nattempting to load as `NetworkOld`:\n{}", err, old_err)
                 })?
@@ -617,7 +617,10 @@ mod tests {
         let tempdir = tempfile::tempdir().unwrap();
         let temp_file_path = tempdir.path().join("links_test2.yaml");
         links.to_file(temp_file_path.clone()).unwrap();
-        assert_eq!(Vec::<Link>::from_file(temp_file_path).unwrap(), links);
+        assert_eq!(
+            Vec::<Link>::from_file(temp_file_path, false).unwrap(),
+            links
+        );
         tempdir.close().unwrap();
     }
 
@@ -626,7 +629,7 @@ mod tests {
         let network_file_path = project_root::get_project_root()
             .unwrap()
             .join("../python/altrios/resources/networks/Taconite.yaml");
-        let network_speed_sets = Network::from_file(network_file_path).unwrap();
+        let network_speed_sets = Network::from_file(network_file_path, false).unwrap();
         let mut network_speed_set = network_speed_sets.clone();
         network_speed_set
             .set_speed_set_for_train_type(TrainType::Freight)
diff --git a/rust/altrios-core/src/train/set_speed_train_sim.rs b/rust/altrios-core/src/train/set_speed_train_sim.rs
index 3e063ef..1b15d74 100644
--- a/rust/altrios-core/src/train/set_speed_train_sim.rs
+++ b/rust/altrios-core/src/train/set_speed_train_sim.rs
@@ -205,11 +205,11 @@ pub struct SpeedTraceElement {
         save_interval: Option<usize>,
     ) -> Self {
         let path_tpc = match path_tpc_file {
-            Some(file) => PathTpc::from_file(file).unwrap(),
+            Some(file) => PathTpc::from_file(file, false).unwrap(),
             None => PathTpc::valid()
         };
         let train_res = match train_res_file {
-            Some(file) => TrainRes::from_file(file).unwrap(),
+            Some(file) => TrainRes::from_file(file, false).unwrap(),
             None => TrainRes::valid()
         };
 
diff --git a/rust/altrios-core/src/train/speed_limit_train_sim.rs b/rust/altrios-core/src/train/speed_limit_train_sim.rs
index 9e4e70a..e9cfe43 100644
--- a/rust/altrios-core/src/train/speed_limit_train_sim.rs
+++ b/rust/altrios-core/src/train/speed_limit_train_sim.rs
@@ -101,7 +101,7 @@ impl From<&Vec<LinkIdxTime>> for TimedLinkPath {
 
     #[pyo3(name = "extend_path")]
     pub fn extend_path_py(&mut self, network_file_path: String, link_path: Vec<LinkIdx>) -> anyhow::Result<()> {
-        let network = Vec::<Link>::from_file(network_file_path).unwrap();
+        let network = Vec::<Link>::from_file(network_file_path, false).unwrap();
 
         self.extend_path(&network, &link_path)?;
         Ok(())
diff --git a/rust/altrios-core/src/traits.rs b/rust/altrios-core/src/traits.rs
index be167ed..81afe4f 100644
--- a/rust/altrios-core/src/traits.rs
+++ b/rust/altrios-core/src/traits.rs
@@ -150,20 +150,20 @@ pub trait SerdeAPI: Serialize + for<'a> Deserialize<'a> {
     ///
     /// * `filepath`: The filepath from which to read the object
     ///
-    fn from_file<P: AsRef<Path>>(filepath: P) -> anyhow::Result<Self> {
+    fn from_file<P: AsRef<Path>>(filepath: P, skip_init: bool) -> anyhow::Result<Self> {
         let filepath = filepath.as_ref();
         let extension = filepath
             .extension()
             .and_then(OsStr::to_str)
             .with_context(|| format!("File extension could not be parsed: {filepath:?}"))?;
-        let file = File::open(filepath).with_context(|| {
+        let mut file = File::open(filepath).with_context(|| {
             if !filepath.exists() {
                 format!("File not found: {filepath:?}")
             } else {
                 format!("Could not open file: {filepath:?}")
             }
         })?;
-        Self::from_reader(file, extension)
+        Self::from_reader(&mut file, extension, skip_init)
     }
 
     /// Write (serialize) an object into a string
@@ -190,11 +190,11 @@ pub trait SerdeAPI: Serialize + for<'a> Deserialize<'a> {
     /// * `contents` - The string containing the object data
     /// * `format` - The source format, any of those listed in [`ACCEPTED_STR_FORMATS`](`SerdeAPI::ACCEPTED_STR_FORMATS`)
     ///
-    fn from_str<S: AsRef<str>>(contents: S, format: &str) -> anyhow::Result<Self> {
+    fn from_str<S: AsRef<str>>(contents: S, format: &str, skip_init: bool) -> anyhow::Result<Self> {
         Ok(
             match format.trim_start_matches('.').to_lowercase().as_str() {
-                "yaml" | "yml" => Self::from_yaml(contents)?,
-                "json" => Self::from_json(contents)?,
+                "yaml" | "yml" => Self::from_yaml(contents, skip_init)?,
+                "json" => Self::from_json(contents, skip_init)?,
                 _ => bail!(
                     "Unsupported format {format:?}, must be one of {:?}",
                     Self::ACCEPTED_STR_FORMATS
@@ -210,20 +210,24 @@ pub trait SerdeAPI: Serialize + for<'a> Deserialize<'a> {
     /// * `rdr` - The reader from which to read object data
     /// * `format` - The source format, any of those listed in [`ACCEPTED_BYTE_FORMATS`](`SerdeAPI::ACCEPTED_BYTE_FORMATS`)
     ///
-    fn from_reader<R>(rdr: R, format: &str) -> anyhow::Result<Self>
-    where
-        R: std::io::Read,
-    {
+    fn from_reader<R: std::io::Read>(
+        rdr: &mut R,
+        format: &str,
+        skip_init: bool,
+    ) -> anyhow::Result<Self> {
         let mut deserialized: Self = match format.trim_start_matches('.').to_lowercase().as_str() {
             "yaml" | "yml" => serde_yaml::from_reader(rdr)?,
             "json" => serde_json::from_reader(rdr)?,
-            "bin" => bincode::deserialize_from(rdr)?,
+            #[cfg(feature = "msgpack")]
+            "msgpack" => rmp_serde::decode::from_read(rdr)?,
             _ => bail!(
                 "Unsupported format {format:?}, must be one of {:?}",
                 Self::ACCEPTED_BYTE_FORMATS
             ),
         };
-        deserialized.init()?;
+        if !skip_init {
+            deserialized.init()?;
+        }
         Ok(deserialized)
     }
 
@@ -232,15 +236,17 @@ pub trait SerdeAPI: Serialize + for<'a> Deserialize<'a> {
         Ok(serde_json::to_string(&self)?)
     }
 
-    /// Read (deserialize) an object to a JSON string
+    /// Read (deserialize) an object from a JSON string
     ///
     /// # Arguments
     ///
     /// * `json_str` - JSON-formatted string to deserialize from
     ///
-    fn from_json<S: AsRef<str>>(json_str: S) -> anyhow::Result<Self> {
+    fn from_json<S: AsRef<str>>(json_str: S, skip_init: bool) -> anyhow::Result<Self> {
         let mut json_de: Self = serde_json::from_str(json_str.as_ref())?;
-        json_de.init()?;
+        if !skip_init {
+            json_de.init()?;
+        }
         Ok(json_de)
     }
 
@@ -276,9 +282,11 @@ pub trait SerdeAPI: Serialize + for<'a> Deserialize<'a> {
     ///
     /// * `yaml_str` - YAML-formatted string to deserialize from
     ///
-    fn from_yaml<S: AsRef<str>>(yaml_str: S) -> anyhow::Result<Self> {
+    fn from_yaml<S: AsRef<str>>(yaml_str: S, skip_init: bool) -> anyhow::Result<Self> {
         let mut yaml_de: Self = serde_yaml::from_str(yaml_str.as_ref())?;
-        yaml_de.init()?;
+        if !skip_init {
+            yaml_de.init()?;
+        }
         Ok(yaml_de)
     }
 

From 6aa951bf5b57753a5f4a183a9df69549304a6a84 Mon Sep 17 00:00:00 2001
From: Chad Baker <chad.baker@nrel.gov>
Date: Wed, 15 Jan 2025 15:32:26 -0700
Subject: [PATCH 08/11] all tests pass

---
 python/altrios/altrios_pyo3.pyi                     | 2 +-
 python/altrios/demos/sim_manager_demo.py            | 2 +-
 python/altrios/demos/version_migration_demo.py      | 4 ++--
 python/altrios/rollout.py                           | 4 ++--
 python/altrios/tests/test_serde.py                  | 9 ++++++---
 python/altrios/train_planner.py                     | 2 +-
 rust/altrios-core/src/consist/consist_model.rs      | 2 +-
 rust/altrios-core/src/consist/consist_utils.rs      | 1 +
 rust/altrios-core/src/track/link/speed/speed_set.rs | 2 +-
 9 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/python/altrios/altrios_pyo3.pyi b/python/altrios/altrios_pyo3.pyi
index 45f6948..f6cbd04 100644
--- a/python/altrios/altrios_pyo3.pyi
+++ b/python/altrios/altrios_pyo3.pyi
@@ -16,7 +16,7 @@ class SerdeAPI(object):
     @classmethod
     def from_yaml(cls) -> Self: ...
     @classmethod
-    def from_file(cls, skip_init=false) -> Self: ...
+    def from_file(cls, skip_init=False) -> Self: ...
     def to_file(self): ...
     def to_bincode(self) -> bytes: ...
     def to_json(self) -> str: ...
diff --git a/python/altrios/demos/sim_manager_demo.py b/python/altrios/demos/sim_manager_demo.py
index 48327a2..f197573 100644
--- a/python/altrios/demos/sim_manager_demo.py
+++ b/python/altrios/demos/sim_manager_demo.py
@@ -23,7 +23,7 @@
 t0_import = time.perf_counter()
 t0_total = time.perf_counter()
 
-rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=false) 
+rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=False) 
                for vehicle_file in Path(alt.resources_root() / "rolling_stock/").glob('*.yaml')]
 
 location_map = alt.import_locations(alt.resources_root() / "networks/default_locations.csv")
diff --git a/python/altrios/demos/version_migration_demo.py b/python/altrios/demos/version_migration_demo.py
index 8170548..0c05936 100644
--- a/python/altrios/demos/version_migration_demo.py
+++ b/python/altrios/demos/version_migration_demo.py
@@ -13,8 +13,8 @@ def migrate_network() -> Tuple[alt.Network, alt.Network]:
     old_network_path = alt.resources_root() / "networks/Taconite_v0.1.6.yaml"
     new_network_path = alt.resources_root() / "networks/Taconite.yaml"
 
-    network_from_old = alt.Network.from_file(old_network_path, skip_init=false)
-    network_from_new = alt.Network.from_file(new_network_path, skip_init=false)
+    network_from_old = alt.Network.from_file(old_network_path, skip_init=False)
+    network_from_new = alt.Network.from_file(new_network_path, skip_init=False)
 
     # `network_from_old` could be used to overwrite the file in the new format with 
     # ```
diff --git a/python/altrios/rollout.py b/python/altrios/rollout.py
index edcd8fe..f841dde 100644
--- a/python/altrios/rollout.py
+++ b/python/altrios/rollout.py
@@ -59,13 +59,13 @@ def simulate_prescribed_rollout(
         else:
             demand_paths.append(demand_file)
 
-    rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=false) 
+    rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=False) 
                 for vehicle_file in Path(alt.resources_root() / "rolling_stock/").glob('*.yaml')]
 
     location_map = alt.import_locations(
         str(alt.resources_root() / "networks/default_locations.csv")
     )
-    network = alt.Network.from_file(network_filename_path, skip_init=false)
+    network = alt.Network.from_file(network_filename_path, skip_init=False)
     sim_days = defaults.SIMULATION_DAYS
     scenarios = []
     for idx, scenario_year in enumerate(years):
diff --git a/python/altrios/tests/test_serde.py b/python/altrios/tests/test_serde.py
index 768aae0..d9d5c0b 100644
--- a/python/altrios/tests/test_serde.py
+++ b/python/altrios/tests/test_serde.py
@@ -117,6 +117,9 @@ def test_pydict():
     print(f"Elapsed time for json: {t_json:.3e} ns ")
     print(f"JSON time per MessagePack time: {(t_json / t_msg):.3e} ")
 
-    # `to_yaml` is probably needed because of NAN variables
-    assert ts_msg == ts
-    assert ts_yaml == ts
+    # `to_pydict` is necessary because of some funkiness with direct equality comparison
+    assert ts_msg.to_pydict() == ts.to_pydict()
+    assert ts_yaml.to_pydict() == ts.to_pydict()
+
+if __name__ == "__main__":
+    test_pydict()
diff --git a/python/altrios/train_planner.py b/python/altrios/train_planner.py
index 7279d89..e906c21 100644
--- a/python/altrios/train_planner.py
+++ b/python/altrios/train_planner.py
@@ -1129,7 +1129,7 @@ def run_train_planner(
 
 if __name__ == "__main__":
 
-    rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=false) 
+    rail_vehicles=[alt.RailVehicle.from_file(vehicle_file, skip_init=False) 
                 for vehicle_file in Path(alt.resources_root() / "rolling_stock/").glob('*.yaml')]
 
     location_map = alt.import_locations(
diff --git a/rust/altrios-core/src/consist/consist_model.rs b/rust/altrios-core/src/consist/consist_model.rs
index bbfa809..e175f80 100644
--- a/rust/altrios-core/src/consist/consist_model.rs
+++ b/rust/altrios-core/src/consist/consist_model.rs
@@ -58,7 +58,7 @@ use super::*;
         );
     }
 
-    fn get_hct(&self) -> String {
+    fn get_pdct(&self) -> String {
         // make a `describe` function
         match &self.pdct {
             PowerDistributionControlType::RESGreedy(val) => format!("{val:?}"),
diff --git a/rust/altrios-core/src/consist/consist_utils.rs b/rust/altrios-core/src/consist/consist_utils.rs
index 13f669b..3a6055d 100644
--- a/rust/altrios-core/src/consist/consist_utils.rs
+++ b/rust/altrios-core/src/consist/consist_utils.rs
@@ -267,6 +267,7 @@ impl SolvePower for FrontAndBack {
         todo!() // not needed urgently
     }
 }
+
 /// Variants of this enum are used to determine what control strategy gets used for distributing
 /// power required from or delivered to during negative tractive power each locomotive.
 #[derive(PartialEq, Clone, Deserialize, Serialize, Debug, SerdeAPI)]
diff --git a/rust/altrios-core/src/track/link/speed/speed_set.rs b/rust/altrios-core/src/track/link/speed/speed_set.rs
index 4498aff..ca50786 100644
--- a/rust/altrios-core/src/track/link/speed/speed_set.rs
+++ b/rust/altrios-core/src/track/link/speed/speed_set.rs
@@ -5,7 +5,7 @@ use std::collections::HashMap;
 
 #[derive(Debug, Default, Clone, Copy, Serialize, Deserialize, PartialEq, Eq, SerdeAPI, Hash)]
 #[repr(u8)]
-#[cfg_attr(feature = "pyo3", pyclass(eq, eq_int))]
+#[cfg_attr(feature = "pyo3", pyclass(eq))]
 /// Enum with variants representing train types
 pub enum TrainType {
     #[default]

From 41753e9168ad534a6d7d13eacf427649f7edea56 Mon Sep 17 00:00:00 2001
From: Chad Baker <calbaker@users.noreply.github.com>
Date: Wed, 15 Jan 2025 16:47:31 -0700
Subject: [PATCH 09/11] Update pyproject.toml

Bumped minimum python version
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 28d3299..32ea8b1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ authors = [
 description = "Tool for modeling and optimization of advanced locomotive powertrains for freight rail decarbonization."
 readme = "README.md"
 license = { file = "LICENSE.md" }
-requires-python = ">=3.9, <3.12"
+requires-python = ">=3.10, <3.12"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: BSD License",

From 228c21527ae71d6273223ca73616c11571e5a656 Mon Sep 17 00:00:00 2001
From: Chad Baker <calbaker@users.noreply.github.com>
Date: Wed, 15 Jan 2025 16:48:55 -0700
Subject: [PATCH 10/11] Update py-tests.yaml

Bumped minimum python version
---
 .github/workflows/py-tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/py-tests.yaml b/.github/workflows/py-tests.yaml
index 0e46f53..16dcf92 100644
--- a/.github/workflows/py-tests.yaml
+++ b/.github/workflows/py-tests.yaml
@@ -26,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11']
 
     env:
       PYTHON: ${{ matrix.python-version }}

From 47df893e151c381024ae76acc1afbf7b07c7055b Mon Sep 17 00:00:00 2001
From: Chad Baker <calbaker@users.noreply.github.com>
Date: Wed, 15 Jan 2025 16:50:05 -0700
Subject: [PATCH 11/11] Update wheels.yaml

Bumped minimum python version
---
 .github/workflows/wheels.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/wheels.yaml b/.github/workflows/wheels.yaml
index 2e23a88..03d2dfb 100644
--- a/.github/workflows/wheels.yaml
+++ b/.github/workflows/wheels.yaml
@@ -21,7 +21,6 @@ jobs:
           - macos
           - windows
         python-version:
-          - "9"
           - "10"
           - "11"
         include:
@@ -36,7 +35,7 @@ jobs:
       - name: set up python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
 
       - name: set up rust
         if: matrix.os != 'ubuntu'