Dev

.dockerignore

@@ -5,9 +5,7 @@ static/*
 !static/images/*
 deploy/*
 !deploy/docker/seqr/*
-!deploy/docker/hail_search/*
 !deploy/docker/vlm/*
-hail_search/fixtures/*
 .git
 .vscode
 .idea

.github/workflows/docker-lint.yaml

@@ -9,7 +9,6 @@ on:
       - master
     paths:
       - deploy/docker/seqr/Dockerfile
-      - hail_search/deploy/Dockerfile
       - vlm/deploy/Dockerfile
       - .hadolint.yaml
       - .docker-compose.yaml
@@ -21,7 +20,6 @@ on:
       - master
     paths:
       - deploy/docker/seqr/Dockerfile
-      - hail_search/deploy/Dockerfile
       - vlm/deploy/Dockerfile
       - .hadolint.yaml
       - .docker-compose.yaml
@@ -37,9 +35,6 @@ jobs:
       - uses: hadolint/hadolint-action@v1.5.0
         with:
           dockerfile: deploy/docker/seqr/Dockerfile
-      - uses: hadolint/hadolint-action@v1.5.0
-        with:
-          dockerfile: hail_search/deploy/Dockerfile
       - uses: hadolint/hadolint-action@v1.5.0
         with:
           dockerfile: vlm/deploy/Dockerfile

.github/workflows/unit-tests.yml

@@ -8,16 +8,12 @@ on:
       - master
       - dev
     paths-ignore:
-      - 'hail_search/**'
       - 'vlm/**'
-      - '.github/workflows/*hail-search*.yaml'
       - '.github/workflows/*vlm*.yaml'
   pull_request:
     types: [opened, synchronize, reopened]
     paths-ignore:
-      - 'hail_search/**'
       - 'vlm/**'
-      - '.github/workflows/*hail-search*.yaml'
       - '.github/workflows/*vlm*.yaml'
 
 jobs:
@@ -73,11 +69,6 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: actions/setup-java@v1
-        with:
-          java-version: "8" # The JDK version needed by hail
-          java-package: jdk # (jre, jdk, or jdk+fx) - defaults to jdk
-          architecture: x64 # (x64 or x86) - defaults to x64
       - name: Use pip cache
         uses: actions/cache@v4
         with:
@@ -118,5 +109,7 @@ jobs:
       - run: npm install -g npm@7.24.2
       - run: npm ci
         working-directory: ./ui
+      - run: npm run lint
+        working-directory: ./ui
       - run: npm test
         working-directory: ./ui

.github/workflows/vlm-unit-tests.yaml

@@ -12,35 +12,13 @@ on:
     paths:
       - 'vlm/**'
       - '.github/workflows/*vlm*.yaml'
-      - 'hail_search/fixtures/*'
   pull_request:
     types: [opened, synchronize, reopened]
     paths:
       - 'vlm/**'
       - '.github/workflows/*vlm*.yaml'
-      - 'hail_search/fixtures/*'
 
 jobs:
-  vlm_hail_backend:
-    runs-on: ubuntu-latest
-    container: hailgenetics/hail:0.2.128
-
-    steps:
-      - uses: actions/checkout@v2
-      - name: Install dependencies
-        run: |
-          python3 -m pip install --upgrade pip wheel
-          pip install -r vlm/requirements-test.txt
-      - name: Run coverage tests
-        run: |
-          export VLM_DATA_DIR=./hail_search/fixtures
-          export SEQR_BASE_URL=https://test-seqr.org/
-          export NODE_ID=TestVLM
-          export MACHINE_MEM=24
-          export JAVA_OPTS_XSS=16M
-          coverage run --source="./vlm" --omit="./vlm/__main__.py","./vlm/setup_clickhouse_test_data.py","./vlm/clickhouse_utils.py" -m pytest vlm/
-          coverage report --fail-under=95
-
   vlm_clickhouse:
     runs-on: ubuntu-latest
     container: hailgenetics/hail:0.2.128
@@ -78,6 +56,6 @@ jobs:
           export CLICKHOUSE_VLM_USERNAME=vlm_test_user
           export CLICKHOUSE_VLM_PASSWORD=vlm_test_password
           export CLICKHOUSE_DATABASE=test_seqr
-          coverage run --source="./vlm" --omit="./vlm/__main__.py","./vlm/setup_clickhouse_test_data.py","./vlm/hail_backend_utils.py" -m pytest vlm/
+          coverage run --source="./vlm" --omit="./vlm/__main__.py","./vlm/setup_clickhouse_test_data.py" -m pytest vlm/
           coverage report --fail-under=95
 

CHANGELOG.md

@@ -2,6 +2,9 @@
 
 ## dev
 
+## 9/18/25
+# Deprecate hail backend support
+
 ## 8/7/25
 * Deprecate support for lifting existing projects from GRCH37 to GRCh38