Update develop branch and include hot fixes

docs/components/components-definition.md

@@ -45,9 +45,7 @@ By default any outputr is stored in the S3 Server. However, when dealing with sp
 
 Checkout the following topis:
 
--  [How to run a component](how-to-run-a-component)
--  [How to create a component](components-development)
-
-
-
+-  [How to run a component](components//how-to-run-a-component)
+-  [How to create a component](components/components-development)
 
+<script src="https://hypothes.is/embed.js" async></script>

docs/components/components-development.md

@@ -162,4 +162,6 @@ schema-output: PATH_TO_OUTPUT_SCHEMA
 # If applicable, define devices needed such as GPU.
 devices:
   gpu: false
-```
+```
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/components/how-to-run-a-component.md

@@ -47,4 +47,6 @@ odtp component delete-image --image_name image_test
 
 To start using component in Digital Twin's executions, first you need to register the component into odtp, and using it. 
 
-See the [tutorial](tutorials/components-and-versions.md) on how to do this.
+See the [tutorial](tutorials/components-and-versions.md) on how to do this.
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/development/odtp-db-schema.md

@@ -207,4 +207,6 @@ results = {
     "created_at": datetime.utcnow(),
     "updated_at": datetime.utcnow(),
 }
-```
+```
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/development/roadmap.md

@@ -14,4 +14,6 @@
 - Definition and exporting of digital twin in `odtp-compose.yml`
 - I/O operations optimization
 - Automatic executions planner
-- Enhancement of DB Schema
+- Enhancement of DB Schema
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/index.md

@@ -47,4 +47,6 @@ Component Zoo Template: The template for the Component Zoo operates under the BS
 Alternative commercial licensing options for the core platform and other components are available and can be negotiated through the EPFL Technology Transfer Office (https://tto.epfl.ch) or ETH Zürich Technology Transfer Office (https://ethz.ch/en/industry/transfer.html).
 
 ## Ethical Use and Legal Compliance Disclaimer
-Please note that this software should not be used to harm any individual or entity. Users and developers must adhere to ethical guidelines and use the software responsibly and legally. This disclaimer serves to remind all parties involved in the use or development of this software to engage in practices that are ethical, lawful, and in accordance with the intended purpose of the software.
+Please note that this software should not be used to harm any individual or entity. Users and developers must adhere to ethical guidelines and use the software responsibly and legally. This disclaimer serves to remind all parties involved in the use or development of this software to engage in practices that are ethical, lawful, and in accordance with the intended purpose of the software.
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/installation/docker-compose.md

@@ -84,4 +84,6 @@ odtp new user-entry \
 user ID: 65c3648260106cc50f650bc1
 ```
 
-Now that everything has been set up, you are ready to work. Head over to the [tutorials](tutorials/getting-started.md) 
+Now that everything has been set up, you are ready to work. Head over to the [tutorials](tutorials/getting-started.md) 
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/installation/odtp-installation.md

@@ -34,5 +34,4 @@ For test and development purposes we recommend to use the former, however this m
 1. First deploy all third-party dependencies following this [guide](odtp-third-party-services.md)
 2. Then install ODTP locally following these [instructions](odtp-local-installation.md)
 
-
-
+<script src="https://hypothes.is/embed.js" async></script>

docs/installation/odtp-local-installation.md

@@ -89,4 +89,6 @@ odtp new user-entry \
 user ID: 65c3648260106cc50f650bc1
 ```
 
-Now that everything has been set up, you are ready to work. Head over to the [tutorials](tutorials/getting-started.md) 
+Now that everything has been set up, you are ready to work. Head over to the [tutorials](tutorials/getting-started.md) 
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/installation/odtp-third-party-services.md

@@ -78,3 +78,4 @@ user ID: 65c3648260106cc50f650bc1
 
 Now that everything has been set up, you are ready to work. Head over to the [tutorials](tutorials/getting-started.md) 
 
+<script src="https://hypothes.is/embed.js" async></script>

docs/odtp-concepts.md

@@ -66,3 +66,5 @@ These modules are the different parts that we are developing for the ODTP. These
 
 ### Services
 One service or micro-service, in a micro-services architecture refers to one logical unit that performs one specific task in an independent manner. In ODTP we use different servers to support core modules, such as MongoDB for the database, Minion for the storage, or GraphDB for the knowledge graph storing. But also, from a technical standpoint every component is turned into a micro-service when running. I think this is the part that’s bringing more confusion. 
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/odtp-digital-twin.md

@@ -36,4 +36,4 @@ One of the limitations in `ODTP v0.2.x` is that we only offer compatibility with
 
 The goal of ODTP is to prioritize the flexibility and independence of the Digital Twins generated. That's why we are developing the exporting of each digital twin into an `odtp-compose.yml` file that can be executed directly by Docker. This file will offer the user the possibility to run one specific execution in an isolated and reproducible environment, ensuring consistency across different executions and facilitating collaboration and sharing among users. The `odtp-compose.yml` will include definitions for all the services involved in the execution, their configuration, inter-service dependencies, and any necessary environment variables or volume mounts.
 
-
+<script src="https://hypothes.is/embed.js" async></script>

docs/tutorials/components-and-versions.md

@@ -99,3 +99,5 @@ commit will be taken.
     component_id_: 65c3ab02b4afbca32db08738
     version_id_: 65e00bc02c01a56f2b8c95f9
     ```
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/tutorials/executions.md

@@ -56,3 +56,5 @@ An execution consists of components and can have extra port mappings and paramet
     execution_id: 65c3ab980c57d37eb076b6ba
     step_ids 65c3ab980c57d37eb076b6bb, 65c3ab980c57d37eb076b6bc
     ```
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/tutorials/getting-started.md

@@ -40,4 +40,7 @@ Checkout the following topis:
 
 -  [add users and digital twins](../users-and-digital-twins)
 -  [add components and versions](../components-and-versions)
--  [add users and digital twins](../executions)
+-  [add executions](../executions)
+-  [run executions](../run-executions)
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/tutorials/run-executions.md

@@ -97,6 +97,7 @@ In this step the docker container for the components will run and produce the ac
     ![Dashboard Add execution](../static/tutorials/run-executions/run-completed.png){ width="800" } 
 
     Now the output folders should have outputs:
+
     ![Dashboard Add execution](../static/tutorials/run-executions/project-folder-after-run.png){ width="300" }
 
 
@@ -109,3 +110,5 @@ In this step the docker container for the components will run and produce the ac
     --execution-id 65c3ab980c57d37eb076b6ba \
     --projecoject-path 
     ```
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/tutorials/users-and-digital-twins.md

@@ -51,3 +51,5 @@ Once you have a user, you can set up a digital twin
     ```
     A digital twin has been added: 65a7c735732ae1d3fee2b946
     ``` 
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/use-cases/mobility-causal-interventions.md

@@ -15,4 +15,6 @@ TBD
 
 ## Reference and contact
 
-TBD
+TBD
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/use-cases/mobility-eqasim-matsim.md

@@ -26,4 +26,6 @@ graph LR;
 
 ## Reference and contact
 
-TBD
+TBD
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/use-cases/use-cases.md

@@ -6,4 +6,6 @@ The development of ODTP is made in parallel to the adaptation of different use c
 ## List of Use Cases
 
 - [Mobility: Eqasim and Matsim Simulation](mobility-eqasim-matsim.md)
-- [Mobility: Causal Inference](mobility-causal-inference.md)
+- [Mobility: Causal Inference](mobility-causal-interventions.md)
+
+<script src="https://hypothes.is/embed.js" async></script>

docs/zoo/zoo-definition.md

@@ -36,4 +36,6 @@ In order to submit a component you need to make an entry in `components` directo
 
 ## How to deploy your own zoo
 
-TO BE DEVELOPED
+TO BE DEVELOPED
+
+<script src="https://hypothes.is/embed.js" async></script>