Refact component type

docs/examples/PINT_walkthrough.md

@@ -6,7 +6,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.2'
-      jupytext_version: 1.4.1
+      jupytext_version: 1.4.0
   kernelspec:
     display_name: Python 3
     language: python

docs/examples/build_model_from_scratch.md

@@ -6,7 +6,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.2'
-      jupytext_version: 1.4.1
+      jupytext_version: 1.4.0
   kernelspec:
     display_name: Python 3
     language: python
@@ -84,7 +84,7 @@ tm = TimingModel("NGC6400E", component_instances)
 
 To view all the components in `TimingModel` instance, we can use the property `.components`, which returns a dictionary (name as the key, component instance as the value).
 
-Internally, the components are stored in a list(ordered list, you will see why this is important below) according to their types. All the delay type of components (subclasses of `DelayComponent` class) are stored in the `DelayComponent_list`, and the phase type of components (subclasses of `PhaseComponent` class) in the `PhaseComponent_list`.
+Internally, the components are stored in the `.model_sectors`, a dictionary with the component type name as the key and `ModelSector` subclasses as the value. `ModelSector` class also have the methods to collect results from each component. For instance, `DelaySector` has `delay()` that compute the total delay from all the `DelayComponent` objects and `PhaseSector` has `phase()` for total phase. But these methods can be accessed from the `TimingModel` class. 
 
 ```python
 # print the components in the timing model
@@ -100,10 +100,10 @@ for (cp_name, cp_instance) in tm.components.items():
 * `TimingModel.params()`               : List all the parameters in the timing model from all components.
 * `TimingModel.setup()`                : Setup the components (e.g., register the derivatives).
 * `TimingModel.validate()`             : Validate the components see if the parameters are setup properly.
-* `TimingModel.delay()`                : Compute the total delay.
-* `TimingModel.phase()`                : Compute the total phase.
-* `TimingModel.delay_funcs()`          : List all the delay functions from all the delay components.
-* `TimingModel.phase_funcs()`          : List all the phase functions from all the phase components.
+* `TimingModel.delay()`                : Compute the total delay, if DelayComponent exists.
+* `TimingModel.phase()`                : Compute the total phase, if PhaseComponent exists.
+* `TimingModel.delay_funcs()`          : List all the delay functions from all the delay components, if DelayComponent exists.
+* `TimingModel.phase_funcs()`          : List all the phase functions from all the phase components, if DelayComponent exists.
 * `TimingModel.get_component_type()`   : Get all the components from one category
 * `TimingModel.map_component()`        : Get the component location. It returns the component's instance, order in                                          the list, host list and its type.
 * `TimingModel.get_params_mapping()`   : Report which component each parameter comes from.
@@ -201,10 +201,10 @@ print("All components in timing model:")
 display(tm.components)
 
 print("\n")
-print("Delay components in the DelayComponent_list (order matters!):")
+print("Delay components in the DelayComponent sector (order matters!):")
 
 # print the delay component order, dispersion should be after the astrometry
-display(tm.DelayComponent_list)
+display(tm.model_sectors['DelayComponent'].component_list)
 ```
 
 The DM value can be set as we set the parameters above.

docs/examples/understanding_timing_models.md

@@ -6,7 +6,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.2'
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+      jupytext_version: 1.4.0
   kernelspec:
     display_name: Python 3
     language: python
@@ -56,12 +56,12 @@ The TimingModel class stores lists of the delay model components and phase compo
 
 ```python
 # When this list gets printed, it shows the parameters that are associated with each component as well.
-m.DelayComponent_list
+m.model_sectors['DelayComponent'].component_list
 ```
 
 ```python
 # Now let's look at the phase components. These include the absolute phase, the spindown model, and phase jumps
-m.PhaseComponent_list
+m.model_sectors['PhaseComponent'].component_list
 ```
 
 We can add a component to an existing model
@@ -82,7 +82,7 @@ m.add_component(a, validate=False)
 ```
 
 ```python
-m.DelayComponent_list  # The new instance is added to delay component list
+m.model_sectors['DelayComponent'].component_list  # The new instance is added to delay component list
 ```
 
 There are two ways to remove a component from a model. This simplest is to use the `remove_component` method to remove it by name.
@@ -112,7 +112,7 @@ from_list.remove(component)
 ```
 
 ```python
-m.DelayComponent_list  # AstrometryEcliptic has been removed from delay list.
+m.model_sectors['DelayComponent'].component_list  # AstrometryEcliptic has been removed from delay list.
 ```
 
 To switch the order of a component, just change the order of the component list
@@ -121,7 +121,7 @@ To switch the order of a component, just change the order of the component list
 
 ```python
 # Let's look at the order of the components in the delay list first
-_ = [print(dc.__class__) for dc in m.DelayComponent_list]
+_ = [print(dc.__class__) for dc in m.model_sectors['DelayComponent'].component_list]
 ```
 
 ```python
@@ -133,7 +133,7 @@ from_list[order], from_list[new_order] = from_list[new_order], from_list[order]
 
 ```python
 # Print the classes to see the order switch
-_ = [print(dc.__class__) for dc in m.DelayComponent_list]
+_ = [print(dc.__class__) for dc in m.model_sectors['DelayComponent'].component_list]
 ```
 
 Delays are always computed in the order of the DelayComponent_list
@@ -181,3 +181,7 @@ for comp, tp in Component.component_types.items():
 
 special
 ```
+
+```python
+
+```

src/pint/fitter.py

@@ -743,6 +743,7 @@ def fit_toas(self, maxiter=1, threshold=False, full_cov=False):
         accuracy where they both can be applied.
         """
         chi2 = 0
+        has_noise_model = "NoiseComponent" in self.model.component_types
         for i in range(max(maxiter, 1)):
             fitp = self.get_fitparams()
             fitpv = self.get_fitparams_num()
@@ -758,8 +759,12 @@ def fit_toas(self, maxiter=1, threshold=False, full_cov=False):
 
             # get any noise design matrices and weight vectors
             if not full_cov:
-                Mn = self.model.noise_model_designmatrix(self.toas)
-                phi = self.model.noise_model_basis_weight(self.toas)
+                if has_noise_model:
+                    Mn = self.model.noise_model_designmatrix(self.toas)
+                    phi = self.model.noise_model_basis_weight(self.toas)
+                else:
+                    Mn = None
+                    phi = None
                 phiinv = np.zeros(M.shape[1])
                 if Mn is not None and phi is not None:
                     phiinv = np.concatenate((phiinv, 1 / phi))
@@ -844,7 +849,10 @@ def fit_toas(self, maxiter=1, threshold=False, full_cov=False):
 
             # Compute the noise realizations if possible
             if not full_cov:
-                noise_dims = self.model.noise_model_dimensions(self.toas)
+                if has_noise_model:
+                    noise_dims = self.model.noise_model_dimensions(self.toas)
+                else:
+                    noise_dims = {}
                 noise_resids = {}
                 for comp in noise_dims.keys():
                     p0 = noise_dims[comp][0] + ntmpar

src/pint/models/__init__.py

@@ -27,6 +27,7 @@
     "StandardTimingModel",
     [AstrometryEquatorial(), Spindown(), DispersionDM(), SolarSystemShapiro()],
 )
+
 # BTTimingModel = generate_timing_model("BTTimingModel",
 #         (Astrometry, Spindown, Dispersion, SolarSystemShapiro, BT))
 # DDTimingModel = generate_timing_model("DDTimingModel",