deps: upgrade deps to latest versions (20240611) (datavisyn#344)

* feat: upgrade backend deps to latest version (20240611)

* update all frontend deps

* deps(npm): [email protected]

* deps(npm): [email protected]

---------

Co-authored-by: Holger Stitz <[email protected]>

.yarnrc.yml

@@ -1,3 +1,3 @@
 nodeLinker: node-modules
 
-yarnPath: .yarn/releases/yarn-4.1.0.cjs
+yarnPath: .yarn/releases/yarn-4.3.0.cjs

package.json

@@ -76,53 +76,53 @@
   },
   "dependencies": {
     "@emotion/css": "^11.11.2",
-    "@emotion/react": "^11.9.3",
-    "@fortawesome/fontawesome-free": "^6.1.1",
-    "@fortawesome/fontawesome-svg-core": "^6.1.2",
-    "@fortawesome/free-regular-svg-icons": "^6.1.2",
-    "@fortawesome/free-solid-svg-icons": "^6.1.2",
-    "@fortawesome/react-fontawesome": "^0.2.0",
-    "@mantine/code-highlight": "~7.6.1",
-    "@mantine/core": "~7.8.1",
-    "@mantine/dates": "~7.8.1",
-    "@mantine/dropzone": "~7.8.1",
-    "@mantine/form": "~7.8.1",
-    "@mantine/hooks": "~7.8.1",
-    "@mantine/modals": "~7.8.1",
-    "@mantine/notifications": "~7.8.1",
+    "@emotion/react": "^11.11.4",
+    "@fortawesome/fontawesome-free": "^6.5.2",
+    "@fortawesome/fontawesome-svg-core": "^6.5.2",
+    "@fortawesome/free-regular-svg-icons": "^6.5.2",
+    "@fortawesome/free-solid-svg-icons": "^6.5.2",
+    "@fortawesome/react-fontawesome": "^0.2.2",
+    "@mantine/code-highlight": "~7.10.1",
+    "@mantine/core": "~7.10.1",
+    "@mantine/dates": "~7.10.1",
+    "@mantine/dropzone": "~7.10.1",
+    "@mantine/form": "~7.10.1",
+    "@mantine/hooks": "~7.10.1",
+    "@mantine/modals": "~7.10.1",
+    "@mantine/notifications": "~7.10.1",
     "@mantine/styles": "~6.0.21",
-    "@mantine/tiptap": "~7.8.1",
+    "@mantine/tiptap": "~7.10.1",
     "@mantine6/core": "npm:@mantine/core@~6.0.21",
-    "@sentry/react": "^8.5.0",
-    "@types/d3-hexbin": "^0.2.3",
-    "@types/d3v7": "npm:@types/d3@^7.4.0",
-    "@types/plotly.js-dist-min": "^2.3.0",
-    "@types/react": "^18.2.0",
-    "@types/react-dom": "^18.2.0",
-    "@types/react-plotly.js": "^2.5.0",
-    "arquero": "^5.2.0",
+    "@sentry/react": "^8.8.0",
+    "@types/d3-hexbin": "^0.2.5",
+    "@types/d3v7": "npm:@types/d3@^7.4.3",
+    "@types/plotly.js-dist-min": "^2.3.4",
+    "@types/react": "^18.3.3",
+    "@types/react-dom": "^18.3.0",
+    "@types/react-plotly.js": "^2.6.3",
+    "arquero": "^5.4.0",
     "d3-force-boundary": "^0.0.3",
     "d3-hexbin": "^0.2.2",
-    "d3v7": "npm:d3@^7.4.0",
+    "d3v7": "npm:d3@^7.9.0",
     "fit-curve": "^0.2.0",
     "html-to-image": "^1.11.11",
-    "i18next": "^22.4.15",
+    "i18next": "^23.11.5",
     "jstat": "^1.9.6",
-    "lineupjs": "4.10.0",
-    "lodash": "~4.17.20",
-    "plotly.js-dist-min": "~2.12.0",
-    "react": "~18.2.0",
-    "react-dom": "~18.2.0",
+    "lineupjs": "4.11.0",
+    "lodash": "~4.17.21",
+    "plotly.js-dist-min": "~2.33.0",
+    "react": "~18.3.1",
+    "react-dom": "~18.3.1",
     "react-highlight-words": "^0.20.0",
-    "react-plotly.js": "^2.5.1",
-    "react-spring": "^9.7.1",
-    "use-deep-compare-effect": "^1.8.0",
+    "react-plotly.js": "^2.6.0",
+    "react-spring": "^9.7.3",
+    "use-deep-compare-effect": "^1.8.1",
     "visyn_scripts": "^9.0.0"
   },
   "devDependencies": {
-    "@chromatic-com/storybook": "^1.3.2",
-    "chromatic": "^11.3.0",
-    "cypress": "^13.2.0"
+    "@chromatic-com/storybook": "^1.5.0",
+    "chromatic": "^11.5.3",
+    "cypress": "^13.11.0"
   },
   "visyn": {
     "entries": {
@@ -135,5 +135,5 @@
       }
     }
   },
-  "packageManager": "yarn@4.1.0"
+  "packageManager": "yarn@4.3.0"
 }

requirements.txt

@@ -1,34 +1,44 @@
 # a2wsgi==1.6.0 # This WSIGMiddleware is not compatible with starlette_context
 alembic==1.13.1
 cachetools==5.3.3
-fastapi==0.110.1
+fastapi==0.111.0
 json-cfg==0.4.2
-openpyxl==3.1.2
-opentelemetry-api==1.24.0
-opentelemetry-exporter-otlp==1.24.0
-opentelemetry-exporter-prometheus==0.45b0
-opentelemetry-instrumentation-fastapi==0.45b0
-opentelemetry-instrumentation-httpx==0.45b0
-opentelemetry-instrumentation-logging==0.45b0
-opentelemetry-instrumentation-requests==0.45b0
-opentelemetry-instrumentation-sqlalchemy==0.45b0
-opentelemetry-instrumentation-system-metrics==0.45b0
-opentelemetry-sdk==1.24.0
-psycopg==3.1.18
+openpyxl==3.1.3
+opentelemetry-api==1.25.0
+opentelemetry-exporter-otlp==1.25.0
+opentelemetry-exporter-prometheus==0.46b0
+opentelemetry-instrumentation-fastapi==0.46b0
+opentelemetry-instrumentation-httpx==0.46b0
+opentelemetry-instrumentation-logging==0.46b0
+opentelemetry-instrumentation-requests==0.46b0
+opentelemetry-instrumentation-sqlalchemy==0.46b0
+opentelemetry-instrumentation-system-metrics==0.46b0
+opentelemetry-sdk==1.25.0
+psycopg==3.1.19
 psycopg2==2.9.9
-pydantic==1.10.14
+pydantic==1.10.15
 pyjwt[crypto]==2.8.0
 pytest-postgresql==6.0.0
 python-dateutil==2.9.0.post0
-python-multipart==0.0.9
-requests==2.32.0
+requests==2.32.3
 SQLAlchemy>=1.4.40,<=1.4.49
 starlette-context==0.3.6
-uvicorn[standard]==0.29.0
-# Extras from fastapi[all], which we can't install because it requires pydantic v2: https://github.com/tiangolo/fastapi/blob/f7e3559bd5997f831fb9b02bef9c767a50facbc3/pyproject.toml#L57-L67
-httpx>=0.23.0
-jinja2>=2.11.2
-itsdangerous>=1.1.0
-pyyaml>=5.3.1
-ujson>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0
-orjson>=3.2.1
+uvicorn[standard]==0.30.1
+# Extras from fastapi[all], which we can't install because it requires pydantic v2: https://github.com/tiangolo/fastapi/blob/master/pyproject.toml#L79-L103
+fastapi-cli >=0.0.4
+# # For the test client
+httpx >=0.27.0
+# For templates
+jinja2 >=2.11.2
+# For forms and file uploads
+python-multipart >=0.0.7
+# For Starlette's SessionMiddleware, not commonly used with FastAPI
+itsdangerous >=1.1.0
+# For Starlette's schema generation, would not be used with FastAPI
+pyyaml >=5.3.1
+# For UJSONResponse
+ujson >=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0
+# For ORJSONResponse
+orjson >=3.2.1
+# To validate email fields
+email_validator >=2.0.0

requirements_dev.txt

@@ -1,5 +1,5 @@
 black~=24.4.2
-pyright==1.1.356
+pyright==1.1.366
 pytest-runner~=6.0.1
-pytest~=8.2.1
-ruff==0.4.7
+pytest~=8.2.2
+ruff==0.4.8

src/i18n/I18nextManager.ts

@@ -1,5 +1,5 @@
 // In case of failing tests due to i18next, check if the `esModuleInterop` flag is set to true in the jest config (in "tsConfig" object under "ts-jest" in globals property).
-import i18next from 'i18next';
+import i18next, { i18n as i18nType } from 'i18next';
 import { pluginRegistry } from '../plugin/PluginRegistry';
 import { EP_PHOVEA_CORE_LOCALE, ILocaleEPDesc } from '../plugin/extensions';
 
@@ -13,7 +13,7 @@ export class I18nextManager {
    * Thus allowing the existence of multiple i18next instances with different configurations
    * without one overwriting the other
    */
-  public i18n = i18next.createInstance();
+  public i18n: i18nType = i18next.createInstance();
 
   /**
    *  Awaits the translation files registered at the EP_PHOVEA_CORE_LOCALE extension point

visyn_core/tests/test_telemetry.py

@@ -29,12 +29,12 @@ def test_fastapi_metrics(client: TestClient):
     parsed = {m.name: m for m in text_string_to_metric_families(metrics_text)}
 
     # Check for app info
-    fastapi_app_info_metric = parsed["fastapi_app_info_1"]  # TODO: Why _1?
+    fastapi_app_info_metric = parsed["fastapi_app_info"]  # TODO: Why _1?
     assert len(fastapi_app_info_metric.samples) == 1
     assert fastapi_app_info_metric.samples[0].labels["app_name"] == "visyn.app.datavisyn.io"
 
     # Check for request counts
-    fastapi_requests_metric = parsed["fastapi_requests_1"]  # TODO: Why _1?
+    fastapi_requests_metric = parsed["fastapi_requests"]  # TODO: Why _1?
     assert len(fastapi_requests_metric.samples) == 2
     assert fastapi_requests_metric.samples[0].labels["path"] == "/api/health"
     assert fastapi_requests_metric.samples[0].value == 1
@@ -47,7 +47,7 @@ def test_fastapi_metrics(client: TestClient):
     parsed = {m.name: m for m in text_string_to_metric_families(metrics_text)}
 
     # And check for increased counts
-    fastapi_requests_metric = parsed["fastapi_requests_1"]  # TODO: Why _1?
+    fastapi_requests_metric = parsed["fastapi_requests"]  # TODO: Why _1?
     assert len(fastapi_requests_metric.samples) == 2
     assert fastapi_requests_metric.samples[0].labels["path"] == "/api/health"
     assert fastapi_requests_metric.samples[0].value == 2