- 
- 
+ 
+ 
+ 
@@ -16,11 +16,11 @@
SciLifeLab Serve ([https://serve.scilifelab.se](https://serve.scilifelab.se)) is a platform offering machine learning model serving, app hosting (Shiny, Streamlit, Dash, etc.), web-based integrated development environments, and other tools to life science researchers affiliated with a Swedish research institute. It is developed and operated by the [SciLifeLab Data Centre](https://github.com/ScilifelabDataCentre), part of [SciLifeLab](https://scilifelab.se/). See [this page for information about funders and mandate](https://serve.scilifelab.se/about/).
-This repository contains source code for SciLifeLab Serve. It is based on the open-source platform [Stackn](https://github.com/scaleoutsystems/stackn).
+This repository contains source code for the main Django application of SciLifeLab Serve.
## Reporting bugs and requesting features
-If you are using SciLifeLab Serve and notice a bug or if there is a feature you would like to be added feel free to [create an issue](https://github.com/ScilifelabDataCentre/stackn/issues/new/choose) with a bug report or feature request.
+If you are using SciLifeLab Serve and notice a bug or if there is a feature you would like to be added feel free to [create an issue](https://github.com/ScilifelabDataCentre/serve/issues/new/choose) with a bug report or feature request.
## Development and contributions
@@ -30,14 +30,20 @@ We welcome contributions to the code. When you want to make a contribution pleas
The `main` branch contains code behind the version that is currently deployed in production - https://serve.scilifelab.se. The branches `develop` and `staging` contain current development versions at different stages.
+### Local development setup
+
+There are multiple ways to set up a local development environment for SciLifeLab Serve. Below you can find instructions on how to set up a local development environment using Docker Compose or Rancher Desktop.
+
+Both have their pros and cons. Docker Compose is easier to set up but does not provide a full Kubernetes environment. Rancher Desktop provides a full Kubernetes environment but is more complex to set up.
+
### Deploy Serve for local development with Docker Compose
It is possible to deploy and work with the user interface of Serve without a running Kubernetes cluster, in that case you can skip the step related to that below. However, in order to be able to deploy and modify resources (apps, notebooks, persistent storage, etc.) a running local cluster is required; it can be created for example with [microk8s](https://microk8s.io/).
1. Clone this repository locally:
```
-$ git clone https://github.com/ScilifelabDataCentre/stackn
-$ cd stackn
+$ git clone https://github.com/ScilifelabDataCentre/serve
+$ cd serve
```
2. Create a copy of the .env template file
@@ -75,6 +81,89 @@ This assumes you have the correct ssh key in your ssh-agent. If you like to give
$ docker compose up -d
```
+### Deploy Serve for local development with Rancher Desktop
+
+Start with instructions in [Serve Charts > How to Deploy](https://github.com/ScilifelabDataCentre/serve-charts?tab=readme-ov-file#how-to-deploy) and come back here when you get to the point of building the studio image.
+
+Again, this setup assumes you have [Rancher Desktop](https://rancherdesktop.io/) installed and running.
+
+```bash
+$ git clone git@github.com:ScilifelabDataCentre/stackn.git
+$ cd stackn
+$ git checkout develop
+$ cp .env.template .env
+$ cp ~/.kube/config cluster.conf
+$ cp ~/.ssh/id_rsa.pub id_rsa.pub
+$ cat Dockerfile local.Dockerfile > local_.dockerfile
+$ nerdctl build --namespace k8s.io -t mystudio -f local_.dockerfile .
+```
+
+Now continue setting up serve charts until you get to the PyCharm setup.
+
+##### PyCharm setup
+
+> Prerequisite: This setup assumes you have PyCharm Professional installed.
+
+1. Do this weirdness due to [this](https://youtrack.jetbrains.com/issue/PY-55338/Connection-to-python-console-refused-with-docker-interpreter-on-Linux)
+ 1. go to Help | Find Action | Registry
+ 2. disable python.use.targets.api
+ 3. recreate the interpreter from scratch
+2. Setup ssh interpreter
+```bash
+# This will open ssh connection from the pod to our host machine
+# Because we made everything super NOT secure for local development you can ssh there without password and as root
+$ sudo kubectl port-forward svc/serve-studio 22:22
+```
+3. Set up the interpreter in PyCharm
+ 1. Go to `PyCharm | Settings | Project: stackn | Python Interpreter`
+ 2. Add new interpreter
+ 3. Choose SSH
+ 4. Host: localhost
+ 5. Port: 22
+ 6. Username: root
+ 7. Auth type: Password
+ 8. Password: root
+ 9. Interpreter path: /usr/local/bin/python
+ 10. Python interpreter path: /usr/local/bin/python
+ 11. **Important** Don't accept synchronization option from PyCharm. There is no need for it because we already synchronize the code with the pod using volume mounts provided by Rancher Desktop.
+4. Set up the environment variables
+ 1. Go to Run | Edit Configurations
+ 2. Add new configuration
+ 3. Choose `Django server`
+ 4. Name: `Serve`
+ 5. Host: `0.0.0.0`
+ 6. Port: `8080`
+ 7. Click Modify options and select `No reload` and `Environment variables`
+ 8. Add environment variables from the studio pod
+ 9. Make sure the Working directory is /app.
+ 10. The Path mappings should be /path/to/your/stackn=/app.
+
+```bash
+$ kubectl get po
+# find the studio pod serve-studio-123
+$ kubectl exec -it + Error code: 500 +
+SciLifeLab Serve (beta) is developed and operated by the SciLifeLab Data Centre. SciLifeLab Serve is free to use for all life science researchers affiliated with a Swedish research institution and their collaborators. The service is hosted on a Kubernetes cluster. The code behind SciLifeLab Serve is available on Github.
+SciLifeLab Serve (beta) is developed and operated by the SciLifeLab Data Centre. SciLifeLab Serve is free to use for all life science researchers affiliated with a Swedish research institution and their collaborators. The service is hosted on a Kubernetes cluster. The code behind SciLifeLab Serve is available on Github.
Please email serve@scilifelab.se with any questions.
version {{version_text}}
diff --git a/templates/common/navbar.html b/templates/common/navbar.html
index 1941291b0..912b6ad4b 100644
--- a/templates/common/navbar.html
+++ b/templates/common/navbar.html
@@ -8,6 +8,7 @@
-
{{ obj.message_in_header | safe }}
-+
{{ obj.message_in_header | safe }}
+Below you can find an overview of events organized by the SciLifeLab Serve team. Life science researchers in Sweden is our primary focus but some webinars may also be interesting for an international audience. Our events are open to everyone (regardless of affiliation) so feel free to sign up and attend. However, please pay attention to the described target audience of each event as some of them are prepared for groups with specific prior knowledge. When possible, we try to record our webinars and provide links to the recorded video afterwards on this page.
+If you have any questions about the events below or if you would like to collaborate with us on organising an event, feel free to get in touch with us (serve@scilifelab.se).
+{{ event.description_html|safe }}
{% endif %} +Date and time: + {% if event.start_time|date:"Y-m-d" == event.end_time|date:"Y-m-d" %} + {{ event.start_time|date:"M. j, Y" }} {{ event.start_time|date:"H:i" }}-{{ event.end_time|date:"H:i" }} + {% else %} + {{ event.start_time|date:"M. j, Y, H:i" }} - {{ event.end_time|date:"M. j, Y, H:i" }} + {% endif %} +
+ {% if event.speaker %}Speaker(s): {{ event.speaker }}
{% endif %} +Venue: {{ event.venue }}
+ Register for this event +{{ event.description_html|safe }}
{% endif %} +Date and time: + {% if event.start_time|date:"Y-m-d" == event.end_time|date:"Y-m-d" %} + {{ event.start_time|date:"M. j, Y" }} {{ event.start_time|date:"H:i" }}-{{ event.end_time|date:"H:i" }} + {% else %} + {{ event.start_time|date:"M. j, Y, H:i" }} - {{ event.end_time|date:"M. j, Y, H:i" }} + {% endif %} +
Venue: {{ event.venue }}
+ {% if event.recording_url %}See the recording{% endif %} +SciLifeLab Serve (beta) is a platform for serving applications and machine learning models that is offered to life science researchers affiliated with a Swedish research institute and their collaborators. Currently, the service is running in beta testing mode. The service is available free of charge to researchers with and without an affiliation to SciLifeLab, to collaborators of these researchers, as well as to data-producing infrastructures in Sweden.
+If you use SciLifeLab Serve for sharing apps and models that accompany your publications, presentations, etc., you can add the following acknowledgement text: “Technical infrastructure for hosting the [app ‘xxx’/model ‘xxx’] was provided by SciLifeLab Serve (https://serve.scilifelab.se), a platform developed and supported by SciLifeLab Data Centre.”
SciLifeLab Serve is developed and maintained by the SciLifeLab Data Centre. Initially the service was based on STACKn, a platform developed by Scaleout systems (a spinoff from the Department of Information Technology at Uppsala University). Since then, the SciLifeLab Data Centre team has expanded and improved the platform. The most up to date source code behind SciLifeLab Serve is available with an open source license on GitHub. We welcome any other organisations running a similar service using our code.
-The main SciLifeLab Serve application is built with Python on Django. SciLifeLab Serve components include a number of open source applications: JupyterLab (source code), RStudio Server (source code, modifications), code-server (VS Code, source code), ShinyProxy (source code), MinIO (unmodified), TensorFlow Serving (source code), TorchServe (source code), MLflow (source code). We use Bootstrap and Bootstrap Icons for user interface styling, JavaScript libraries jQuery and aos for dynamic elements of the website.
+SciLifeLab Serve is developed and maintained by the SciLifeLab Data Centre. Initially the service was based on STACKn, a platform developed by Scaleout systems (a spinoff from the Department of Information Technology at Uppsala University). Since then, the SciLifeLab Data Centre team has expanded and improved the platform. The most up to date source code behind SciLifeLab Serve is available with an open source license on GitHub. We welcome any other organisations running a similar service using our code.
+The main SciLifeLab Serve application is built with Python on Django. SciLifeLab Serve components include a number of open source applications: JupyterLab (source code), RStudio Server (source code, modifications), code-server (VS Code, source code), ShinyProxy (source code), filebrowser (source code, modifications), TensorFlow Serving (source code), TorchServe (source code), MLflow (source code). We use Bootstrap and Bootstrap Icons for user interface styling, JavaScript libraries jQuery and aos for dynamic elements of the website.
SciLifeLab Serve as well as the applications and models deployed through the service are hosted on a Kubernetes cluster located and administered on hardware at the KTH Royal Institute of Technology in Stockholm and managed by the SciLifeLab Data Centre.
- This user user account cannot be deleted because you are the owner of at least one Serve project. + This user account cannot be deleted because you are the owner of at least one Serve project. Please delete or transfer ownership to another user account.
{% endif %}