Copier update (biome)

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v0.0.55
+_commit: v0.0.57
 _src_path: gh:LabAutomationAndScreening/copier-base-template.git
 description: Copier template for creating Python libraries and executables
 python_ci_versions:

.devcontainer/devcontainer.json

@@ -61,5 +61,5 @@
   "initializeCommand": "sh .devcontainer/initialize-command.sh",
   "onCreateCommand": "sh .devcontainer/on-create-command.sh",
   "postStartCommand": "sh .devcontainer/post-start-command.sh"
-  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): 6ebb97a5 # spellchecker:disable-line
+  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): 01ec0f62 # spellchecker:disable-line
 }

.devcontainer/install-ci-tooling.py

@@ -8,7 +8,7 @@
 from pathlib import Path
 
 UV_VERSION = "0.7.12"
-PNPM_VERSION = "10.12.1"
+PNPM_VERSION = "10.13.1"
 COPIER_VERSION = "9.7.1"
 COPIER_TEMPLATES_EXTENSION_VERSION = "0.3.1"
 PRE_COMMIT_VERSION = "4.2.0"

.github/dependabot.yml

@@ -9,6 +9,9 @@ updates:
       time: "16:00"
     open-pull-requests-limit: 5
     ignore:
+      - dependency-name: "*"
+        update-types:
+          - "version-update:semver-patch" # we don't want to be bothered with patch updates for anything except security updates
       - dependency-name: "boto3" # boto3 gets patch updates way too frequently and they're usually not important
         update-types:
           - "version-update:semver-patch"

.pre-commit-config.yaml

@@ -42,9 +42,16 @@ repos:
 
   # Reformatting (should generally come before any file format or other checks, because reformatting can change things)
   - repo: https://github.com/crate-ci/typos
-    rev: 0f0ccba9ed1df83948f0c15026e4f5ccfce46109  # frozen: v1.32.0
+    rev: 392b78fe18a52790c53f42456e46124f77346842  # frozen: v1.34.0
     hooks:
       - id: typos
+        exclude:
+          |
+          (?x)^(
+              .*\.min.js|
+              .*\.min.css|
+              .*\.umd.js|
+          )$
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: cef0300fd0fc4d2a87a85fa2093c6b283ea36f4b # frozen: v5.0.0
     hooks:
@@ -77,17 +84,21 @@ repos:
               .*devcontainer.json|
               .*pyrightconfig.json|
               .*tsconfig.json|
+              .*biome.jsonc|
               .*/vendor_files/.*|
           )$
         args: [--autofix, --no-sort-keys]
 
   - repo: https://github.com/biomejs/pre-commit
-    rev: 748e40d32e076a6aaaf3353a2564c8fe43764f79  # frozen: v2.0.0-beta.1
+    rev: a450e9c04887b1305951c298db5999cd30155f74  # frozen: v2.1.1
     hooks:
       - id: biome-check
+        # exclude generated files from codegen and strawberry
         exclude: |
           (?x)^(
               .*generated/graphql.ts|
+              .*/schema.graphql|
+              .*pyrightconfig\.json|
           )$
 
   - repo: https://github.com/pre-commit/mirrors-prettier # TODO: switch to a different approach...this was archived in 2024
@@ -102,10 +113,17 @@ repos:
               .*devcontainer.json|
               .*pyrightconfig.json|
               .*tsconfig.json|
+              .*/__snapshots__/.*|
+              .*.min.js|
+              .*.min.css|
+              .*.umd.js|
               .*.yaml|
               .*.yml|
               .*.md|
+              .*.jsonc|
               .*/vendor_files/.*|
+              .*/schema.graphql|
+              .*generated/graphql.ts|
           )$
         files: (.*.json)|(.*.ts)|(.*.jsx)|(.*.tsx)|(.*.yaml)|(.*.yml)|(.*.md)|(.*.html)|(.*.css)|(.*.scss)|(.*.less)|(.*.vue)|(.*.graphql)|(.*.gql)
 
@@ -204,7 +222,7 @@ repos:
         description: Runs hadolint to lint Dockerfiles
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 24e02b24b8ab2b7c76225602d13fa60e12d114e6  # frozen: v0.11.9
+    rev: 3d44372123ca5e8617fdb65d9f11facd159b9e95  # frozen: v0.12.3
     hooks:
       - id: ruff
         name: ruff-src

biome.jsonc

@@ -0,0 +1,16 @@
+{
+  "formatter": {
+    "enabled": false,
+  },
+  "linter": {
+    "enabled": false,
+  },
+  "files": {
+    "includes": [
+      "**",
+      "!template/template/biome.jsonc",
+      "!template/biome.jsonc",
+      "!**/*.css", // still too many false positives, so we exclude CSS files
+    ],
+  },
+}

extensions/context.py

@@ -11,30 +11,30 @@ class ContextUpdater(ContextHook):
     @override
     def hook(self, context: dict[Any, Any]) -> dict[Any, Any]:
         context["uv_version"] = "0.7.12"
-        context["pnpm_version"] = "10.12.1"
+        context["pnpm_version"] = "10.13.1"
         context["pre_commit_version"] = "4.2.0"
-        context["pyright_version"] = "1.1.402"
+        context["pyright_version"] = "1.1.403"
         context["pytest_version"] = "8.4.0"
         context["pytest_randomly_version"] = "3.16.0"
         context["pytest_cov_version"] = "6.2.1"
         context["copier_version"] = "9.7.1"
         context["copier_templates_extension_version"] = "0.3.1"
         context["sphinx_version"] = "8.1.3"
-        context["pulumi_version"] = "3.177.0"
+        context["pulumi_version"] = "3.181.0"
         context["pulumi_aws_version"] = "6.83.0"
         context["pulumi_aws_native_version"] = "1.30.0"
         context["pulumi_command_version"] = "1.1.0"
         context["pulumi_github_version"] = "6.7.2"
         context["pulumi_okta_version"] = "4.20.0"
         context["boto3_version"] = "1.38.38"
         context["ephemeral_pulumi_deploy_version"] = "0.0.4"
-        context["pydantic_version"] = "2.11.5"
+        context["pydantic_version"] = "2.11.7"
         context["pyinstaller_version"] = "6.13.0"
         context["setuptools_version"] = "80.7.1"
         context["strawberry_graphql_version"] = "0.270.4"
-        context["fastapi_version"] = "0.115.12"
-        context["uvicorn_version"] = "0.34.2"
-        context["lab_auto_pulumi_version"] = "0.1.14"
+        context["fastapi_version"] = "0.115.14"
+        context["uvicorn_version"] = "0.35.0"
+        context["lab_auto_pulumi_version"] = "0.1.15"
 
         context["nuxt_ui_version"] = "^3.1.2"
         context["nuxt_version"] = "^3.17.3"

pyproject.toml

@@ -9,7 +9,7 @@ dependencies = [
     "pytest>=8.4.0",
     "pytest-cov>=6.2.1",
     "pytest-randomly>=3.16.0",
-    "pyright[nodejs]>=1.1.402",
+    "pyright[nodejs]>=1.1.403",
     "copier>=9.7.1",
     "copier-templates-extensions>=0.3.1"
 

ruff.toml

@@ -61,6 +61,7 @@ ignore = [
     "TD002", # Adding author names to TODOs erodes shared ownership of codebase. Git history provides information about who originally created the TODO if that information is vitally needed
     "TD003", # Up to the author's judgement whether a TODO requires a link to an issue or not
     "TID252", # Sometimes it makes sense to use relative imports, that's a judgement call for us, not ruff
+    "TC006", # Adding quotes around classes unnecessarily confuses the IDE for automatic refactoring
 ]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.

template/.github/workflows/publish.yaml.jinja

@@ -152,19 +152,38 @@ jobs:
   install-from-staging:
     name: Install package from staging registry
     needs: [ publish-to-staging, get-values ]
-    runs-on: {% endraw %}{{ gha_linux_runner }}{% raw %}
+    strategy:
+      matrix:
+        os:
+          - "{% endraw %}{{ gha_linux_runner }}{% raw %}"
+{% endraw %}{% if use_windows_in_ci %}          - {{ gha_windows_runner }}{% endif %}{% raw %}
+        python-version:
+{% endraw %}{% for item in python_ci_versions %}
+          - {{ item }}
+{% endfor %}{% raw %}
+        include:
+          - os: "{% endraw %}{{ gha_linux_runner }}{% raw %}"
+            python-version: "{% endraw %}{{ python_ci_versions[0] }}{% raw %}"
+            JOB_MATCHING_DEV_ENV: true
+
+    runs-on: ${{ matrix.os }}
+
     steps:
+      - name: Checkout code
+        uses: actions/checkout@{% endraw %}{{ gha_checkout }}{% raw %}
       - name: Setup python
         uses: actions/setup-python@{% endraw %}{{ gha_setup_python }}{% raw %}
         with:
-          python-version: {% endraw %}{{ python_version }}{% raw %}
+          python-version: ${{ matrix.python-version }}
 {% endraw %}{% if python_package_registry == "PyPI" %}{% raw %}
       - name: Sleep to allow PyPI Index to update before proceeding to the next step
         uses: juliangruber/sleep-action@{% endraw %}{{ gha_sleep }}{% raw %}
         with:
           time: 60s{% endraw %}{% endif %}{% raw %}
       - name: Install from staging registry
         run: pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://www.pypi.org/simple {% endraw %}{{ package_name | replace('_', '-') }}{% raw %}==${{ needs.get-values.outputs.package-version }}
+      - name: Display dependencies
+        run: pip list
       - name: Confirm library can be imported successfully
         run: python -c "import {% endraw %}{{ package_name | replace('-', '_') }}{% raw %}"
 
@@ -224,18 +243,37 @@ jobs:
     name: Install package from primary registry
     if: ${{ github.event.inputs.publish_to_primary }}
     needs: [ publish-to-primary, get-values ]
-    runs-on: {% endraw %}{{ gha_linux_runner }}{% raw %}
+    strategy:
+      matrix:
+        os:
+          - "{% endraw %}{{ gha_linux_runner }}{% raw %}"
+{% endraw %}{% if use_windows_in_ci %}          - {{ gha_windows_runner }}{% endif %}{% raw %}
+        python-version:
+{% endraw %}{% for item in python_ci_versions %}
+          - {{ item }}
+{% endfor %}{% raw %}
+        include:
+          - os: "{% endraw %}{{ gha_linux_runner }}{% raw %}"
+            python-version: "{% endraw %}{{ python_ci_versions[0] }}{% raw %}"
+            JOB_MATCHING_DEV_ENV: true
+
+    runs-on: ${{ matrix.os }}
+
     steps:
+      - name: Checkout code
+        uses: actions/checkout@{% endraw %}{{ gha_checkout }}{% raw %}
       - name: Setup python
         uses: actions/setup-python@{% endraw %}{{ gha_setup_python }}{% raw %}
         with:
-          python-version: {% endraw %}{{ python_version }}{% raw %}
+          python-version: ${{ matrix.python-version }}
 {% endraw %}{% if python_package_registry == "PyPI" %}{% raw %}
       - name: Sleep to allow PyPI Index to update before proceeding to the next step
         uses: juliangruber/sleep-action@{% endraw %}{{ gha_sleep }}{% raw %}
         with:
           time: 60s{% endraw %}{% endif %}{% raw %}
       - name: Install from primary registry
         run: pip install {% endraw %}{{ package_name | replace('_', '-') }}{% raw %}==${{ needs.get-values.outputs.package-version }}
+      - name: Display dependencies
+        run: pip list
       - name: Confirm library can be imported successfully
         run: python -c "import {% endraw %}{{ package_name | replace('-', '_') }}{% raw %}"{% endraw %}

template/.pre-commit-config.yaml

@@ -42,9 +42,16 @@ repos:
 
   # Reformatting (should generally come before any file format or other checks, because reformatting can change things)
   - repo: https://github.com/crate-ci/typos
-    rev: 0f0ccba9ed1df83948f0c15026e4f5ccfce46109  # frozen: v1.32.0
+    rev: 392b78fe18a52790c53f42456e46124f77346842  # frozen: v1.34.0
     hooks:
       - id: typos
+        exclude:
+          |
+          (?x)^(
+              .*\.min.js|
+              .*\.min.css|
+              .*\.umd.js|
+          )$
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: cef0300fd0fc4d2a87a85fa2093c6b283ea36f4b # frozen: v5.0.0
     hooks:
@@ -77,17 +84,21 @@ repos:
               .*devcontainer.json|
               .*pyrightconfig.json|
               .*tsconfig.json|
+              .*biome.jsonc|
               .*/vendor_files/.*|
           )$
         args: [--autofix, --no-sort-keys]
 
   - repo: https://github.com/biomejs/pre-commit
-    rev: 748e40d32e076a6aaaf3353a2564c8fe43764f79  # frozen: v2.0.0-beta.1
+    rev: a450e9c04887b1305951c298db5999cd30155f74  # frozen: v2.1.1
     hooks:
       - id: biome-check
+        # exclude generated files from codegen and strawberry
         exclude: |
           (?x)^(
               .*generated/graphql.ts|
+              .*/schema.graphql|
+              .*pyrightconfig\.json|
           )$
 
   - repo: https://github.com/pre-commit/mirrors-prettier # TODO: switch to a different approach...this was archived in 2024
@@ -102,10 +113,17 @@ repos:
               .*devcontainer.json|
               .*pyrightconfig.json|
               .*tsconfig.json|
+              .*/__snapshots__/.*|
+              .*.min.js|
+              .*.min.css|
+              .*.umd.js|
               .*.yaml|
               .*.yml|
               .*.md|
+              .*.jsonc|
               .*/vendor_files/.*|
+              .*/schema.graphql|
+              .*generated/graphql.ts|
           )$
         files: (.*.json)|(.*.ts)|(.*.jsx)|(.*.tsx)|(.*.yaml)|(.*.yml)|(.*.md)|(.*.html)|(.*.css)|(.*.scss)|(.*.less)|(.*.vue)|(.*.graphql)|(.*.gql)
 
@@ -204,7 +222,7 @@ repos:
         description: Runs hadolint to lint Dockerfiles
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 24e02b24b8ab2b7c76225602d13fa60e12d114e6  # frozen: v0.11.9
+    rev: 3d44372123ca5e8617fdb65d9f11facd159b9e95  # frozen: v0.12.3
     hooks:
       - id: ruff
         name: ruff-src

template/biome.jsonc

@@ -0,0 +1,16 @@
+{
+  "formatter": {
+    "enabled": false,
+  },
+  "linter": {
+    "enabled": false,
+  },
+  "files": {
+    "includes": [
+      "**",
+      "!template/template/biome.jsonc",
+      "!template/biome.jsonc",
+      "!**/*.css", // still too many false positives, so we exclude CSS files
+    ],
+  },
+}

template/ruff.toml

@@ -61,6 +61,7 @@ ignore = [
     "TD002", # Adding author names to TODOs erodes shared ownership of codebase. Git history provides information about who originally created the TODO if that information is vitally needed
     "TD003", # Up to the author's judgement whether a TODO requires a link to an issue or not
     "TID252", # Sometimes it makes sense to use relative imports, that's a judgement call for us, not ruff
+    "TC006", # Adding quotes around classes unnecessarily confuses the IDE for automatic refactoring
 ]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.