Fix Sphinx API documentation warnings

docs/source/conf.py

@@ -39,6 +39,7 @@
 add_module_names = False
 autodoc_member_order = "bysource"
 napoleon_google_docstring = True
+napoleon_use_ivar = True
 autodoc_default_options = {"member-order": "bysource", "undoc-members": True}
 nb_execution_mode = "off"
 

src/pyprobound/aggregate.py

@@ -76,7 +76,7 @@ def components(self) -> Iterator[Binding]:
         yield self.binding
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "Contribution.unfreezable" = "all") -> None:
         if parameter in ("activity", "all") and self.train_activity:
             if torch.isneginf(self.log_activity):
                 raise ValueError(
@@ -216,7 +216,7 @@ def _contributing(self) -> Iterator[Contribution]:
                 yield ctrb
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "Aggregate.unfreezable" = "all") -> None:
         if parameter in ("concentration", "all"):
             if self.train_concentration:
                 self.log_target_concentration.requires_grad_()

src/pyprobound/base.py

@@ -310,7 +310,7 @@ def freeze(self) -> None:
         for p in self.parameters():
             p.requires_grad_(False)
 
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "Component.unfreezable" = "all") -> None:
         """Turns on gradient calculation for the specified parameter.
 
         Args:

src/pyprobound/cooperativity.py

@@ -177,7 +177,7 @@ def components(self) -> Iterator[Component]:
         return iter(())
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "Spacing.unfreezable" = "all") -> None:
         if parameter in ("spacing", "all"):
             self.log_spacing.requires_grad_()
         if parameter != "spacing":
@@ -672,7 +672,7 @@ def check_length_consistency(self) -> None:
                 )
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "Cooperativity.unfreezable" = "all") -> None:
         if parameter in ("hill", "all") and self.train_hill:
             self.log_hill.requires_grad_()
         if parameter in ("posbias", "all") and self.train_posbias:

src/pyprobound/layers/conv0d.py

@@ -175,7 +175,7 @@ def check_length_consistency(self) -> None:
             )
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "Conv0d.unfreezable" = "all") -> None:
         if parameter in ("posbias", "all") and self.train_posbias:
             self.log_posbias.requires_grad_()
         if parameter != "posbias":

src/pyprobound/layers/conv1d.py

@@ -29,8 +29,10 @@ class Conv1d(Layer):
     :math:`-\log K^{rel}_{\text{D}}` of each sliding window.
 
     .. math::
+
             \log \frac{1}{K^{rel}_{\text{D}, a} (S_{i, x})}
             = \omega(x) + \sum_{\phi} \beta_\phi \mathbb{1}_\phi(S_{i, x})
+
     where :math:`\mathbb{1}_\phi(S_{i, x})` is the indicator function of when
     window :math:`x` of sequence :math:`i` contains feature :math:`\phi`.
 
@@ -298,7 +300,7 @@ def check_length_consistency(self) -> None:
             )
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "Conv1d.unfreezable" = "all") -> None:
         if parameter in ("posbias", "all") and self.train_posbias:
             self.log_posbias.requires_grad_()
         if parameter != "posbias":

src/pyprobound/layers/psam.py

@@ -426,7 +426,7 @@ def _seed(
                     torch.nn.init.constant_(parameter, val)
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "PSAM.unfreezable" = "all") -> None:
         if self.train_betas:
             if parameter in ("monomer", "pairwise", "all"):
                 if self.train_bias:

src/pyprobound/mode.py

@@ -301,7 +301,7 @@ def check_length_consistency(self) -> None:
                 )
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "Mode.unfreezable" = "all") -> None:
         if parameter in ("hill", "all") and self.train_hill:
             self.log_hill.requires_grad_()
         if parameter != "hill":

src/pyprobound/rounds.py

@@ -117,7 +117,7 @@ def __setattr__(self, name: str, value: Any) -> None:
     def components(self) -> Iterator[Aggregate]: ...
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "BaseRound.unfreezable" = "all") -> None:
         if parameter in ("depth", "all") and self.train_depth:
             self.log_depth.requires_grad_()
         if parameter != "depth":
@@ -532,7 +532,7 @@ def from_binding(
         )
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(self, parameter: "RhoGammaRound.unfreezable" = "all") -> None:
         if parameter in ("rho", "all"):
             self.rho.requires_grad_()
             self.gamma.requires_grad_()
@@ -683,7 +683,9 @@ def from_binding(
         )
 
     @override
-    def unfreeze(self, parameter: unfreezable = "all") -> None:
+    def unfreeze(
+        self, parameter: "ExponentialRound.unfreezable" = "all"
+    ) -> None:
         if parameter in ("delta", "all") and self.train_delta:
             self.delta.requires_grad_()
         if parameter != "delta":