73 migrate docs here

.gitignore

@@ -1,2 +1,35 @@
 kubeconfig
 uscd.yaml
+# Created by https://www.toptal.com/developers/gitignore/api/osx
+# Edit at https://www.toptal.com/developers/gitignore?templates=osx
+
+### OSX ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+# End of https://www.toptal.com/developers/gitignore/api/osx
+

.readthedocs.yml

@@ -0,0 +1,19 @@
+# Required
+version: 2
+
+# Build documentation with MkDocs
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"

charts/mint/Chart.yaml

@@ -15,7 +15,7 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 3.4.0
+version: 3.4.1
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.

charts/mint/README.md

@@ -1,6 +1,6 @@
 # MINT
 
-![Version: 3.4.0](https://img.shields.io/badge/Version-3.4.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 1.16.3](https://img.shields.io/badge/AppVersion-1.16.3-informational?style=flat-square)
+![Version: 3.4.1](https://img.shields.io/badge/Version-3.4.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 1.16.3](https://img.shields.io/badge/AppVersion-1.16.3-informational?style=flat-square)
 
 A Helm chart for MINT
 

docs/admin-guide/catalog-configuration/model-catalog-configuration.md

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+The Model Catalog Endpoint is a [SPARQL](https://www.w3.org/TR/sparql11-overview/) endpoint that provides access to the model catalog data. The Model Catalog Endpoint is implemented using [Apache Jena Fuseki](https://jena.apache.org/documentation/fuseki2/). The Model Catalog Endpoint is used by the MINT platform to store and retrieve model metadata.
+
+The Model Catalog Endpoint is password protected. The default username and password are `admin` and `CHANGEME`, respectively. You can change the username and password by editing the `values.yaml` file in the `mint` directory. The `values.yaml` file contains the following sections:
+
+The default url is [http://endpoint.models.mint.local](http://endpoint.models.mint.local)
+
+```yaml
+secrets:
+  database:
+    model_catalog_endpoint:
+      # -- Username for Model Catalog Apache Jena Fuseki database
+      username: admin
+      # -- Password for Model Catalog Apache Jena Fuseki database
+      password: CHANGEME
+```
+
+### Initial Data
+
+Helm charts are configured to populate the database with initial data. You can configure the initial data by editing the `values.yaml` file in the `mint` directory. The `values.yaml` file contains the following sections:
+
+!!! Note
+
+    The initial data file must be in the [Turtle](https://www.w3.org/TR/turtle/) format.
+    The process of loading the initial data is done only once when the Model Catalog Endpoint is installed.
+
+```yaml
+components:
+  model_catalog_endpoint:
+    environment:
+      seeds_url: https://raw.githubusercontent.com/mintproject/model-catalog-endpoint/main/data/wifire-2023-09-22.trig
+```
+
+The `seeds_url` key specifies the URL of the initial data. You can change the URL to point to a different initial data file. The initial data file must be in the [Turtle](https://www.w3.org/TR/turtle/) format.

docs/admin-guide/catalog-configuration/region-configuration.md

@@ -0,0 +1,54 @@
+Helm charts are configured to populate the database with initial data containing multiple regions. You can remove the regions by querying the database and deleting the regions. The following sections describe how to query the database and delete the regions.
+
+## Open the database
+
+To open the database, use the following command:
+
+```bash
+$ kubectl exec -ti $(kubectl get pod -l app=mint-hasura -o jsonpath='{.items[0].metadata.name}') -c hasura-db -- sh
+```
+
+## Query the database
+
+To query the database, use the following command:
+
+```bash
+$ psql -U postgres -d hasura
+```
+
+The following SQL query will remove all region geometry that are not California:
+
+```sql
+SELECT
+    rg.region_id
+FROM
+    region
+INNER JOIN
+    region_geometry rg
+ON
+    region.id = rg.region_id
+WHERE
+    region.parent_region_id IS NULL
+    AND region.parent_region_id != 'california';
+```
+
+```sql
+DELETE FROM region_geometry
+USING region
+WHERE region_geometry.region_id = region.id
+AND region.parent_region_id != 'california';
+```
+
+The following SQL query will remove all region geometry that are not California and are not a child of California:
+
+```sql
+DELETE FROM region
+WHERE  region.parent_region_id != 'california' AND region.id != 'california';
+```
+
+Delete all region that the id is not `california` and the `parent_region_id` is `NULL`:
+
+```sql
+DELETE FROM region
+WHERE  region.parent_region_id IS NULL AND region.id != 'california';
+```

docs/admin-guide/catalog-configuration/solution-catalog-configuration.md

@@ -0,0 +1,22 @@
+MINT uses [hasura](https://hasura.io/) to store the task, problem, execution and other metadata.
+
+The Hasura database is password protected. The default secret is `CHANGEME` can change the username and password by editing the `values.yaml` file in the `mint` directory. The `values.yaml` file contains the following sections:
+
+The default url is [http://graphql.mint.local](http://graphql.mint.local)
+
+```yml
+secrets:
+  hasura:
+    # -- Admin secret for Hasura used to access the console
+    admin_secret: CHANGEME
+```
+
+## Initial Data
+
+Helm charts are configured to populate the database with initial data.
+
+!!! Note
+
+    The process of loading the initial data is done only once when the Hasura is installed.
+
+To delete existing regions, please go to the [Region Configuration](region-configuration.md) page.

docs/admin-guide/ckan-configuration.md

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+MINT supports CKAN as a data catalog. CKAN is a powerful data management system that makes data accessible by providing tools to streamline publishing, sharing, finding, and using data. CKAN is aimed at data publishers (national and regional governments, companies, and organizations) wanting to make their data open and available.
+
+## Features
+
+MINT CKAN provides the following features:
+
+- Query and search for datasets
+- View dataset metadata
+- Publish datasets and resources from the execution of a workflow
+
+## Configuration
+
+The CKAN configuration is stored in the `values.yaml` file in the `mint` directory. The `values.yaml` file contains the following sections:
+
+```yaml
+external_services:
+  ckan:
+    # -- Enable or disable CKAN service
+    enabled: true
+    # -- CKAN url
+    url: "http://localhost:5000"
+    # -- CKAN service type
+    type: "CKAN"
+    extra:
+      # -- Owner organization ID for CKAN service
+      owner_organization_id: ""
+      # -- Owner provenance ID for CKAN service
+      owner_provenance_id: ""``
+secrets:
+  external_services:
+    ckan:
+      # -- API key for CKAN service. Used by Ensemble Manager to upload data
+      api_key: CHANGEME
+```

docs/admin-guide/execution-configuration/execution-configuration-kubernetes.md

@@ -0,0 +1,20 @@
+# Kubernetes
+
+MINT can run models as job on Kubernetes clusters. This guide explains how to set up a Kubernetes cluster for MINT execution.
+
+Configure the Kubernetes cluster in the `values.yaml`.
+
+```yaml
+external_services:
+  kubernetes:
+    # -- Enable or disable Kubernetes service to run jobs used by Ensemble Manager
+    enabled: true
+    # -- Kubernetes namespace
+    namespace: 'default'
+    # -- Job CPU limit
+    cpu_limit: '256m'
+    # -- Job memory limit
+    memory_limit: '512Mi'
+    # -- Toggle for node affinity. The job will be scheduled on the same node as the Ensemble Manager
+    node_affinity: true
+```

docs/admin-guide/execution-configuration/execution-configuration-tapis.md

@@ -0,0 +1,5 @@
+# Tapis
+
+MINT can run models as job on Tapis clusters. The models should be existing Tapis apps. This guide explains how to set up a Tapis cluster for MINT execution.
+
+TODO: Add instructions for setting up Tapis cluster for MINT execution.

docs/admin-guide/index.md

@@ -0,0 +1,7 @@
+# Overview
+
+This guide is for Administrators who need to set up a new [MINT](https://mint.isi.edu) installation.
+
+!!! Note
+    Please make sure you have completed the User guide  before you start.
+

docs/admin-guide/installation.md

@@ -0,0 +1,90 @@
+# Install
+
+MINT can be easily deployed on large Kubernetes clusters using Helm. Useful for production instances.
+
+## Pre-requisites
+
+- A Kubernetes `v1.16.3` cluster or later.
+- Helm `v3.2.x` or later.
+
+If you don't have a Kubernetes cluster and you want to test MINT, we **strongly** recommend to use [Microk8s](https://microk8s.io/) to create a local cluster on your machine. Follow the instructions in the [MINT](https://github.com/mintproject/mint/?tab=readme-ov-file#mint) to install Microk8s on your machine.
+
+## Install MINT
+
+Add the MINT Helm repository:
+
+```bash
+$ helm repo add mint https://mintproject.github.io/mint
+```
+
+Update the Helm repository:
+
+```bash
+$ helm repo update
+```
+
+Install MINT:
+
+```bash
+$ helm install mint mint/mint --namespace mint --create-namespace
+```
+
+If you using MacOS Silicon, you need to install the `arm64` version of the postgresql database.
+
+**WARNING:** The arm64 image has not been tested and may not work as expected. Please use it at your own risk.
+
+```bash
+$ helm install mint mint/mint --namespace mint --create-namespace --set arm_support=true
+```
+
+Helm will returns the URL to access the MINT services. You can use the following command to get the URL:
+
+```txt
+The MINT system has been installed!
+
+Please remember to edit your `/etc/hosts/`
+
+After that, you can access to the MINT services
+
+
+http://mint.local
+http://ensemble-manager.mint.local
+http://cromo.mint.local
+http://mic.mint.local
+http://datacatalog.mint.local
+```
+
+If you are using microk8s on a VM (macOS or windows) need to get the IP address of the VM to access the MINT services. You can use the following command to get the IP address of the VM:
+
+```bash
+$ kubectl get node -o json | jq '.items[].status.addresses[] | select(.type=="InternalIP") | .address'
+10.211.59.16
+```
+
+Then, edit the `/etc/hosts` file and add the following lines:
+
+```bash
+$ sudo vim /etc/hosts
+```
+
+Add the following lines (replace the IP address with the IP address of the VM):
+
+```text
+10.211.59.16 mint.local
+10.211.59.16 cromo.mint.local
+10.211.59.16 mic.mint.local
+10.211.59.16 api.mic.mint.local
+10.211.59.16 datacatalog.mint.local
+10.211.59.16 endpoint.models.mint.local
+10.211.59.16 graphql.mint.local
+10.211.59.16 models.mint.local
+10.211.59.16 api.models.mint.local
+10.211.59.16 endpoint.models.mint.local
+```
+
+Got to the URL returned by Helm to access the MINT services.
+
+The default username and password are:
+
+- Username: `[email protected]`
+- Password: `mint123!`

docs/assets/extra.css

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+.md-grid {
+    max-width: 80rem;
+}
+.md-nav__item--active {
+    font-weight: bold;
+}