Copier update (python install scripts)

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v0.0.44
+_commit: v0.0.49
 _src_path: gh:LabAutomationAndScreening/copier-base-template.git
 description: Copier template for creating Python libraries and executables
 python_ci_versions:

.devcontainer/Dockerfile

@@ -1,4 +1,7 @@
-FROM mcr.microsoft.com/vscode/devcontainers/universal:2.9.0-focal
+# base image tags available at https://mcr.microsoft.com/v2/devcontainers/universal/tags/list
+# added the platform flag to override any local settings since this image is only compatible with linux/amd64. since this image is only x64 compatible, suppressing the hadolint rule
+# hadolint ignore=DL3029
+FROM --platform=linux/amd64 mcr.microsoft.com/devcontainers/universal:2.13.1-focal
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 

.devcontainer/devcontainer.json

@@ -3,12 +3,13 @@
   "service": "devcontainer",
   "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
   "features": {
-    "ghcr.io/devcontainers/features/aws-cli:1": {
+    "ghcr.io/devcontainers/features/aws-cli:1.1.1": {
+      // 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": "2.24.24"
+      "version": "2.27.14"
     },
-    "ghcr.io/devcontainers/features/python:1": {
-      // https://github.com/devcontainers/features/tree/main/src/python
+    "ghcr.io/devcontainers/features/python:1.7.1": {
+      // https://github.com/devcontainers/features/blob/main/src/python/devcontainer-feature.json
       "version": "3.12.7",
       "installTools": false,
       "optimize": true
@@ -20,16 +21,16 @@
       "extensions": [
         // basic tooling
         "eamodio.gitlens@15.5.1",
-        "ms-vscode.live-server@0.5.2024091601",
+        "ms-vscode.live-server@0.5.2025051301",
         "MS-vsliveshare.vsliveshare@1.0.5905",
-        "github.copilot@1.304.1523",
-        "github.copilot-chat@0.27.2025042301",
+        "github.copilot@1.320.1564",
+        "github.copilot-chat@0.28.2025051402",
 
         // Python
-        "ms-python.python@2024.14.1",
-        "ms-python.vscode-pylance@2024.9.2",
-        "ms-vscode-remote.remote-containers@0.383.0",
-        "charliermarsh.ruff@2024.54.0",
+        "ms-python.python@2025.7.2025051401",
+        "ms-python.vscode-pylance@2025.4.104",
+        "ms-vscode-remote.remote-containers@0.414.0",
+        "charliermarsh.ruff@2025.22.0",
 
         // Misc file formats
         "bierner.markdown-mermaid@1.28.0",
@@ -42,6 +43,7 @@
         "editor.accessibilitySupport": "off", // turn off sounds
         "extensions.autoUpdate": false,
         "extensions.autoCheckUpdates": false,
+        "livePreview.portNumber": 3025, // arbitrary not to conflict with default 3000 Nuxt port number
         "[python]": {
           "editor.formatOnSave": true,
           "editor.defaultFormatter": "charliermarsh.ruff"
@@ -59,5 +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): a16b1f65 # spellchecker:disable-line
+  // Devcontainer context hash (do not manually edit this, it's managed by a pre-commit hook): dfcd01a5 # spellchecker:disable-line
 }

.devcontainer/envs.json

@@ -0,0 +1,7 @@
+[
+  {
+    "description": "main",
+    "relative_directory": ".",
+    "package_manager": "uv"
+  }
+]

.devcontainer/install-ci-tooling.py

@@ -0,0 +1,114 @@
+import argparse
+import os
+import platform
+import shutil
+import subprocess
+import sys
+
+UV_VERSION = "0.7.8"
+PNPM_VERSION = "10.11.0"
+COPIER_VERSION = "9.7.1"
+COPIER_TEMPLATES_EXTENSION_VERSION = "0.3.1"
+PRE_COMMIT_VERSION = "4.2.0"
+GITHUB_WINDOWS_RUNNER_BIN_PATH = r"C:\Users\runneradmin\.local\bin"
+parser = argparse.ArgumentParser(description="Install CI tooling for the repo")
+_ = parser.add_argument(
+    "--no-python",
+    default=False,
+    action="store_true",
+    help="Do not process any environments using python package managers",
+)
+_ = parser.add_argument(
+    "--python-version",
+    default=f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}",
+    type=str,
+    help="What version to install.",
+)
+_ = parser.add_argument(
+    "--no-node", action="store_true", default=False, help="Do not process any environments using node package managers"
+)
+
+
+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_path = ((GITHUB_WINDOWS_RUNNER_BIN_PATH + "\\") if is_windows else "") + "uv"
+    if is_windows:
+        pwsh = shutil.which("pwsh") or shutil.which("powershell")
+        if not pwsh:
+            raise FileNotFoundError("Neither 'pwsh' nor 'powershell' found on PATH")
+    if not args.no_python:
+        if is_windows:
+            uv_env.update({"PATH": rf"{GITHUB_WINDOWS_RUNNER_BIN_PATH};{uv_env['PATH']}"})
+            # invoke installer in a pwsh process
+            _ = subprocess.run(
+                [
+                    pwsh,  # type: ignore[reportPossiblyUnboundVariable] # this matches the conditional above that defines pwsh
+                    "-NoProfile",
+                    "-NonInteractive",
+                    "-Command",
+                    f"irm https://astral.sh/uv/{UV_VERSION}/install.ps1 | iex",
+                ],
+                check=True,
+                env=uv_env,
+            )
+        else:
+            _ = subprocess.run(
+                f"curl -fsSL https://astral.sh/uv/{UV_VERSION}/install.sh | sh",
+                check=True,
+                shell=True,
+                env=uv_env,
+            )
+            # TODO: add uv autocompletion to the shell https://docs.astral.sh/uv/getting-started/installation/#shell-autocompletion
+        _ = subprocess.run(
+            [
+                uv_path,
+                "tool",
+                "install",
+                f"copier=={COPIER_VERSION}",
+                "--with",
+                f"copier-templates-extensions=={COPIER_TEMPLATES_EXTENSION_VERSION}",
+            ],
+            check=True,
+            env=uv_env,
+        )
+        _ = subprocess.run(
+            [
+                uv_path,
+                "tool",
+                "install",
+                f"pre-commit=={PRE_COMMIT_VERSION}",
+            ],
+            check=True,
+            env=uv_env,
+        )
+        _ = subprocess.run(
+            [
+                uv_path,
+                "tool",
+                "list",
+            ],
+            check=True,
+            env=uv_env,
+        )
+    if not args.no_node:
+        pnpm_install_sequence = ["npm -v", f"npm install -g pnpm@{PNPM_VERSION}", "pnpm -v"]
+        for cmd in pnpm_install_sequence:
+            cmd = (
+                [
+                    pwsh,  # type: ignore[reportPossiblyUnboundVariable] # this matches the conditional above that defines pwsh
+                    "-NoProfile",
+                    "-NonInteractive",
+                    "-Command",
+                    cmd,
+                ]
+                if is_windows
+                else [cmd]
+            )
+            _ = subprocess.run(cmd, shell=True, check=True)
+
+
+if __name__ == "__main__":
+    main()

.devcontainer/manual-setup-deps.py

@@ -0,0 +1,120 @@
+import argparse
+import enum
+import json
+import os
+import platform
+import shutil
+import subprocess
+import sys
+from pathlib import Path
+from typing import Any
+
+REPO_ROOT_DIR = Path(__file__).parent.parent.resolve()
+ENVS_CONFIG = REPO_ROOT_DIR / ".devcontainer" / "envs.json"
+parser = argparse.ArgumentParser(description="Manual setup for dependencies in the repo")
+_ = parser.add_argument(
+    "--python-version",
+    type=str,
+    default=f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}",
+    help="What version to install.",
+)
+_ = parser.add_argument("--skip-check-lock", action="store_true", default=False, help="Skip the lock file check step")
+_ = parser.add_argument(
+    "--optionally-check-lock", action="store_true", default=False, help="Check the lock file IFF it exists"
+)
+_ = parser.add_argument(
+    "--no-python",
+    action="store_true",
+    default=False,
+    help="Do not process any environments using python package managers",
+)
+_ = parser.add_argument(
+    "--no-node", action="store_true", default=False, help="Do not process any environments using node package managers"
+)
+
+
+class PackageManager(str, enum.Enum):
+    UV = "uv"
+    PNPM = "pnpm"
+
+
+class EnvConfig:
+    def __init__(self, json_dict: dict[str, Any]):
+        super().__init__()
+        self.package_manager = PackageManager(json_dict["package_manager"])
+        self.path = REPO_ROOT_DIR
+        if "relative_directory" in json_dict:
+            self.path = REPO_ROOT_DIR / json_dict["relative_directory"]
+        if self.package_manager == PackageManager.UV:
+            self.lock_file = self.path / "uv.lock"
+        elif self.package_manager == PackageManager.PNPM:
+            self.lock_file = self.path / "pnpm-lock.yaml"
+        else:
+            raise NotImplementedError(f"Package manager {self.package_manager} is not supported")
+
+
+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})
+    skip_check_lock = args.skip_check_lock
+    if skip_check_lock and args.optionally_check_lock:
+        print("Cannot skip and optionally check the lock file at the same time.")
+        sys.exit(1)
+
+    with ENVS_CONFIG.open("r") as f:
+        envs = json.load(f)
+
+    for env_dict in envs:
+        env = EnvConfig(env_dict)
+        if args.no_python and env.package_manager == PackageManager.UV:
+            print(f"Skipping environment {env.path} as it uses a Python package manager and --no-python is set")
+            continue
+        if args.no_node and env.package_manager == PackageManager.PNPM:
+            print(f"Skipping environment {env.path} as it uses a Node package manager and --no-node is set")
+            continue
+        env_skip_check_lock = skip_check_lock
+        if args.optionally_check_lock and env.lock_file.exists():
+            env_skip_check_lock = False
+        if not env_skip_check_lock:
+            if env.package_manager == PackageManager.UV:
+                _ = subprocess.run(["uv", "lock", "--check", "--directory", str(env.path)], check=True, env=uv_env)
+            elif env.package_manager == PackageManager.PNPM:
+                pass  # doesn't seem to be a way to do this https://github.com/orgs/pnpm/discussions/3202
+            else:
+                raise NotImplementedError(f"Package manager {env.package_manager} does not support lock file checking")
+        if env.package_manager == PackageManager.UV:
+            sync_command = ["uv", "sync", "--directory", str(env.path)]
+            if not env_skip_check_lock:
+                sync_command.append("--frozen")
+            _ = subprocess.run(
+                sync_command,
+                check=True,
+                env=uv_env,
+            )
+        elif env.package_manager == PackageManager.PNPM:
+            pnpm_command = ["pnpm", "install", "--dir", str(env.path)]
+            if not env_skip_check_lock:
+                pnpm_command.append("--frozen-lockfile")
+            if is_windows:
+                pwsh = shutil.which("pwsh") or shutil.which("powershell")
+                if not pwsh:
+                    raise FileNotFoundError("Neither 'pwsh' nor 'powershell' found on PATH")
+                pnpm_command = [
+                    pwsh,
+                    "-NoProfile",
+                    "-NonInteractive",
+                    "-Command",
+                    " ".join(pnpm_command),
+                ]
+            _ = subprocess.run(
+                pnpm_command,
+                check=True,
+            )
+        else:
+            raise NotImplementedError(f"Package manager {env.package_manager} is not supported for installation")
+
+
+if __name__ == "__main__":
+    main()

.devcontainer/on-create-command-boilerplate.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 set -ex
 
-sh .devcontainer/install-ci-tooling.sh
+python .devcontainer/install-ci-tooling.py
 
 git config --global --add --bool push.autoSetupRemote true
 git config --local core.symlinks true

.devcontainer/on-create-command.sh

@@ -9,4 +9,4 @@ sh .devcontainer/on-create-command-boilerplate.sh
 
 pre-commit install --install-hooks
 
-sh .devcontainer/manual-setup-deps.sh --optionally-lock
+python .devcontainer/manual-setup-deps.py --optionally-check-lock