Precommit changes

.deployments/backend_dep.yaml

@@ -1,34 +1,34 @@
-apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: taxoniumbackend
-  labels:
-    app: taxoniumbackend
-spec:
-  replicas: 1
-  selector:
-    matchLabels:
-      app: taxoniumbackend
-  template:
-    metadata:
-      labels:
-        app: taxoniumbackend
-    spec:
-      containers:
-        - name: taxoniumbackend
-          image: theosanderson/taxonium:master
-          imagePullPolicy: Always
-          ports:
-            - containerPort: 80
-          livenessProbe:
-            httpGet:
-              path: /
-              port: 80
-            initialDelaySeconds: 180
-            periodSeconds: 180
-          readinessProbe:
-            httpGet:
-              path: /
-              port: 80
-            initialDelaySeconds: 30
-            periodSeconds: 5
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: taxoniumbackend
+  labels:
+    app: taxoniumbackend
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: taxoniumbackend
+  template:
+    metadata:
+      labels:
+        app: taxoniumbackend
+    spec:
+      containers:
+        - name: taxoniumbackend
+          image: theosanderson/taxonium:master
+          imagePullPolicy: Always
+          ports:
+            - containerPort: 80
+          livenessProbe:
+            httpGet:
+              path: /
+              port: 80
+            initialDelaySeconds: 180
+            periodSeconds: 180
+          readinessProbe:
+            httpGet:
+              path: /
+              port: 80
+            initialDelaySeconds: 30
+            periodSeconds: 5

.devcontainer/setup.sh

@@ -1,2 +1,2 @@
 cd taxonium_web_client
-yarn install &
+yarn install &

.github/workflows/docker-publish-backend.yml

@@ -9,24 +9,22 @@ on:
   repository_dispatch:
   workflow_dispatch:
   schedule:
-    - cron: '37 18 * * *'
+    - cron: "37 18 * * *"
   push:
-    branches: [ master, staging ]
+    branches: [master, staging]
     # Publish semver tags as releases.
-    tags: [ 'v*.*.*' ]
+    tags: ["v*.*.*"]
   pull_request:
-    branches: [ master, staging ]
+    branches: [master, staging]
 
 env:
   # Use docker.io for Docker Hub if empty
   REGISTRY: docker.io
   # github.repository as <account>/<repo>
   IMAGE_NAME: theosanderson/taxonium_backend
 
-
 jobs:
   build:
-
     runs-on: ubuntu-latest
     permissions:
       contents: read
@@ -45,8 +43,7 @@ jobs:
         if: github.event_name != 'pull_request'
         uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
         with:
-          cosign-release: 'v1.7.1'
-
+          cosign-release: "v1.7.1"
 
       # Workaround: https://github.com/docker/build-push-action/issues/461
       - name: Setup Docker buildx

.github/workflows/docker-publish-frontend.yml

@@ -9,24 +9,22 @@ on:
   repository_dispatch:
   workflow_dispatch:
   schedule:
-    - cron: '37 18 * * *'
+    - cron: "37 18 * * *"
   push:
-    branches: [ master ]
+    branches: [master]
     # Publish semver tags as releases.
-    tags: [ 'v*.*.*' ]
+    tags: ["v*.*.*"]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 env:
   # Use docker.io for Docker Hub if empty
   REGISTRY: docker.io
   # github.repository as <account>/<repo>
   IMAGE_NAME: theosanderson/taxonium_frontend
 
-
 jobs:
   build:
-
     runs-on: ubuntu-latest
     permissions:
       contents: read
@@ -45,8 +43,7 @@ jobs:
         if: github.event_name != 'pull_request'
         uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
         with:
-          cosign-release: 'v1.7.1'
-
+          cosign-release: "v1.7.1"
 
       # Workaround: https://github.com/docker/build-push-action/issues/461
       - name: Setup Docker buildx
@@ -81,4 +78,3 @@ jobs:
           push: ${{ github.event_name != 'pull_request' }}
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-

.github/workflows/frontend-test.yml

@@ -1,28 +1,28 @@
-name: Frontend
-
-on:
-   workflow_call:
-
-jobs:
-  test:
-    env:
-      CI: false
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v3
-        with:
-          node-version: 17.5
-      - name: NPM build
-        run: |
-          cd taxonium_web_client
-          npm install -g yarn
-          yarn install
-          yarn build
-          cd build
-      - name: 'Upload Artifact'
-        uses: actions/upload-artifact@v3
-        with:
-          name: taxonium_web_client_build
-          path: taxonium_web_client/build
-          retention-days: 5
+name: Frontend
+
+on:
+  workflow_call:
+
+jobs:
+  test:
+    env:
+      CI: false
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 17.5
+      - name: NPM build
+        run: |
+          cd taxonium_web_client
+          npm install -g yarn
+          yarn install
+          yarn build
+          cd build
+      - name: "Upload Artifact"
+        uses: actions/upload-artifact@v3
+        with:
+          name: taxonium_web_client_build
+          path: taxonium_web_client/build
+          retention-days: 5

.github/workflows/integration-test.yml

@@ -1,18 +1,18 @@
-name: Integration Test
-
-on:
-  repository_dispatch:
-  workflow_dispatch:
-  push:
-  pull_request:
-    branches: [master]
-  schedule:
-    - cron: "0 0 * * *"
-jobs:
-  build:
-    uses:  ./.github/workflows/frontend-test.yml
-  python:
-    uses:  ./.github/workflows/python-test.yml
-  selenium:
-    needs: [build, python]
-    uses:  ./.github/workflows/selenium-test.yml
+name: Integration Test
+
+on:
+  repository_dispatch:
+  workflow_dispatch:
+  push:
+  pull_request:
+    branches: [master]
+  schedule:
+    - cron: "0 0 * * *"
+jobs:
+  build:
+    uses: ./.github/workflows/frontend-test.yml
+  python:
+    uses: ./.github/workflows/python-test.yml
+  selenium:
+    needs: [build, python]
+    uses: ./.github/workflows/selenium-test.yml

.github/workflows/prettier.yml

@@ -22,4 +22,4 @@ jobs:
       - name: Prettify code
         uses: creyD/[email protected]
         with:
-           prettier_options: --write **/*.{js,md,jsx}
+          prettier_options: --write **/*.{js,md,jsx}

.github/workflows/python-build.yml

@@ -1,9 +1,9 @@
 name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
 
-on: 
+on:
   push:
     paths:
-    - 'taxoniumtools/**'
+      - "taxoniumtools/**"
 jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI

.github/workflows/python-format.yaml2

@@ -21,8 +21,8 @@ jobs:
       - name: Push changes
         if: steps.git-check.outputs.modified == 'true'
         run: |
-          git config --global user.name 'github-actions' 
-          git config --global user.email '[email protected]' 
+          git config --global user.name 'github-actions'
+          git config --global user.email '[email protected]'
           git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}
           git commit -am "Automated autoyapf fixes"
           git push