Bump Pydantic to v2+

.github/dependabot.yml

@@ -1,34 +1,32 @@
 version: 2
 updates:
-- package-ecosystem: pip
-  directory: "./pydatalab"
-  schedule:
-    interval: monthly
-    day: monday
-    time: "05:43"
-  target-branch: main
-  labels:
-  - dependency_updates
-  versioning-strategy: "increase-if-necessary"
-  ignore:
-    - dependency-name: "pydantic"
-      versions: [ ">=2" ]
-    - dependency-name: "bokeh"
-      versions: [ ">=3" ]
-    - dependency-name: "langchain"
-      versions: [ ">=0.3" ]
-# Updates GH actions versions as often as needed
-- package-ecosystem: github-actions
-  directory: "/"
-  schedule:
-    day: monday
-    interval: monthly
-    time: "05:33"
-  target-branch: main
-  labels:
-  - CI
-  - dependency_updates
-  groups:
-    github-actions:
-      applies-to: version-updates
-      dependency-type: production
+  - package-ecosystem: pip
+    directory: "./pydatalab"
+    schedule:
+      interval: monthly
+      day: monday
+      time: "05:43"
+    target-branch: main
+    labels:
+      - dependency_updates
+    versioning-strategy: "increase-if-necessary"
+    ignore:
+      - dependency-name: "bokeh"
+        versions: [">=3"]
+      - dependency-name: "langchain"
+        versions: [">=0.3"]
+  # Updates GH actions versions as often as needed
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      day: monday
+      interval: monthly
+      time: "05:33"
+    target-branch: main
+    labels:
+      - CI
+      - dependency_updates
+    groups:
+      github-actions:
+        applies-to: version-updates
+        dependency-type: production

.github/workflows/ci.yml

@@ -90,7 +90,7 @@ jobs:
       - name: Run all tests
         working-directory: ./pydatalab
         run: |
-          uv run pytest -rs -vvv ./tests
+          uv run pytest -rs --cov=pydatalab --cov-report=term --cov-report=xml -vvv ./tests
 
       - name: Upload coverage to Codecov
         if: matrix.python-version == '3.10' && github.repository == 'datalab-org/datalab'
@@ -149,7 +149,7 @@ jobs:
           files: docker-compose.yml
           load: true
           source: .
-          targets: 'app,api,database'
+          targets: "app,api,database"
           set: |
             app.cache-from=type=gha,scope=${{ github.ref_name }}-${{ matrix.browser-backend }}-build-app
             app.cache-from=type=gha,scope=main-${{ matrix.browser-backend }}-build-app

.github/workflows/license-check.yml

@@ -12,30 +12,30 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        submodules: true
-        fetch-depth: 0
-        ref: ${{ env.PUBLISH_UPDATE_BRANCH }}
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 0
+          ref: ${{ env.PUBLISH_UPDATE_BRANCH }}
 
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
 
-    - name: Set up uv
-      uses: astral-sh/setup-uv@v6
-      with:
-        version: ${{ env.UV_VERSION }}
-        working-directory: "./pydatalab"
-        enable-cache: true
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: ${{ env.UV_VERSION }}
+          working-directory: "./pydatalab"
+          enable-cache: true
 
-    - name: Run liccheck
-      working-directory: ./pydatalab
-      run: |
-        uv venv
-        uv sync --all-extras --dev
-        uv export --locked --all-extras --no-hashes --no-dev > requirements.txt
-        uv pip install liccheck==0.9.2 pip
-        uv run liccheck -r requirements.txt
+      - name: Run liccheck
+        working-directory: ./pydatalab
+        run: |
+          uv venv
+          uv sync --all-extras --dev
+          uv export --locked --all-extras --no-hashes --no-dev > requirements.txt
+          uv pip install liccheck==0.9.2 pip
+          uv run liccheck -r requirements.txt

.pre-commit-config.yaml

@@ -66,7 +66,13 @@ repos:
     hooks:
       - id: mypy
         additional_dependencies:
-          ["types-python-dateutil", "types-requests", "types-paramiko", "pydantic~=1.10"]
+          [
+            "types-python-dateutil",
+            "types-requests",
+            "types-paramiko",
+            "pydantic>=2.0,<3.0",
+            "pydantic-settings>=2.0",
+          ]
         args: ["--config-file", "pydatalab/pyproject.toml"]
 
   - repo: local
@@ -75,6 +81,6 @@ repos:
         name: Regenerate item model JSONSchemas
         files: "^pydatalab/src/pydatalab/models/.*.$"
         description: Check if the current code changes have enacted changes to the resulting JSONSchemas
-        entry: invoke -r pydatalab dev.generate-schemas
+        entry: uv run invoke -r pydatalab dev.generate-schemas
         pass_filenames: false
         language: system

pydatalab/pyproject.toml

@@ -23,7 +23,9 @@ dependencies = [
     "bokeh ~= 2.4, < 3.0",
     "matplotlib ~= 3.8",
     "periodictable ~= 1.7",
-    "pydantic[email, dotenv] < 2.0",
+    "pydantic[email] ~= 2.11",
+    "python-dotenv ~= 1.1",
+    "pydantic-settings ~= 2.10",
     "pint ~= 0.24",
     "pandas[excel] ~= 2.2",
     "pymongo ~= 4.7",
@@ -134,7 +136,6 @@ dev-dependencies = [
 datalab-app-plugin-insitu = { git = "https://github.com/datalab-org/datalab-app-plugin-insitu.git", rev = "v0.2.0" }
 
 [tool.pytest.ini_options]
-addopts = "--cov-report=term --cov-report=xml --cov ./src/pydatalab"
 filterwarnings = [
     "error",
     "ignore:.*np.bool8*:DeprecationWarning",