Merge pull request #63 from Caleydo/release-5.0.0

Release 5.0.0

.github/workflows/build.yml

@@ -2,6 +2,10 @@ name: build
 
 on: [push, workflow_dispatch]
 
+permissions:
+  contents: write
+  id-token: write
+
 jobs:
   build:
     uses: datavisyn/github-workflows/.github/workflows/build-node-python.yml@main

coral/__init__.py

@@ -5,7 +5,7 @@
 ###############################################################################
 from os import path
 
-from tdp_core.plugin.model import AVisynPlugin, RegHelper
+from visyn_core.plugin.model import AVisynPlugin, RegHelper
 
 from .settings import CoralSettings
 

coral/migration/env.py

@@ -1,3 +1,3 @@
-import tdp_core.dbmigration.env
+import visyn_core.dbmigration.env
 
-tdp_core.dbmigration.env.run_migrations_online()
+visyn_core.dbmigration.env.run_migrations_online()

coral/migration/versions/20220414_1158_ddd776aa28c3_.py

@@ -19,15 +19,15 @@ def upgrade():
     for cmd in [
         """
 CREATE SCHEMA IF NOT EXISTS cohort;
-CREATE SEQUENCE cohort.cohort_id_seq
+CREATE SEQUENCE IF NOT EXISTS cohort.cohort_id_seq
     INCREMENT 1
     START 1
     MINVALUE 1
     MAXVALUE 2147483647
     CACHE 1;
 """,
         """
-CREATE TABLE cohort.cohort
+CREATE TABLE IF NOT EXISTS cohort.cohort
 (
     id integer NOT NULL DEFAULT nextval('cohort.cohort_id_seq'::regclass),
     name character varying COLLATE pg_catalog."default" NOT NULL,

coral/settings.py

@@ -1,5 +1,5 @@
 from pydantic import BaseModel
-from tdp_core import manager
+from visyn_core import manager
 
 
 class CoralSettings(BaseModel):

coral/sql.py

@@ -1,7 +1,7 @@
 import logging
 
 from flask import Flask, abort, jsonify, request
-from tdp_core.security import login_required
+from visyn_core.security import login_required
 
 from .settings import get_settings
 from .sql_query_mapper import QueryElements

coral/sql_query_mapper.py

@@ -7,7 +7,7 @@
 from sqlalchemy import create_engine, exc, inspect, text
 from sqlalchemy.exc import NoInspectionAvailable
 from sqlalchemy.orm import sessionmaker
-from tdp_core import manager
+from visyn_core import manager
 
 from .settings import get_settings
 from .sql_tables import Cohort

coral/tests/conftest.py

@@ -1,10 +1,10 @@
 import pytest
 from fastapi import FastAPI
 from fastapi.testclient import TestClient
-from tdp_core.security.manager import SecurityManager
-from tdp_core.security.model import User
-from tdp_core.server.visyn_server import create_visyn_server
-from tdp_core.tests.fixtures.postgres_db import postgres_db
+from visyn_core.security.manager import SecurityManager
+from visyn_core.security.model import User
+from visyn_core.server.visyn_server import create_visyn_server
+from visyn_core.tests.fixtures.postgres_db import postgres_db
 
 assert postgres_db  # silence unused import warning
 

package.json

@@ -2,7 +2,7 @@
   "name": "coral",
   "description": "Coral is a web-based cohort analysis tool to interactively create, refine, and analyze patient cohorts.",
   "homepage": "https://caleydo.org",
-  "version": "4.1.0",
+  "version": "5.0.0",
   "author": {
     "name": "PatrickAdelberger",
     "email": "[email protected]",
@@ -32,7 +32,7 @@
     "dist": "mkdir lib && cd dist && tar cvzf ../lib/bundle.tar.gz *",
     "docs": "visyn_scripts docs",
     "lint:fix": "visyn_scripts lint --fix",
-    "lint": "visyn_scripts lint || true",
+    "lint": "visyn_scripts lint",
     "prepack": "yarn run build",
     "start": "visyn_scripts start --env workspace_mode=single",
     "storybook:build": "NODE_OPTIONS=--max_old_space_size=4096 build-storybook",
@@ -72,27 +72,30 @@
     "react-dom": "^16.13.0",
     "react-router-dom": "^5.2.0",
     "split-grid": "^1.0.9",
-    "tdp_core": "^17.0.0",
-    "tdp_publicdb": "git+ssh://[email protected]/caleydo/tdp_publicdb#semver:^13.0.3",
+    "tdp_core": "^20.1.0",
+    "tdp_publicdb": "git+ssh://[email protected]:Caleydo/tdp_publicdb#semver:^14.0.0",
     "tippy.js": "^6.2.6",
-    "tourdino": "git+ssh://[email protected]/caleydo/tourdino#semver:^7.0.1",
+    "tourdino": "git+ssh://[email protected]:Caleydo/tourdino#semver:^8.0.0",
     "vega": "~5.20.0",
     "vega-embed": "6.19.1",
     "vega-functions": "5.12.0",
     "vega-lite": "5.1.1",
     "vega-parser": "6.1.3",
-    "visyn_scripts": "^1.1.1"
+    "visyn_scripts": "^4.1.0"
   },
   "devDependencies": {
     "@types/d3-selection": "^3.0.2",
     "@types/d3-transition": "^3.0.1",
-    "@types/react": "^16.14.6",
-    "@types/react-dom": "^16.9.5",
-    "@types/react-router-dom": "^5.1.7",
     "mkdirp": "0.5.1",
     "tslint": "~5.20.1",
     "worker-loader": "^2.0.0"
   },
+  "resolutions": {
+    "@types/react": "~18.2.0",
+    "@types/react-dom": "~18.2.0",
+    "react": "~18.2.0",
+    "react-dom": "~18.2.0"
+  },
   "browser": {
     "fs": false,
     "os": false,

requirements.txt

@@ -1 +1,2 @@
-tdp_core>=17.0.0,<18.0.0
+tdp_publicdb@git+https://github.com/Caleydo/[email protected]#egg=tdp_publicdb
+tdp_core>=20.1.0,<21.0.0