Change API docs links and readme following repo move (#156)

* update links to page deployements

* change message about examples

CHANGELOG.md

@@ -40,9 +40,9 @@ refers to `DeterministicGlobalWorkspace`.
 # 0.5.0
 * Replace loss coef buffers by a `LossCoef` TypedDict.
 * Add
-  [`RepeatedDataset`](https://bdvllrs.github.io/shimmer/shimmer/dataset.html#RepeatedDataset)
+  [`RepeatedDataset`](https://ruflab.github.io/shimmer/shimmer/dataset.html#RepeatedDataset)
   to shimmer.
-* Add docs in `docs/`, API documentation in https://bdvllrs.github.io/shimmer/, and
+* Add docs in `docs/`, API documentation in https://ruflab.github.io/shimmer/, and
     some code examples.
 * Replace Black, isort, and flake8 with Ruff (see
       https://github.com/bdvllrs/shimmer/pull/8).
@@ -65,9 +65,9 @@ refers to `DeterministicGlobalWorkspace`.
 * Rename all "with_uncertainty" methods to "bayesian". Note, BayesianGlobalWorkspaces
   are still a work in progress.
 * Added selection mechanisms (inheriting from `SelectionBase`, [see
-  docs](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/selection.html#SelectionBase))
+  docs](https://ruflab.github.io/shimmer/latest/shimmer/modules/selection.html#SelectionBase))
   to fuse representations according to different mechanisms (e.g. Attention).
 * `GlobalWorkspace` (and associated `GWModule`, `GWLosses`, ...) now uses the
-  [`RandomSelection`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/selection.html#RandomSelection)
+  [`RandomSelection`](https://ruflab.github.io/shimmer/latest/shimmer/modules/selection.html#RandomSelection)
   mechanism. For the old behavior, use
-  [`GlobalWorkspace2Domains`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspace2Domains).
+  [`GlobalWorkspace2Domains`](https://ruflab.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspace2Domains).

README.md

@@ -6,9 +6,8 @@ This repository is the barebones API to build a global workspace.
 ## Install
 See [Installation instructions](docs/installation.md).
 
-## Examples
-You can find code examples in the `examples` folder. Each subfolder is a different
-example.
+## Example
+You can find a code example in the `examples` folder.
 
 ## Tutorial
 You can also follow a tutorial on the basics of shimmer [here](docs/shimmer_basics.md).
@@ -17,7 +16,7 @@ You can also find some additional information in the [Q&A](docs/q_and_a.md).
 
 ## API Documentation
 The full API documentation is available here:
-[https://bdvllrs.github.io/shimmer/](https://bdvllrs.github.io/shimmer/).
+[https://ruflab.github.io/shimmer/](https://ruflab.github.io/shimmer/).
 
 # Contributing
 See [CONTRIBUTING.md](CONTRIBUTING.md).

docs/q_and_a.md

@@ -1,7 +1,7 @@
 # Q&A
 
 ## How can I customize my GlobalWorkspace
-[`GlobalWorkspaceBase`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspaceBase) 
+[`GlobalWorkspaceBase`](https://ruflab.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspaceBase) 
 is a very generic implementation of the global workspace and uses different building
 blocks (given as arguments) to function:
 * **gw_mod**: a class implementation of `GWModuleBase` which defines how to encode, 
@@ -14,32 +14,32 @@ Different implementations have been made to initialize the Global Workspace more
 but you may need to implement a new one if you have very specific needs.
 
 To get insipiration, you can look at the source code of
-[`GlobalWorkspace`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspace).
+[`GlobalWorkspace`](https://ruflab.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspace).
 
 ## How can I change the loss function?
 If you are using pre-made GW architecture
-([`GlobalWorkspace`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspace),
-[`GlobalWorkspaceBayesian`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspaceBayesian),
-[`GlobalWorkspaceFusion`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspaceFusion)) and want to update the loss
+([`GlobalWorkspace`](https://ruflab.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspace),
+[`GlobalWorkspaceBayesian`](https://ruflab.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspaceBayesian),
+[`GlobalWorkspaceFusion`](https://ruflab.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspaceFusion)) and want to update the loss
 used for demi-cycles, cycles, translations or broadcast, you can do so directly from
 your definition of the
-[`DomainModule`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule.compute_loss)
+[`DomainModule`](https://ruflab.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule.compute_loss)
 when defining the `compute_loss` method.
 
 You also can have different losses for demi-cycles, cycles, ... by implementing
 the corresponding methods
-([`compute_dcy_loss`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule.compute_dcy_loss),
-[`compute_tr_loss`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule.compute_tr_loss), ...).
+([`compute_dcy_loss`](https://ruflab.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule.compute_dcy_loss),
+[`compute_tr_loss`](https://ruflab.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule.compute_tr_loss), ...).
 
 You can use your own contrastive loss function by passing it as an argument to the
 `GlobalWorkspace` class with the `contrastive_loss` loss argument.
 
 If you have more specific needs, like change how the different loss interact, or
 completely replace the loss combination we provide, you will need to implement a new
 Loss Module inheriting from
-[`GWLossesBase`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/losses.html#GWLossesBase).
+[`GWLossesBase`](https://ruflab.github.io/shimmer/latest/shimmer/modules/losses.html#GWLossesBase).
 Then, you can create a new implementation of
-[`GlobalWorkspaceBase`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspaceBase)
+[`GlobalWorkspaceBase`](https://ruflab.github.io/shimmer/latest/shimmer/modules/global_workspace.html#GlobalWorkspaceBase)
 (see section "How can I customize my GlobalWorkspace" for more details.)
 
 

docs/shimmer_basics.md

@@ -13,7 +13,7 @@ to make a GW in shimmer:
 ![architecture](assets/shimmer_architecture.png)
 
 Let's detail:
-- [`DomainModule`](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule)s
+- [`DomainModule`](https://ruflab.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule)s
     are the individual domain modules which encode domain data into a latent vector;
 - the `GWModule` has access to the domain modules, and defines how to encode, decode and merge representations of the domains into a unique GW representation.
 - finally `GlobalWorkspaceBase` takes all building blocks to make a [Pytorch Lightning](https://lightning.ai/docs/pytorch/stable/) module
@@ -87,7 +87,7 @@ class DomainDataModule(LightningDataModule):
 Now that our data module is defined, let's create `DomainModule`s.
 
 ## `DomainModule`
-For more details about DomainModules, see the [DomainModule API docs](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule).
+For more details about DomainModules, see the [DomainModule API docs](https://ruflab.github.io/shimmer/latest/shimmer/modules/domain.html#DomainModule).
 The `DomainModule` class extends from a LightningModule and requires you to define some
 methods:
 
@@ -422,7 +422,7 @@ class GenericDomain(DomainModule):
         return LossOutput(loss=F.mse_loss(pred, target))
 ```
 
-To learn more about LossOutput, see [API docs](https://bdvllrs.github.io/shimmer/latest/shimmer/modules/domain.html#LossOutput).
+To learn more about LossOutput, see [API docs](https://ruflab.github.io/shimmer/latest/shimmer/modules/domain.html#LossOutput).
 
 ## Let's make a GW!