Merge pull request #114 from databio/dev

Deployment updates

.github/workflows/deploy-api-dev.yml

@@ -24,18 +24,10 @@
 #    and best practices on handling the access key credentials.
 
 on:
-  push:
-    branches:
-      - master
-    paths:
-      - deployment/config/api-dev.bedbase.org.yaml
   workflow_dispatch:
     inputs: null
-
-  workflow_run:
-    workflows: [ "Build and push dev image to Dockerhub" ]
-    types:
-      - completed
+    paths:
+      - deployment/config/api-dev.bedbase.org.yaml
 
 name: Deploy to Amazon ECS - dev1
 
@@ -46,8 +38,6 @@ jobs:
     name: Deploy
     runs-on: ubuntu-latest
 
-    needs: [dockerhub-dev]
-
     steps:
     - name: Checkout
       uses: actions/checkout@v4
@@ -79,7 +69,7 @@ jobs:
       id: task-def
       uses: aws-actions/amazon-ecs-render-task-definition@v1
       with:
-        task-definition: task_defs/port82.json
+        task-definition: deployment/task_defs/port82.json
         container-name: bedhost
         image: ${{ steps.build-image.outputs.image }}
 

.github/workflows/deploy-api.yml

@@ -24,13 +24,10 @@
 #    and best practices on handling the access key credentials.
 
 on:
-  push:
-    branches:
-      - master
+  workflow_dispatch:
+    inputs: null
     paths:
       - deployment/config/api.bedbase.org.yaml
-  workflow_dispatch:
-    inputs: null   
 
 name: Deploy to Amazon ECS - primary
 
@@ -70,7 +67,7 @@ jobs:
       id: task-def
       uses: aws-actions/amazon-ecs-render-task-definition@v1
       with:
-        task-definition: task_defs/port81.json
+        task-definition: deployment/task_defs/port81.json
         container-name: bedhost
         image: ${{ steps.build-image.outputs.image }}
 

README.md

@@ -21,53 +21,3 @@ It needs a path to the *bedbase configuration file*, which can be provided eithe
 **DEV UI**: <a href="https://dev.bedhost.pages.dev/" target="_blank">https://dev.bedhost.pages.dev/</a>
 
 **Source Code**: <a href="https://github.com/databio/bedhost/" target="_blank">https://github.com/databio/bedhost/</a>
-
----
-
-## Running for development
-
-Running with `uvicorn` provides auto-reload. To configure, this assumes you have previously set up `databio/secrets`. 
-
-1. Source `.env` file to populate the environment variables referenced in the configuration file.
-2. Start `bedhost` using `uvicorn` and pass the configuration file via the `BEDBASE_CONFIG` env var.
-
-
-```console
-source ../bedbase.org/environment/production.env
-BEDBASE_CONFIG=../bedbase.org/config/api.bedbase.org.yaml uvicorn bedhost.main:app --reload
-```
-
-You can change the database you're connecting to by using a different config file:
-- Using a local config: `BEDBASE_CONFIG=../bbconf/tests/data/config.yaml uvicorn bedhost.main:app --reload`
-- With new database: `BEDBASE_CONFIG=../bedbase.org/config/bedbase2.yaml uvicorn bedhost.main:app --reload`
-
-Now, you can access the service at [http://127.0.0.1:8000](http://127.0.0.1:8000). Example endpoints:
-- 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/img/open_chromatin
-- 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/img_path/open_chromatin
-- 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/file/bedfile
-- 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/file_path/bedfile
-- 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata
-- 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata?attr_ids=md5sum&attr_ids=genome
-
-----
-## Running the server in Docker
-
-### Building image
-
-- Primary image: `docker build -t databio/bedhost -f .Dockerfile .`
-- Dev image `docker build -t databio/bedhost:dev -f dev.Dockerfile .`
-- Test image: `docker build -t databio/bedhost:dev -f test.Dockerfile .`
-
-Existing images can be found [at dockerhub](https://hub.docker.com/r/databio/bedhost).
-
-### Running container for development
-
-Configuration settings and deployment instructions are in the `bedbase.org` repository.
-
----
-
-## Deploying updates automatically
-
-The `bedhost/databio` image is built by a github action. It will build and push the `latest` image whenever a release is made. It will also tag that release with a tag for the release name.
-
-For the dev tag, you must deploy this through manual dispatch

deployment/Dockerfiles/dev1.Dockerfile

@@ -1,6 +1,6 @@
 FROM databio/bedhost:dev
 
-COPY config/api-dev.bedbase.org.yaml /bedbase.yaml
+COPY deployment/config/api-dev.bedbase.org.yaml /bedbase.yaml
 ENV BEDBASE_CONFIG=/bedbase.yaml
 
 RUN mkdir -p /data/outputs/bedstat_output

deployment/Dockerfiles/primary.Dockerfile

@@ -1,6 +1,6 @@
 FROM databio/bedhost:latest
 
-COPY config/api.bedbase.org.yaml /bedbase.yaml
+COPY deployment/config/api.bedbase.org.yaml /bedbase.yaml
 ENV BEDBASE_CONFIG=/bedbase.yaml
 
 RUN mkdir -p /data/outputs/bedstat_output

ui/src/motions/landing-animations.tsx

@@ -2,7 +2,7 @@ import { motion } from 'framer-motion';
 import { PRIMARY_COLOR } from '../const';
 
 const STROKE_WIDTH = 2;
-const STROKE_SPEAD = 8;
+const STROKE_SPEAD = 0;
 
 export const InPaths = () => {
   return (