DOC: Use more canonical links in docs

skipci

Author: cortadocodes

docs/authentication.md

@@ -8,7 +8,7 @@ Authentication is provided by a GCP service account.
 ## Creating a service account
 
 By setting up your Twined service network with the
-[Twined Terraform modules](/deploying_services), a set of maintainer service accounts have already been
+[Twined Terraform modules](core_concepts/deploying_services.md), a set of maintainer service accounts have already been
 created with the required permissions. These will have names starting with `maintainer-`.
 
 ## Using a service account

docs/core_concepts/asking_questions.md

@@ -21,7 +21,7 @@ to a child for processing/analysis. Questions can be:
     or custom logic in your own webserver.
 
 Questions are always asked to a _revision_ of a service. You can ask a
-service a question if you have its [SRUID](../services/#service-names), project ID, and the necessary permissions.
+service a question if you have its [SRUID](services.md/#service-names), project ID, and the necessary permissions.
 
 ## Asking a question
 
@@ -49,7 +49,7 @@ answer["output_manifest"]["my_dataset"].files
 
     If you're using an environment other than the `main` environment, then before asking any questions to your Twined
     services, set the `TWINED_SERVICES_TOPIC_NAME` environment variable to the name of the Twined services Pub/Sub topic
-    (this is set when [deploying a service network](../deploying_services/#deploying-services-advanced-developers-guide).
+    (this is set when [deploying a service network](deploying_services.md).
     It will be in the form `<environment-name>.octue.twined.services`
 
 !!! note
@@ -242,10 +242,10 @@ at once instead of one after another.
 ## Asking a question within a service
 
 If you have
-[created your own Twined service](../creating_services) and want to ask children questions, you can do this more
+[created your own Twined service](creating_services.md) and want to ask children questions, you can do this more
 easily than above. Children are accessible from the `analysis` object by
 the keys you give them in the
-[service configuration](../creating_services/#octueyaml) file. For example, you can ask an `elevation` service a
+[service configuration](creating_services.md/#octueyaml) file. For example, you can ask an `elevation` service a
 question like this:
 
 ```python
@@ -314,7 +314,7 @@ you want it to use (dynamic children) to the
 children will instead go to the dynamic children. Note that:
 
 - You must provide the children in the same format as they're provided
-  in the [service configuration](../../core_concepts/creating_services/#octueyaml)
+  in the [service configuration](../core_concepts/creating_services.md/#octueyaml)
 - If you override one static child, you must override others, too
 - The dynamic children must have the same keys as the static children
   (so the child knows which service to ask which questions)

docs/core_concepts/creating_services.md

@@ -16,12 +16,12 @@ A Twined service is defined by the following files (located in the repository ro
 
 ### app.py
 
-This is the entrypoint into your code - read more [here](../creating_apps).
+This is the entrypoint into your code - read more [here](creating_apps.md).
 
 ### twine.json
 
-This file defines the schema for the service's configuration, input, and output data. Read more [here](../twines) and
-see an example [here](../twine_file_quickstart).
+This file defines the schema for the service's configuration, input, and output data. Read more [here](twines.md) and
+see an example [here](twine_file_quickstart.md).
 
 ### Dependencies file
 
@@ -98,7 +98,7 @@ are supported.
 
 ### Where to specify the namespace, name, and revision tag
 
-See [here](../services/#service-names) for service naming requirements.
+See [here](services.md/#service-names) for service naming requirements.
 
 **Namespace**
 
@@ -149,4 +149,4 @@ Automated deployment with Octue means:
   other services are sent to it, meaning there are minimal costs to
   having it deployed but not in use.
 
-If you'd like help deploying services, [contact us](../../support). To do it yourself, see [here](../deploying_services).
+If you'd like help deploying services, [contact us](../support.md). To do it yourself, see [here](deploying_services.md).

docs/core_concepts/available_filters.md renamed to docs/core_concepts/data_containers/available_filters.md

@@ -51,7 +51,7 @@ Datafile content isn't downloaded until you:
 - Call its `download` method
 - Use its `local_path` property
 
-Read more about downloading files [here](../../downloading_datafiles).
+Read more about downloading files [here](downloading_datafiles.md).
 
 ### CLI command friendly
 

docs/core_concepts/data_containers/datafiles.md

@@ -202,7 +202,7 @@ dataset.files.filter(extension="csv", labels__contains="a")
 >>> <FilterSet({<Datafile('my_file.csv')>})>
 ```
 
-For the full list of available filters, [click here](../../available_filters).
+For the full list of available filters, [click here](available_filters.md).
 
 ### Order datasets
 

docs/core_concepts/data_containers/datasets.md

@@ -3,7 +3,7 @@
 One of the main features of Twined is making using, creating, and
 sharing scientific datasets easy. There are three main data classes that do this:
 
-- **Datafile** - [a single local or cloud file](datafiles) and its metadata.
-- **Dataset** - [a set of related datafiles](datasets) that exist in the same location, plus metadata.
-- **Manifest** - [a set of related datasets](manifests) that exist anywhere, plus metadata. Typically produced by or for
+- **Datafile** - [a single local or cloud file](datafiles.md) and its metadata.
+- **Dataset** - [a set of related datafiles](datasets.md) that exist in the same location, plus metadata.
+- **Manifest** - [a set of related datasets](manifests.md) that exist anywhere, plus metadata. Typically produced by or for
   one analysis.

docs/core_concepts/data_containers/index.md

@@ -2,7 +2,7 @@
 
 !!! tip
 
-    Use a manifest to send [datasets](../datasets) to a Twined service as a question (for processing) - the
+    Use a manifest to send [datasets](datasets.md) to a Twined service as a question (for processing) - the
     service will send an output manifest back with its answer if the answer includes output datasets.
 
 ## Key features
@@ -39,7 +39,7 @@ child = Child(
 answer, question_uuid = child.ask(input_manifest=manifest)
 ```
 
-See [here](../../asking_questions) for more information.
+See [here](../asking_questions.md) for more information.
 
 ### Receive datasets from a service
 

docs/core_concepts/data_containers/manifests.md

@@ -42,7 +42,7 @@ done automatically:
   including automated pre-deployment testing and creation of a GitHub
   release
 
-You can now [ask your service some questions](../asking_questions)! It will be available in the service network as
+You can now [ask your service some questions](asking_questions.md)! It will be available in the service network as
 `<namespace>/<name>:<version>` (e.g. `octue/example-service-kueue:0.1.1`).
 
 ## Deploying the infrastructure

docs/core_concepts/deploying_services.md

@@ -13,7 +13,7 @@ processing). You can:
 ### Via the CLI
 
 1.  Ensure you've created a valid
-    [`octue.yaml`](../../core_concepts/creating_services/#octueyaml)
+    [`octue.yaml`](../core_concepts/creating_services.md/#octueyaml)
     file for your service
 
 2.  Run:
@@ -50,7 +50,7 @@ See the `Runner` API documentation for more advanced usage including providing c
 ### Via the CLI
 
 1.  Ensure you've created a valid
-    [`octue.yaml`](../../core_concepts/creating_services/#octueyaml)
+    [`octue.yaml`](../core_concepts/creating_services.md/#octueyaml)
     file for your service
 
 2.  Run: