fix: check for pixi before installing

backend/Dockerfile

@@ -1,24 +1,19 @@
 FROM pypy:3.11-slim
-
 ENV PYTHONUNBUFFERED=1
 WORKDIR /app
-
 RUN apt-get update && apt-get install -y \
-    build-essential pkg-config \
+    build-essential pkg-config libuv1 \
     libffi-dev libssl-dev libsodium-dev make libpq-dev \
     && rm -rf /var/lib/apt/lists/*
-
 COPY requirements.txt .
 RUN  pip install --upgrade pip && pip install --no-cache-dir -r requirements.txt
-
 COPY app ./app
 COPY domain ./domain
 COPY migrations ./migrations
 COPY pyproject.toml .
 COPY settings.yaml .
 COPY run_server.sh ./
 RUN chmod +x run_server.sh
-RUN apt-get update && apt-get install -y libuv1
 EXPOSE 8000
 
 RUN useradd -m appuser

backend/app/service_analysis/controller.py

@@ -95,7 +95,7 @@ async def get_analysis(
 
         return ok(
             {
-                "item": result,
+                "items": result,
                 "page": page,
                 "page_size": page_size,
                 "total": total_count,

backend/app/service_analysis/tests/test_analysis.py

@@ -51,13 +51,13 @@ async def test_basic_analysis(
 
     # list instance as admin
     res_admin = await list_instance(test_client, f"{BASE_URL}/", cookies_admin, 200)
-    assert len(res_admin["item"]) == 1
-    assert_instance_fields(res_admin["item"][0], EXPECTED_FIELDS)
+    assert len(res_admin["items"]) == 1
+    assert_instance_fields(res_admin["items"][0], EXPECTED_FIELDS)
 
     # list instance as contributor
     res_contrib = await list_instance(test_client, f"{BASE_URL}/", cookies_contributor, 200)
-    assert len(res_contrib["item"]) == 1
-    assert_instance_fields(res_contrib["item"][0], EXPECTED_FIELDS)
+    assert len(res_contrib["items"]) == 1
+    assert_instance_fields(res_contrib["items"][0], EXPECTED_FIELDS)
 
     # delete as admin (should fail)
     delete_url = f"{BASE_URL}/{res_admin['item'][0]['id']}/"
@@ -93,23 +93,23 @@ async def get_page(page, page_size):
     # page 1
     data = await get_page(1, 10)
     assert data["page"] == 1
-    assert len(data["item"]) == 10
+    assert len(data["items"]) == 10
 
     # page 2
     data = await get_page(2, 10)
     assert data["page"] == 2
-    assert len(data["item"]) == 10
+    assert len(data["items"]) == 10
 
     # last page
     data = await get_page(4, 10)
     assert data["page"] == 4
-    assert len(data["item"]) == 0
+    assert len(data["items"]) == 0
     # too large page
     data = await get_page(99, 10)
-    assert data["item"] == []
+    assert data["items"] == []
 
     # search by url
     res = await test_client.get(f"{BASE_URL}/", query={"search": "repo-1"}, cookies=cookies_admin)
     data = await res.json()
     assert res.status == 200
-    assert any("repo-1" in item["url"] for item in data["item"])
+    assert any("repo-1" in item["url"] for item in data["items"])

backend/app/service_job/controller.py

@@ -149,7 +149,7 @@ async def list_web_job(
 
         return ok(
             {
-                "item": result,
+                "items": result,
                 "page": page,
                 "page_size": page_size,
                 "total": total_count,

backend/app/service_job/tests/test_api_web_job.py

@@ -80,8 +80,8 @@ async def test_create_list_job(
     )
     assert res.status == 200
     result = await res.json()
-    assert "item" in result
-    assert len(result["item"]) == 5
+    assert "items" in result
+    assert len(result["items"]) == 5
     assert result["total"] >= 15
 
     # List jobs with pagination (page=3, page_size=5)
@@ -92,8 +92,8 @@ async def test_create_list_job(
     )
     assert res.status == 200
     result = await res.json()
-    assert "item" in result
-    assert len(result["item"]) == 5
+    assert "items" in result
+    assert len(result["items"]) == 5
 
     # Search for a specific job by name
     search_name = "customer-03"
@@ -104,7 +104,7 @@ async def test_create_list_job(
     )
     assert res.status == 200
     result = await res.json()
-    assert any(job["name"] == search_name for job in result["item"])
+    assert any(job["name"] == search_name for job in result["items"])
 
     # get log of current running job
     # TODO: test job log

backend/app/service_organization/controller.py

@@ -69,7 +69,7 @@ async def list_organization(
 
         return ok(
             {
-                "item": result,
+                "items": result,
                 "page": page,
                 "page_size": page_size,
                 "total": total_count,

backend/app/service_organization/tests/test_organization.py

@@ -45,8 +45,8 @@ async def check_page(page, expected_count):
         res_data = await res.json()
         assert res.status == 200
         assert res_data["page"] == page
-        assert len(res_data["item"]) == expected_count
-        for item in res_data["item"]:
+        assert len(res_data["items"]) == expected_count
+        for item in res_data["items"]:
             assert_instance_fields(item, expected_fields)
 
     await check_page(1, 10)
@@ -58,19 +58,19 @@ async def check_page(page, expected_count):
     res_data = await res.json()
     assert res.status == 200
     assert res_data["total"] == 1
-    assert "29" in res_data["item"][0]["name"]
+    assert "29" in res_data["items"][0]["name"]
 
     # search by description
     res = await test_client.get(f"{BASE_URL}", query={"search": "Description-1"}, cookies=cookies_org_manager)
     res_data = await res.json()
     assert res.status == 200
     assert res_data["total"] == 11
-    assert len(res_data["item"]) == 11
-    for item in res_data["item"]:
+    assert len(res_data["items"]) == 11
+    for item in res_data["items"]:
         assert_instance_fields(item, expected_fields)
 
     # Update
-    update_org = res_data["item"][0]
+    update_org = res_data["items"][0]
     updated_org = await update_instance(
         test_client,
         f"{BASE_URL}/{update_org['id']}/",
@@ -99,4 +99,4 @@ async def check_page(page, expected_count):
         cookies=cookies_org_manager,
     )
     res_data = await res.json()
-    assert len(res_data["item"]) == 29
+    assert len(res_data["items"]) == 29

backend/app/service_project/controller.py

@@ -148,7 +148,7 @@ async def list_projects(
 
         return ok(
             {
-                "item": result,
+                "items": result,
                 "page": page,
                 "page_size": page_size,
                 "total": total_count,

backend/app/service_project/tests/test_project.py

@@ -184,17 +184,17 @@ async def test_project_CRUD_and_search(
     res_data = await res.json()
     assert res.status == 200
     assert res_data["page"] == 1
-    assert len(res_data["item"]) == 5
-    for item in res_data["item"]:
+    assert len(res_data["items"]) == 5
+    for item in res_data["items"]:
         assert_instance_fields(item, expected_fields)
 
     # second page
     res = await test_client.get(f"{BASE_URL}", query={"page": 2, "page_size": 5}, cookies=cookies_admin)
     res_data = await res.json()
     assert res.status == 200
     assert res_data["page"] == 2
-    assert len(res_data["item"]) == 3
-    for item in res_data["item"]:
+    assert len(res_data["items"]) == 3
+    for item in res_data["items"]:
         assert_instance_fields(item, expected_fields)
 
     # Search name
@@ -203,7 +203,7 @@ async def test_project_CRUD_and_search(
     res_data = await res.json()
     assert res.status == 200
     assert res_data["total"] == 2
-    assert "public project 1" in res_data["item"][0]["name"]
+    assert "public project 1" in res_data["items"][0]["name"]
 
     # failed due to invalid format filters
     res = await test_client.get(
@@ -233,7 +233,7 @@ async def test_project_CRUD_and_search(
     res_data = await res.json()
     assert res.status == 200
     assert res_data["total"] == 2
-    assert "public project 1" in res_data["item"][0]["name"]
+    assert "public project 1" in res_data["items"][0]["name"]
 
     # Search by role
     res = await test_client.get(
@@ -265,8 +265,8 @@ async def test_project_CRUD_and_search(
     res_data = await res.json()
     assert res.status == 200
     assert res_data["total"] == 8
-    assert len(res_data["item"]) == 5
-    for item in res_data["item"]:
+    assert len(res_data["items"]) == 5
+    for item in res_data["items"]:
         assert_instance_fields(item, expected_fields)
 
     # Get by desc sorting (asc by default)
@@ -283,13 +283,13 @@ async def test_project_CRUD_and_search(
     res_data = await res.json()
     assert res.status == 200
     assert res_data["total"] == 8
-    assert len(res_data["item"]) == 5
-    for item in res_data["item"]:
+    assert len(res_data["items"]) == 5
+    for item in res_data["items"]:
         assert_instance_fields(item, expected_fields)
-    assert res_data["item"][0]["name"] == "user public project 1"  # this one if not sorting will be last
+    assert res_data["items"][0]["name"] == "user public project 1"  # this one if not sorting will be last
 
     # Test RBAC for update/delete
-    project_id = res_data["item"][0]["id"]
+    project_id = res_data["items"][0]["id"]
     update_data = {"name": "Edited name", "description": "Edited description"}
 
     for cookies in [cookies_contributor, cookies_viewer]:

backend/app/utils/executor/ssh.py

@@ -503,7 +503,12 @@ def _generate_script(self, server: str, job: WebJob, params: dict) -> str:
 mkdir -p $NXF_SINGULARITY_CACHEDIR
 
 # === Install pixi ===
-which pixi || curl -fsSL https://pixi.sh/install.sh | sh
+if [ ! -f "$HOME/.pixi/bin/pixi" ]; then
+    curl -fsSL https://pixi.sh/install.sh | sh
+else
+    echo "Pixi already installed."
+fi
+
 export PATH=$PATH:$HOME/.pixi/bin
 # Only append channels if not already present
 if ! pixi config get default-channels --global | grep -q bioconda; then

backend/perf/install.sh

@@ -12,7 +12,11 @@ tar xf pypy3.11-v7.3.20-linux64.tar.bz2
 ./pypy3.11-v7.3.20-linux64/bin/pypy -mpip install -U pip wheel
 ./pypy3.11-v7.3.20-linux64/bin/pypy -mpip install -r requirements.txt
 
+# download for bombardier
+wget https://github.com/codesenberg/bombardier/releases/download/v2.0.2/bombardier-linux-amd64
+chmod +x bombardier-linux-amd64
 
+./bombardier-linux-amd64 -c 2000 -d 10s -l http://river-backend:8000/api/health
 
 # pypy3.11 socketify
 ./pypy3.11-v7.3.20-linux64/bin/pypy -m socketify app:app --worker 2 --port 8000

backend/requirements.txt

@@ -18,4 +18,5 @@ celery==5.5.3
 socketify==0.0.31
 psycopg[binary]==3.3.2
 psycopg-pool==3.3.0
-anyio==4.12.0
+anyio==4.12.0
+cffi==1.18.0.dev0

backend/run_server.sh

@@ -13,4 +13,4 @@ echo "Starting BlackSheep app..."
 pypy -m socketify app.main:app \
     --host 0.0.0.0 \
     --port 8000 \
-    --workers "$(nproc --all)"
+    --workers 2

frontend/src/features/credential/contexts/CredentialContext.tsx

@@ -137,6 +137,7 @@ export const CredentialContextProvider: React.FC<{ children: ReactNode }> = ({
 				case CredentialTypeEnum.GITHUB:
 					if (
 						existing.type === CredentialTypeEnum.GITHUB
+						&& existing.username
 					) {
 						update = true;
 					}

frontend/src/features/project/components/Projects.tsx

@@ -45,7 +45,7 @@ const Projects: React.FC = () => {
 	const [sorting, setSorting] = useState<MRT_SortingState>([]);
 	const [pagination, setPagination] = useState({
 		pageIndex: 0,
-		pageSize: 5,
+		pageSize: 10,
 	});
 
 	// Fetch projects