Copier update (misc version bumps) (#74)

Pull in upstream template changes

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **New Features**
  * Added optional Claude CLI integration support.
  * Added control over Python version management during setup.

* **Chores**
  * Updated development dependencies and tools to latest versions.
  * Refreshed pre-commit hook configurations and exclusion patterns.
  * Updated documentation branding references.
  * Minor text corrections throughout configuration files.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: ejfine

.copier-answers.yml

@@ -1,7 +1,8 @@
 # Changes here will be overwritten by Copier
-_commit: v0.0.74
+_commit: v0.0.77
 _src_path: gh:LabAutomationAndScreening/copier-base-template.git
 description: Copier template for creating Python libraries and executables
+install_claude_cli: false
 python_ci_versions:
 - 3.12.7
 - 3.13.2

.devcontainer/devcontainer.json

@@ -3,10 +3,10 @@
   "service": "devcontainer",
   "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
   "features": {
-    "ghcr.io/devcontainers/features/aws-cli:1.1.1": {
+    "ghcr.io/devcontainers/features/aws-cli:1.1.2": {
       // https://github.com/devcontainers/features/blob/main/src/aws-cli/devcontainer-feature.json
       // view latest version https://raw.githubusercontent.com/aws/aws-cli/v2/CHANGELOG.rst
-      "version": "2.27.14"
+      "version": "2.31.11"
     },
     "ghcr.io/devcontainers/features/python:1.7.1": {
       // https://github.com/devcontainers/features/blob/main/src/python/devcontainer-feature.json
@@ -20,17 +20,18 @@
       // Add the IDs of extensions you want installed when the container is created.
       "extensions": [
         // basic tooling
-        "[email protected]",
+        // "[email protected]",
+        "[email protected]",
         "[email protected]",
         "[email protected]",
-        "github.copilot@1.366.1775",
-        "github.copilot-chat@0.31.2025090401",
+        "github.copilot@1.380.1802",
+        "github.copilot-chat@0.33.2025101401",
 
         // Python
-        "ms-python.python@2025.13.2025090201",
-        "ms-python.vscode-pylance@2025.7.102",
+        "ms-python.python@2025.17.2025100201",
+        "ms-python.vscode-pylance@2025.8.3",
         "[email protected]",
-        "charliermarsh.ruff@2025.24.0",
+        "charliermarsh.ruff@2025.28.0",
 
         // Misc file formats
         "[email protected]",
@@ -44,6 +45,7 @@
         "extensions.autoUpdate": false,
         "extensions.autoCheckUpdates": false,
         "livePreview.portNumber": 3025, // arbitrary not to conflict with default 3000 Nuxt port number
+        "github.copilot.nextEditSuggestions.allowWhitespaceOnlyChanges": false,
         "[python]": {
           "editor.formatOnSave": true,
           "editor.defaultFormatter": "charliermarsh.ruff"
@@ -61,5 +63,5 @@
   "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): 735908f4 # spellchecker:disable-line
+  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): a5dbeab3 # spellchecker:disable-line
 }

.devcontainer/install-ci-tooling.py

@@ -7,8 +7,8 @@
 import tempfile
 from pathlib import Path
 
-UV_VERSION = "0.8.22"
-PNPM_VERSION = "10.17.1"
+UV_VERSION = "0.9.2"
+PNPM_VERSION = "10.18.3"
 COPIER_VERSION = "9.10.2"
 COPIER_TEMPLATE_EXTENSIONS_VERSION = "0.3.3"
 PRE_COMMIT_VERSION = "4.3.0"
@@ -36,13 +36,21 @@
     default=False,
     help="Skip installing the SSM plugin for AWS CLI",
 )
+_ = parser.add_argument(
+    "--allow-uv-to-install-python",
+    action="store_true",
+    default=False,
+    help="Allow uv to install new versions of Python on the fly. This is typically only needed when instantiating the copier template.",
+)
 
 
 def main():
     args = parser.parse_args(sys.argv[1:])
     is_windows = platform.system() == "Windows"
     uv_env = dict(os.environ)
-    uv_env.update({"UV_PYTHON_PREFERENCE": "only-system", "UV_PYTHON": args.python_version})
+    uv_env.update({"UV_PYTHON": args.python_version})
+    if not args.allow_uv_to_install_python:
+        uv_env.update({"UV_PYTHON_PREFERENCE": "only-system"})
     uv_path = ((GITHUB_WINDOWS_RUNNER_BIN_PATH + "\\") if is_windows else "") + "uv"
     if is_windows:
         pwsh = shutil.which("pwsh") or shutil.which("powershell")

.gitignore

@@ -44,8 +44,6 @@ pytest.log
 tests/__coverage__
 test/__coverage__
 coverage-report-pytest
-.pytest_cache/
-.mypy_cache/
 .coverage
 .coverage.*
 coverage.xml

.pre-commit-config.yaml

@@ -42,7 +42,7 @@ 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: edb4e206047e89b93ebe08f1a2ccc3d581a70cc7  # frozen: v1
+    rev: 6573587991823ef75e4d6ca97fe895f45e9f14e4  # frozen: v1
     hooks:
       - id: typos
         exclude: |
@@ -59,6 +59,7 @@ repos:
           (?x)^(
               .*/vendor_files/.*|
               .*tests/.*/__snapshots__/.*|
+              .*/openapi_codegen/.*|
           )$
       - id: end-of-file-fixer
         # the XML formatter hook doesn't leave a blank line at the end, so excluding XML files from this hook to avoid conflicts
@@ -70,10 +71,12 @@ repos:
               template/template/.copier-answers.yml.jinja|
               template/.copier-answers.yml.jinja|
               .*generated/graphql.ts|
+              .*/openapi_codegen/.*|
               .*tests/.*/__snapshots__/.*|
               .devcontainer/devcontainer-lock.json|
               .copier-answers.yml|
               .*\.xml|
+              .*\.svg|
               .*/vendor_files/.*|
           )$
       - id: pretty-format-json
@@ -85,6 +88,7 @@ repos:
               .*pyrightconfig.json|
               .*tsconfig.json|
               .*biome.jsonc|
+              .*/openapi_codegen/.*|
               .*tests/.*/__snapshots__/.*|
               .*/vendor_files/.*|
           )$
@@ -98,6 +102,7 @@ repos:
         exclude: |
           (?x)^(
               .*generated/graphql.ts|
+              .*/openapi_codegen/.*|
               .*/schema.graphql|
               .*pyrightconfig\.json|
           )$
@@ -124,6 +129,7 @@ repos:
               .*.jsonc|
               .*/vendor_files/.*|
               .*/schema.graphql|
+              .*/openapi_codegen/.*|
               .*generated/graphql.ts|
               template/.*|
           )$
@@ -148,6 +154,7 @@ repos:
           (?x)^(
               .*/__snapshots__/.*|
               .*/vendor_files/.*|
+              .*\.svg|
           )$
 
   # Invalid File Checks
@@ -170,17 +177,19 @@ repos:
       - id: check-yaml
         # .copier-answers.yml is an autogenerated YAML file by Copier that throws 'found unhashable key' errors
         # Helm charts contain other non-YAML markers that cause errors here. they should be checked with helm-lint instead
+        # VCRpy cassettes sometimes contain non-YAML markers that cause errors---but they're autogenerated anyway
         exclude: |
           (?x)^(
               .copier-answers.yml|
-              (.*/helm/.*)|
+              (.*/?helm/.*)|
+              (.*/tests/unit/.*/?cassettes/.*)|
           )$
       - id: check-xml
       - id: check-merge-conflict
       - id: check-case-conflict
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 83987cd6ad8943c7f029b500b14aaf82c00a01fa  # frozen: 0.34.0
+    rev: 83b816d020105076daac266dbf6bfed199a2da93  # frozen: 0.34.1
     hooks:
       - id: check-github-workflows
 
@@ -234,7 +243,7 @@ repos:
         description: Runs hadolint to lint Dockerfiles
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: a113f03edeabb71305f025e6e14bd2cd68660e29  # frozen: v0.13.1
+    rev: f9351c924055bf6c7b4a4670237d3ce141e9f57c  # frozen: v0.14.0
     hooks:
       - id: ruff
         name: ruff-src
@@ -244,6 +253,7 @@ repos:
           (?x)^(
               .*/graphql_codegen/.*|
               .*/openapi_codegen/.*|
+              template/.*|
           )$
       - id: ruff
         name: ruff-tests
@@ -253,6 +263,7 @@ repos:
           (?x)^(
               .*/graphql_codegen/.*|
               .*/openapi_codegen/.*|
+              template/.*|
           )$
       - id: ruff-format
         exclude: |
@@ -262,7 +273,7 @@ repos:
           )$
 
   - repo: https://github.com/pylint-dev/pylint
-    rev: 98942ba4126a6fe1657bad77027bcc11016d16da  # frozen: v3.3.8
+    rev: 9a3035053154ba0c3ca3b300d6bc9fa72b95d552  # frozen: v4.0.1
     hooks:
       - id: pylint
         name: pylint

CONTRIBUTING.md

@@ -27,7 +27,7 @@ By participating in this project, you agree to abide by our [Code of Conduct](./
 1. **Fork the repository** on GitHub.
 
 2. **Set up the Dev Container (Recommended Method)**
-   - Create a Github Codespace (`Code`->`Codespaces` in the Github web console of your cloned repository) OR click on the "Open in Devcontainer" link in the [Readme](./README.md)
+   - Create a GitHub Codespace (`Code`->`Codespaces` in the GitHub web console of your cloned repository) OR click on the "Open in Devcontainer" link in the [Readme](./README.md)
 
 3. **Make Your Changes**
    - Create a branch for your feature or bug fix:

README.md

@@ -10,7 +10,7 @@ To create a new repository using this template:
 1. Inside that devcontainer, run `python .devcontainer/install-ci-tooling.py` to install necessary tooling to instantiate the template (you can copy/paste the script from this repo...and you can paste it in the root of the repo if you want)
 1. Delete all files currently in the repository. Optional...but makes it easiest to avoid git conflicts.
 1. Run copier to instantiate the template: `copier copy --trust gh:LabAutomationAndScreening/copier-python-package-template.git .`
-1. Run `python .devcontainer/manual-setup-deps.py --only-create-lock` to generate the lock file(s)
+1. Run `python .devcontainer/manual-setup-deps.py --only-create-lock --allow-uv-to-install-python` to generate the lock file(s)
 1. Stage all files to prepare for commit (`git add .`)
 1. Run `python3 .github/workflows/hash_git_files.py . --for-devcontainer-config-update` to update the hash for your devcontainer file
 1. Commit the changes (optional)

_typos.toml

@@ -22,5 +22,5 @@ extend-exclude = [
     ".copier-answers.yml",  # this is an autogenerated file, and sometimes the commit sha gets confused as being a word
     "**/__snapshots__/**", # Snapshots need to remain static
     "**/tests/**/cassettes/**/*.yaml", # URLs and other responses in VCR.py generated files should not be altered
-    "**/vendor_files/**" # if vendors mispell things, there may be other implications in other parts of their code, just leave vendor files alone
+    "**/vendor_files/**" # if vendors misspell things, there may be other implications in other parts of their code, just leave vendor files alone
 ]

copier.yml

@@ -11,6 +11,11 @@ description:
     type: str
     help: What is the description of this repository?
 
+install_claude_cli:
+    type: bool
+    help: Should the Claude CLI be installed in the devcontainer?
+    default: no
+
 is_open_source:
     type: bool
     help: Is this library open source?

extensions/context.py

@@ -10,54 +10,55 @@ class ContextUpdater(ContextHook):
 
     @override
     def hook(self, context: dict[Any, Any]) -> dict[Any, Any]:
-        context["uv_version"] = "0.8.22"
-        context["pnpm_version"] = "10.17.1"
+        context["uv_version"] = "0.9.2"
+        context["pnpm_version"] = "10.18.3"
         context["pre_commit_version"] = "4.3.0"
-        context["pyright_version"] = "1.1.405"
+        context["pyright_version"] = "1.1.406"
         context["pytest_version"] = "8.4.2"
         context["pytest_randomly_version"] = "4.0.1"
         context["pytest_cov_version"] = "7.0.0"
         context["copier_version"] = "9.10.2"
         context["copier_template_extensions_version"] = "0.3.3"
         context["sphinx_version"] = "8.1.3"
-        context["pulumi_version"] = "3.197.0"
-        context["pulumi_aws_version"] = "7.7.0"
-        context["pulumi_aws_native_version"] = "1.33.0"
-        context["pulumi_command_version"] = "1.1.0"
-        context["pulumi_github_version"] = "6.7.3"
-        context["pulumi_okta_version"] = "5.2.0"
-        context["boto3_version"] = "1.40.41"
+        context["pulumi_version"] = "3.203.0"
+        context["pulumi_aws_version"] = "7.8.0"
+        context["pulumi_aws_native_version"] = "1.37.0"
+        context["pulumi_command_version"] = "1.1.3"
+        context["pulumi_github_version"] = "6.7.4"
+        context["pulumi_okta_version"] = "6.0.0"
+        context["boto3_version"] = "1.40.51"
         context["ephemeral_pulumi_deploy_version"] = "0.0.5"
-        context["pydantic_version"] = "2.11.7"
+        context["pydantic_version"] = "2.12.2"
         context["pyinstaller_version"] = "6.16.0"
         context["setuptools_version"] = "80.7.1"
-        context["strawberry_graphql_version"] = "0.282.0"
-        context["fastapi_version"] = "0.118.0"
+        context["strawberry_graphql_version"] = "0.283.3"
+        context["fastapi_version"] = "0.119.0"
         context["fastapi_offline_version"] = "1.7.4"
         context["uvicorn_version"] = "0.37.0"
-        context["lab_auto_pulumi_version"] = "0.1.16"
+        context["lab_auto_pulumi_version"] = "0.1.17"
         context["ariadne_codegen_version"] = "0.15.2"
-        context["pytest_mock_version"] = "3.15.0"
+        context["pytest_mock_version"] = "3.15.1"
         context["uuid_utils_version"] = "0.11.0"
+        context["syrupy_version"] = "5.0.0"
 
         context["node_version"] = "24.7.0"
-        context["nuxt_ui_version"] = "^4.0.0"
+        context["nuxt_ui_version"] = "^4.0.1"
         context["nuxt_version"] = "^4.1.0"
         context["nuxt_icon_version"] = "^2.0.0"
-        context["typescript_version"] = "^5.8.2"
-        context["playwright_version"] = "^1.55.0"
+        context["typescript_version"] = "^5.9.3"
+        context["playwright_version"] = "^1.56.0"
         context["vue_version"] = "^3.5.21"
-        context["vue_tsc_version"] = "^3.1.0"
+        context["vue_tsc_version"] = "^3.1.1"
         context["vue_devtools_api_version"] = "^8.0.0"
-        context["vue_router_version"] = "^4.5.1"
+        context["vue_router_version"] = "^4.6.0"
         context["dotenv_cli_version"] = "^10.0.0"
-        context["faker_version"] = "^10.0.0"
+        context["faker_version"] = "^10.1.0"
         context["vitest_version"] = "^3.2.4"
-        context["eslint_version"] = "^9.36.0"
+        context["eslint_version"] = "^9.37.0"
         context["nuxt_eslint_version"] = "^1.9.0"
         context["zod_version"] = "^4.1.5"
         context["zod_from_json_schema_version"] = "^0.5.0"
-        context["types_node_version"] = "^24.6.0"
+        context["types_node_version"] = "^24.7.2"
         context["nuxt_apollo_version"] = "5.0.0-alpha.15"
         context["graphql_codegen_cli_version"] = "^6.0.0"
         context["graphql_codegen_typescript_version"] = "^5.0.0"
@@ -68,7 +69,10 @@ def hook(self, context: dict[Any, Any]) -> dict[Any, Any]:
         context["nuxt_fonts_version"] = "^0.11.4"
         context["nuxtjs_color_mode_version"] = "^3.5.2"
         context["vue_test_utils_version"] = "^2.4.6"
-        context["nuxt_test_utils_version"] = "^3.17.2"
+        context["nuxt_test_utils_version"] = "3.19.1"
+        context["vue_eslint_parser_version"] = "^10.1.3"
+        context["happy_dom_version"] = "^20.0.2"
+        context["node_kiota_bundle_version"] = "1.0.0-preview.99"
 
         context["gha_checkout"] = "v5.0.0"
         context["gha_setup_python"] = "v6.0.0"