env-module-manager 0.3.0__tar.gz → 0.5.0__tar.gz

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/.github/workflows/test.yml

@@ -74,3 +74,24 @@ jobs:
 
       - name: Verify artifacts
         run: ls -l dist/
+
+  integration:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: astral-sh/setup-uv@v3
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: uv sync --group dev
+
+      - name: Test real uv deployment
+        run: uv run pytest tests/test_integration.py -m integration --no-cov

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/.gitignore

@@ -218,6 +218,7 @@ __marimo__/
 
 # Local
 .gitconductor
+/test/
 
 # OS-generated files
 .DS_Store

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/AGENTS.md

@@ -90,6 +90,9 @@ Common settings:
 * `module_root` or `MODULE_MANAGER_MODULE_ROOT`
 * `[python].indexes`, `MODULE_MANAGER_INDEX`, or `MODULE_MANAGER_INDEXES`
 * `[python].find_links` or `MODULE_MANAGER_FIND_LINKS`
+* `[python].uv_config_file` for the uv `--config-file` option. Do not add a
+  `MODULE_MANAGER_*` wrapper for this; users should use uv's `UV_CONFIG_FILE`
+  environment variable when they want environment-based uv configuration.
 
 ## Documentation
 

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: env-module-manager
-Version: 0.3.0
+Version: 0.5.0
 Summary: Deploy Python, Rust, shell, and collective CLI environments behind GNU environment modulefiles
 Project-URL: Homepage, https://github.com/ejb90/module-manager
 Project-URL: Documentation, https://module-manager.readthedocs.io/
@@ -50,6 +50,22 @@ It writes tools and modulefiles into predictable versioned locations:
 /prod/modulefiles/<name>/<version>
 ```
 
+The installation prefix and module root must be different directories.
+
+## Installation
+
+Install from PyPI:
+
+```sh
+pip install env-module-manager
+```
+
+Or install as a uv-managed tool:
+
+```sh
+uv tool install env-module-manager
+```
+
 ## Quick Start
 
 Deploy a Python CLI with `uv tool install`:
@@ -108,12 +124,5 @@ module-manager uninstall ruff 0.8.0 \
 
 ## Documentation
 
-Full documentation lives in `docs/` and can be served with MkDocs:
-
-```sh
-uv run mkdocs serve
-```
-
-Start with `docs/index.md` for installation, configuration, Python tools, Rust
-tools, shell scripts, collective environments, uninstall, and local development
-notes.
+Read the full documentation on
+[Read the Docs](https://module-manager.readthedocs.io/).

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/README.md

@@ -18,6 +18,22 @@ It writes tools and modulefiles into predictable versioned locations:
 /prod/modulefiles/<name>/<version>
 ```
 
+The installation prefix and module root must be different directories.
+
+## Installation
+
+Install from PyPI:
+
+```sh
+pip install env-module-manager
+```
+
+Or install as a uv-managed tool:
+
+```sh
+uv tool install env-module-manager
+```
+
 ## Quick Start
 
 Deploy a Python CLI with `uv tool install`:
@@ -76,12 +92,5 @@ module-manager uninstall ruff 0.8.0 \
 
 ## Documentation
 
-Full documentation lives in `docs/` and can be served with MkDocs:
-
-```sh
-uv run mkdocs serve
-```
-
-Start with `docs/index.md` for installation, configuration, Python tools, Rust
-tools, shell scripts, collective environments, uninstall, and local development
-notes.
+Read the full documentation on
+[Read the Docs](https://module-manager.readthedocs.io/).

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/docs/collective-environments.md

@@ -22,6 +22,7 @@ package = "ruff==0.8.0"
 python = "3.12"
 indexes = ["https://packages.example/simple"]
 find_links = ["/prod/wheels"]
+uv_config_file = "/prod/config/uv.toml"
 
 [[tools]]
 type = "rust"

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/docs/configuration.md

@@ -17,8 +17,13 @@ module_root = "/prod/modulefiles"
 [python]
 indexes = ["https://packages.example/simple"]
 find_links = ["/prod/wheels"]
+uv_config_file = "/prod/config/uv.toml"
 ```
 
+`prefix` and `module_root` must resolve to different directories. Using the
+same root makes `<prefix>/<name>/<version>` both an installation directory and
+a modulefile path.
+
 Use a different config file with `--config`:
 
 ```sh
@@ -36,6 +41,10 @@ export MODULE_MANAGER_FIND_LINKS=/prod/wheels,/prod/more-wheels
 
 `MODULE_MANAGER_CONFIG` can point to an alternate TOML config file.
 
+There is no `MODULE_MANAGER_*` environment variable for uv configuration files.
+Use uv's own `UV_CONFIG_FILE` environment variable when you want to set that via
+the environment.
+
 ## CLI Precedence
 
 CLI options override both environment variables and TOML config:

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/docs/development.md

@@ -14,6 +14,14 @@ uv run ruff format --check .
 uv run pytest
 ```
 
+Run the real `uv tool install` integration test with:
+
+```sh
+uv run pytest tests/test_integration.py -m integration --no-cov
+```
+
+CI runs this integration test on Linux and macOS.
+
 Build distributions:
 
 ```sh

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/docs/installation.md

@@ -38,18 +38,24 @@ in every new shell.
 
 ## Install module-manager
 
-From a local checkout:
+From PyPI with pip:
 
 ```sh
-uv tool install .
+pip install env-module-manager
 ```
 
-From PyPI:
+As a uv-managed tool:
 
 ```sh
 uv tool install env-module-manager
 ```
 
+From a local checkout:
+
+```sh
+uv tool install .
+```
+
 During development, use:
 
 ```sh

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/docs/python-tools.md

@@ -3,6 +3,10 @@
 Python CLIs are installed with `uv tool install`. Each deployed version gets
 isolated `UV_TOOL_DIR` and `UV_TOOL_BIN_DIR` paths.
 
+The install subprocess ignores inherited `UV_TOOL_*` settings so the managed
+destination and install behavior are not changed by the invoking environment.
+Other uv settings, including `UV_CONFIG_FILE`, are preserved.
+
 `uv` is an external runtime requirement for `--execute-install`. It is not a
 Python package dependency because `module-manager` shells out to the `uv`
 executable and is intended to be installable by `uv` itself.
@@ -51,6 +55,29 @@ module-manager deploy-python gitconductor 0.1.0 \
 
 `--find-links` may be used more than once.
 
+## Use a uv Config File
+
+Pass a specific uv configuration file to `uv tool install`:
+
+```sh
+module-manager deploy-python internal-tool 1.2.3 \
+  --package internal-tool==1.2.3 \
+  --uv-config-file /prod/config/uv.toml \
+  --prefix /prod/tools \
+  --module-root /prod/modulefiles \
+  --execute-install
+```
+
+The same option can be set in the module-manager config file:
+
+```toml
+[python]
+uv_config_file = "/prod/config/uv.toml"
+```
+
+Use uv's own `UV_CONFIG_FILE` environment variable if you want to configure uv
+through the environment.
+
 ## Deploy from VCS
 
 `--package` is passed directly to `uv tool install`, so VCS package specs are

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/docs/reference.md

@@ -44,6 +44,7 @@ module-manager deploy-python NAME VERSION \
   [--python PYTHON] \
   [--index URL] \
   [--find-links PATH_OR_URL] \
+  [--uv-config-file PATH] \
   [--prefix PATH] \
   [--module-root PATH] \
   [--no-default] \

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/module_manager/__init__.py

@@ -1,3 +1,3 @@
 """Deployment helpers for HPC environment module files."""
 
-__version__ = "0.1.0"
+__version__ = "0.5.0"

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/module_manager/cli.py

@@ -29,14 +29,61 @@ click.rich_click.STYLE_ARGUMENT = "bold yellow"
 click.rich_click.STYLE_SWITCH = "bold magenta"
 click.rich_click.STYLE_METAVAR = "yellow"
 click.rich_click.HEADER_TEXT = "module-manager"
-click.rich_click.FOOTER_TEXT = (
-    "Examples: [cyan]module-manager deploy-python ruff 0.8.0 --package "
-    "ruff==0.8.0 --prefix /prod/tools --module-root /prod/modulefiles[/cyan]"
-)
 
 PATH = click.Path(path_type=Path)
 ClickCommand = TypeVar("ClickCommand", bound=Command)
 
+TOP_LEVEL_EXAMPLES = (
+    "Examples:\n\n"
+    "[cyan]module-manager deploy-python ruff 0.8.0 --package ruff==0.8.0 "
+    "--prefix /prod/tools --module-root /prod/modulefiles[/cyan]\n\n"
+    "[cyan]module-manager deploy-rust ripgrep 14.1.1 --binary ./target/release/rg "
+    "--prefix /prod/tools --module-root /prod/modulefiles[/cyan]\n\n"
+    "[cyan]module-manager deploy-script my-tool 1.0.0 --script ./scripts/my-tool "
+    "--prefix /prod/tools --module-root /prod/modulefiles[/cyan]\n\n"
+    "[cyan]module-manager deploy-env --file dev-tools.toml[/cyan]\n\n"
+    "[cyan]module-manager uninstall ruff 0.8.0 --prefix /prod/tools --module-root /prod/modulefiles[/cyan]"
+)
+
+DEPLOY_PYTHON_EXAMPLES = (
+    "Examples:\n\n"
+    "[cyan]module-manager deploy-python ruff 0.8.0 --package ruff==0.8.0 "
+    "--prefix /prod/tools --module-root /prod/modulefiles --execute-install[/cyan]\n\n"
+    "[cyan]module-manager deploy-python internal-tool 1.2.3 --package internal-tool==1.2.3 "
+    "--uv-config-file /prod/config/uv.toml --prefix /prod/tools --module-root /prod/modulefiles[/cyan]"
+)
+
+DEPLOY_RUST_EXAMPLES = (
+    "Examples:\n\n"
+    "[cyan]module-manager deploy-rust ripgrep 14.1.1 --binary ./target/release/rg "
+    "--prefix /prod/tools --module-root /prod/modulefiles[/cyan]\n\n"
+    "[cyan]module-manager deploy-rust ripgrep 14.1.1 --binary ./target/release/rg "
+    "--prefix /prod/tools --module-root /prod/modulefiles --dry-run[/cyan]"
+)
+
+DEPLOY_SCRIPT_EXAMPLES = (
+    "Examples:\n\n"
+    "[cyan]module-manager deploy-script my-tool 1.0.0 --script ./scripts/my-tool "
+    "--prefix /prod/tools --module-root /prod/modulefiles[/cyan]\n\n"
+    "[cyan]module-manager deploy-script my-tool 1.0.0 --script ./scripts/my-tool "
+    "--prefix /prod/tools --module-root /prod/modulefiles --dry-run[/cyan]"
+)
+
+DEPLOY_ENV_EXAMPLES = (
+    "Examples:\n\n"
+    "[cyan]module-manager deploy-env --file dev-tools.toml[/cyan]\n\n"
+    "[cyan]module-manager deploy-env --file dev-tools.toml --prefix /scratch/tools "
+    "--module-root /scratch/modulefiles --dry-run[/cyan]"
+)
+
+UNINSTALL_EXAMPLES = (
+    "Examples:\n\n"
+    "[cyan]module-manager uninstall ruff 0.8.0 --prefix /prod/tools "
+    "--module-root /prod/modulefiles[/cyan]\n\n"
+    "[cyan]module-manager uninstall ruff 0.8.0 --prefix /prod/tools "
+    "--module-root /prod/modulefiles --dry-run[/cyan]"
+)
+
 
 def common_options(command: ClickCommand) -> ClickCommand:
     """Attach options shared by deployment commands.
@@ -108,6 +155,7 @@ def location_options(command: ClickCommand) -> ClickCommand:
         "Build versioned modulefiles for Python tools, Rust binaries, shell scripts, "
         "and collective environments."
     ),
+    epilog=TOP_LEVEL_EXAMPLES,
 )
 @click.version_option(__version__)
 @click.option(
@@ -131,7 +179,11 @@ def main(ctx: click.Context, config: Path | None) -> None:
     ctx.obj = load_config(config)
 
 
-@main.command("deploy-python", help="Write a modulefile for a uv tool install Python CLI.")
+@main.command(
+    "deploy-python",
+    help="Write a modulefile for a uv tool install Python CLI.",
+    epilog=DEPLOY_PYTHON_EXAMPLES,
+)
 @common_options
 @click.option("--package", "package", required=True, help="Package spec passed to uv tool install.")
 @click.option("--python", "python", help="Python interpreter/version passed to uv.")
@@ -147,6 +199,11 @@ def main(ctx: click.Context, config: Path | None) -> None:
     multiple=True,
     help="Directory or HTML page of packages passed to uv. May be used more than once.",
 )
+@click.option(
+    "--uv-config-file",
+    type=PATH,
+    help="uv.toml file passed to uv tool install with --config-file.",
+)
 @click.option(
     "--execute-install",
     is_flag=True,
@@ -166,6 +223,7 @@ def deploy_python(
     python: str | None,
     indexes: tuple[str, ...],
     find_links: tuple[str, ...],
+    uv_config_file: Path | None,
     execute_install: bool,
 ) -> None:
     """Write a modulefile for a [cyan]uv tool install[/cyan] Python CLI.
@@ -183,6 +241,7 @@ def deploy_python(
         python: Optional Python interpreter or version passed to uv.
         indexes: Additional package index URLs passed to uv.
         find_links: Wheelhouse directories or HTML package pages passed to uv.
+        uv_config_file: Optional uv configuration file passed to `uv tool`.
         execute_install: Whether to run `uv tool install` immediately.
 
     Raises:
@@ -191,8 +250,10 @@ def deploy_python(
             `PATH`.
         subprocess.CalledProcessError: If `uv tool install` fails.
     """
-    resolved_module_root = require_path(module_root or config.module_root, "module root", "--module-root")
-    resolved_prefix = require_path(prefix or config.prefix, "install prefix", "--prefix")
+    resolved_module_root, resolved_prefix = require_locations(
+        module_root or config.module_root,
+        prefix or config.prefix,
+    )
     paths = deploy_python_tool(
         name=name,
         version=version,
@@ -204,6 +265,7 @@ def deploy_python(
         python=python,
         indexes=indexes or config.indexes,
         find_links=find_links or config.find_links,
+        uv_config_file=(uv_config_file.expanduser() if uv_config_file else config.uv_config_file),
         execute_install=execute_install,
         make_default=make_default,
     )
@@ -212,7 +274,11 @@ def deploy_python(
     )
 
 
-@main.command("deploy-rust", help="Copy a Rust CLI binary and write a modulefile for it.")
+@main.command(
+    "deploy-rust",
+    help="Copy a Rust CLI binary and write a modulefile for it.",
+    epilog=DEPLOY_RUST_EXAMPLES,
+)
 @common_options
 @click.option(
     "--binary",
@@ -255,8 +321,10 @@ def deploy_rust(
     Raises:
         click.UsageError: If required paths are missing.
     """
-    resolved_module_root = require_path(module_root or config.module_root, "module root", "--module-root")
-    resolved_prefix = require_path(prefix or config.prefix, "install prefix", "--prefix")
+    resolved_module_root, resolved_prefix = require_locations(
+        module_root or config.module_root,
+        prefix or config.prefix,
+    )
     paths = deploy_rust_tool(
         name=name,
         version=version,
@@ -277,7 +345,11 @@ def deploy_rust(
     )
 
 
-@main.command("deploy-script", help="Copy a shell script and write a modulefile for it.")
+@main.command(
+    "deploy-script",
+    help="Copy a shell script and write a modulefile for it.",
+    epilog=DEPLOY_SCRIPT_EXAMPLES,
+)
 @common_options
 @click.option(
     "--script",
@@ -319,8 +391,10 @@ def deploy_script(
     Raises:
         click.UsageError: If required paths are missing.
     """
-    resolved_module_root = require_path(module_root or config.module_root, "module root", "--module-root")
-    resolved_prefix = require_path(prefix or config.prefix, "install prefix", "--prefix")
+    resolved_module_root, resolved_prefix = require_locations(
+        module_root or config.module_root,
+        prefix or config.prefix,
+    )
     paths = deploy_script_tool(
         name=name,
         version=version,
@@ -341,7 +415,11 @@ def deploy_script(
     )
 
 
-@main.command("deploy-env", help="Deploy a collective environment from a TOML manifest.")
+@main.command(
+    "deploy-env",
+    help="Deploy a collective environment from a TOML manifest.",
+    epilog=DEPLOY_ENV_EXAMPLES,
+)
 @click.option(
     "--file",
     "manifest",
@@ -399,12 +477,10 @@ def deploy_env(
     except (OSError, TypeError, tomllib.TOMLDecodeError) as error:
         raise click.ClickException(str(error)) from error
 
-    resolved_module_root = require_path(
+    resolved_module_root, resolved_prefix = require_locations(
         module_root or spec.module_root or config.module_root,
-        "module root",
-        "--module-root",
+        prefix or spec.prefix or config.prefix,
     )
-    resolved_prefix = require_path(prefix or spec.prefix or config.prefix, "install prefix", "--prefix")
     if make_default is not None:
         spec = spec.__class__(
             name=spec.name,
@@ -421,7 +497,11 @@ def deploy_env(
     print_environment_result(result, dry_run)
 
 
-@main.command("uninstall", help="Remove a deployed tool version and its modulefile.")
+@main.command(
+    "uninstall",
+    help="Remove a deployed tool version and its modulefile.",
+    epilog=UNINSTALL_EXAMPLES,
+)
 @location_options
 @click.option(
     "--keep-default",
@@ -457,8 +537,10 @@ def uninstall(
     Raises:
         click.UsageError: If required paths are missing.
     """
-    resolved_module_root = require_path(module_root or config.module_root, "module root", "--module-root")
-    resolved_prefix = require_path(prefix or config.prefix, "install prefix", "--prefix")
+    resolved_module_root, resolved_prefix = require_locations(
+        module_root or config.module_root,
+        prefix or config.prefix,
+    )
     result = uninstall_tool(
         name=name,
         version=version,
@@ -493,6 +575,31 @@ def require_path(value: Path | None, label: str, option: str) -> Path:
     return value.expanduser()
 
 
+def require_locations(module_root: Path | None, prefix: Path | None) -> tuple[Path, Path]:
+    """Return distinct configured module and installation roots.
+
+    Args:
+        module_root: Candidate root of the module tree.
+        prefix: Candidate installation prefix.
+
+    Returns:
+        Expanded module root and installation prefix.
+
+    Raises:
+        click.UsageError: If either path is missing or both resolve to the same
+            directory.
+    """
+    resolved_module_root = require_path(module_root, "module root", "--module-root")
+    resolved_prefix = require_path(prefix, "install prefix", "--prefix")
+    if resolved_module_root.resolve() == resolved_prefix.resolve():
+        msg = (
+            "--module-root and --prefix must resolve to different directories; "
+            "otherwise the versioned modulefile collides with the install root."
+        )
+        raise click.UsageError(msg)
+    return resolved_module_root, resolved_prefix
+
+
 def print_result(
     modulefile: Path,
     install_root: Path,

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/module_manager/config.py

@@ -22,12 +22,14 @@ class AppConfig:
         indexes: Default Python package indexes passed to `uv tool install`.
         find_links: Default Python package locations passed to
             `uv tool install`.
+        uv_config_file: Default uv configuration file passed to `uv tool`.
     """
 
     prefix: Path | None = None
     module_root: Path | None = None
     indexes: tuple[str, ...] = ()
     find_links: tuple[str, ...] = ()
+    uv_config_file: Path | None = None
 
 
 def default_config_path() -> Path:
@@ -81,6 +83,7 @@ def load_file_config(path: Path) -> AppConfig:
         module_root=optional_path(data.get("module_root"), "module_root"),
         indexes=string_tuple(python_data.get("indexes"), "python.indexes"),
         find_links=string_tuple(python_data.get("find_links"), "python.find_links"),
+        uv_config_file=optional_path(python_data.get("uv_config_file"), "python.uv_config_file"),
     )
 
 
@@ -98,6 +101,7 @@ def overlay_env_config(config: AppConfig) -> AppConfig:
         module_root=env_path("MODULE_MANAGER_MODULE_ROOT") or config.module_root,
         indexes=env_tuple("MODULE_MANAGER_INDEXES") or env_tuple("MODULE_MANAGER_INDEX") or config.indexes,
         find_links=env_tuple("MODULE_MANAGER_FIND_LINKS") or config.find_links,
+        uv_config_file=config.uv_config_file,
     )
 
 

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/module_manager/deploy.py

@@ -62,6 +62,7 @@ class EnvironmentToolSpec:
         name: Tool name used for copied binaries and reporting.
         version: Optional source tool version for documentation.
         package: Python package spec passed to `uv tool install`.
+        uv_config_file: uv configuration file passed to `uv tool`.
         binary: Rust binary path to copy into the shared `bin` directory.
         script: Shell script path to copy into the shared `bin` directory.
         python: Optional Python interpreter or version passed to uv.
@@ -75,6 +76,7 @@ class EnvironmentToolSpec:
     name: str
     version: str | None = None
     package: str | None = None
+    uv_config_file: Path | None = None
     binary: Path | None = None
     script: Path | None = None
     python: str | None = None
@@ -148,6 +150,7 @@ def uv_install_command(
     python: str | None = None,
     indexes: tuple[str, ...] = (),
     find_links: tuple[str, ...] = (),
+    uv_config_file: Path | None = None,
 ) -> list[str]:
     """Build the uv command used to install a Python CLI tool.
 
@@ -156,11 +159,15 @@ def uv_install_command(
         python: Optional Python interpreter or version passed to uv.
         indexes: Additional package index URLs.
         find_links: Wheelhouse directories or HTML package pages.
+        uv_config_file: Optional uv configuration file passed to `uv tool`.
 
     Returns:
         Tokenized uv command suitable for `subprocess.run`.
     """
-    command = ["uv", "tool", "install"]
+    command = ["uv", "tool"]
+    if uv_config_file:
+        command.extend(["--config-file", str(uv_config_file)])
+    command.append("install")
     if python:
         command.extend(["--python", python])
     for index in indexes:
@@ -171,6 +178,23 @@ def uv_install_command(
     return command
 
 
+def uv_install_environment(tool_dir: Path, bin_dir: Path) -> dict[str, str]:
+    """Build an isolated environment for a managed uv tool installation.
+
+    Args:
+        tool_dir: Directory where uv should store installed tools.
+        bin_dir: Directory where uv should install tool executables.
+
+    Returns:
+        Process environment with inherited `UV_TOOL_*` settings removed and
+        the managed tool destinations set.
+    """
+    env = {key: value for key, value in os.environ.items() if not key.startswith("UV_TOOL_")}
+    env["UV_TOOL_DIR"] = str(tool_dir)
+    env["UV_TOOL_BIN_DIR"] = str(bin_dir)
+    return env
+
+
 def write_text(path: Path, content: str) -> None:
     """Write UTF-8 text to a path, creating parent directories first.
 
@@ -482,6 +506,7 @@ def parse_environment_tool(data: object, base_dir: Path, index: int) -> Environm
         name=name,
         version=optional_string(data, "version"),
         package=optional_string(data, "package"),
+        uv_config_file=optional_manifest_path(data, "uv_config_file", base_dir),
         binary=optional_manifest_path(data, "binary", base_dir),
         script=optional_manifest_path(data, "script", base_dir),
         python=optional_string(data, "python"),
@@ -540,7 +565,13 @@ def environment_actions(spec: EnvironmentSpec, paths: DeploymentPaths) -> tuple[
     tool_dir = paths.install_root / "uv-tools"
     for tool in spec.tools:
         if tool.tool_type == "python" and tool.package:
-            command = uv_install_command(tool.package, tool.python, tool.indexes, tool.find_links)
+            command = uv_install_command(
+                tool.package,
+                tool.python,
+                tool.indexes,
+                tool.find_links,
+                tool.uv_config_file,
+            )
             actions.append(
                 f"install python {tool.name}: "
                 f"UV_TOOL_DIR={shlex.quote(str(tool_dir))} "
@@ -591,13 +622,16 @@ def deploy_environment(
     for tool in spec.tools:
         if tool.tool_type == "python" and tool.package:
             require_executable("uv")
-            env = os.environ.copy()
-            env["UV_TOOL_DIR"] = str(tool_dir)
-            env["UV_TOOL_BIN_DIR"] = str(paths.bin_dir)
             subprocess.run(
-                uv_install_command(tool.package, tool.python, tool.indexes, tool.find_links),
+                uv_install_command(
+                    tool.package,
+                    tool.python,
+                    tool.indexes,
+                    tool.find_links,
+                    tool.uv_config_file,
+                ),
                 check=True,
-                env=env,
+                env=uv_install_environment(tool_dir, paths.bin_dir),
             )
         elif tool.tool_type == "rust" and tool.binary:
             copy_executable(tool.binary, paths.bin_dir / tool.name)
@@ -634,6 +668,7 @@ def deploy_python_tool(
     python: str | None = None,
     indexes: tuple[str, ...] = (),
     find_links: tuple[str, ...] = (),
+    uv_config_file: Path | None = None,
     execute_install: bool = False,
     make_default: bool = True,
 ) -> DeploymentPaths:
@@ -650,6 +685,7 @@ def deploy_python_tool(
         python: Optional Python interpreter or version passed to uv.
         indexes: Additional package index URLs passed to uv.
         find_links: Wheelhouse directories or HTML package pages passed to uv.
+        uv_config_file: Optional uv configuration file passed to `uv tool`.
         execute_install: Whether to run `uv tool install` immediately.
         make_default: Whether to make this version the module default.
 
@@ -664,14 +700,11 @@ def deploy_python_tool(
     paths = deployment_paths(module_root, prefix, name, version)
     paths.bin_dir.mkdir(parents=True, exist_ok=True)
     tool_dir = paths.install_root / "uv-tools"
-    command = uv_install_command(package, python, indexes, find_links)
+    command = uv_install_command(package, python, indexes, find_links, uv_config_file)
 
     if execute_install:
         require_executable("uv")
-        env = os.environ.copy()
-        env["UV_TOOL_DIR"] = str(tool_dir)
-        env["UV_TOOL_BIN_DIR"] = str(paths.bin_dir)
-        subprocess.run(command, check=True, env=env)
+        subprocess.run(command, check=True, env=uv_install_environment(tool_dir, paths.bin_dir))
 
     install_hint = (
         f"UV_TOOL_DIR={shlex.quote(str(tool_dir))} "

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "env-module-manager"
-version = "0.3.0"
+version = "0.5.0"
 description = "Deploy Python, Rust, shell, and collective CLI environments behind GNU environment modulefiles"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -111,8 +111,13 @@ docstring-code-format = true
 [tool.pytest.ini_options]
 minversion = "7.0"
 pythonpath = ["."]
+markers = [
+    "integration: executes external tools for end-to-end verification",
+]
 addopts = [
     "-ra",
+    "-m",
+    "not integration",
     "--strict-markers",
     "--strict-config",
     "--tb=short",

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/tests/test_cli.py

@@ -56,12 +56,16 @@ def test_deploy_python_command_writes_modulefile() -> None:
                 "https://packages.example/simple",
                 "--find-links",
                 "/prod/wheels",
+                "--uv-config-file",
+                "/prod/uv.toml",
             ],
         )
+        modulefile = Path("modules/ruff/0.8.0").read_text(encoding="utf-8")
 
     assert result.exit_code == 0
     assert "modulefile: modules/ruff/0.8.0" in result.output
     assert "default version: modules/ruff/.version" in result.output
+    assert "--config-file /prod/uv.toml" in modulefile
 
 
 def test_deploy_python_command_uses_config_defaults() -> None:
@@ -78,6 +82,7 @@ module_root = "modules"
 [python]
 indexes = ["https://packages.example/simple"]
 find_links = ["/prod/wheels"]
+uv_config_file = "uv.toml"
 """.strip(),
             encoding="utf-8",
         )
@@ -93,9 +98,38 @@ find_links = ["/prod/wheels"]
                 "ruff==0.8.0",
             ],
         )
+        modulefile = Path("modules/ruff/0.8.0").read_text(encoding="utf-8")
 
     assert result.exit_code == 0
     assert "modulefile: modules/ruff/0.8.0" in result.output
+    assert "--config-file uv.toml" in modulefile
+
+
+def test_deploy_command_rejects_matching_prefix_and_module_root() -> None:
+    """Deployment roots must differ to avoid a modulefile path collision."""
+    runner = CliRunner()
+
+    with runner.isolated_filesystem():
+        result = runner.invoke(
+            main,
+            [
+                "deploy-python",
+                "gitconductor",
+                "0.7.0",
+                "--package",
+                "gitconductor",
+                "--prefix",
+                "test",
+                "--module-root",
+                "test",
+            ],
+        )
+        collision_path_exists = Path("test/gitconductor/0.7.0").exists()
+
+    assert result.exit_code != 0
+    output = " ".join(strip_ansi(result.output).split())
+    assert "--module-root and --prefix must resolve to different directories" in output
+    assert not collision_path_exists
 
 
 def test_cli_options_override_config_defaults() -> None:

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/tests/test_config.py

@@ -22,6 +22,7 @@ module_root = "/scratch/modules"
 [python]
 indexes = ["https://packages.example/simple"]
 find_links = ["/scratch/wheels"]
+uv_config_file = "/scratch/uv.toml"
 """.strip(),
         encoding="utf-8",
     )
@@ -31,6 +32,7 @@ find_links = ["/scratch/wheels"]
         module_root=Path("/scratch/modules"),
         indexes=("https://packages.example/simple",),
         find_links=("/scratch/wheels",),
+        uv_config_file=Path("/scratch/uv.toml"),
     )
 
 

env_module_manager-0.5.0/tests/test_integration.py

@@ -0,0 +1,49 @@
+"""Integration tests that execute external deployment tools."""
+
+from pathlib import Path
+
+import pytest
+from click.testing import CliRunner
+
+from module_manager.cli import main
+
+
+@pytest.mark.integration
+def test_deploy_python_real_uv_install_uses_cli_roots(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
+    """A real uv install should use the CLI prefix and module root.
+
+    Args:
+        tmp_path: Temporary deployment root.
+        monkeypatch: Pytest helper used to control inherited uv destinations.
+    """
+    project_root = Path(__file__).parent.parent
+    prefix = tmp_path / "tools"
+    module_root = tmp_path / "modules"
+    inherited_tool_dir = tmp_path / "inherited-tools"
+    inherited_bin_dir = tmp_path / "inherited-bin"
+    monkeypatch.setenv("UV_TOOL_DIR", str(inherited_tool_dir))
+    monkeypatch.setenv("UV_TOOL_BIN_DIR", str(inherited_bin_dir))
+
+    result = CliRunner().invoke(
+        main,
+        [
+            "deploy-python",
+            "module-manager",
+            "0.5.0",
+            "--package",
+            str(project_root),
+            "--prefix",
+            str(prefix),
+            "--module-root",
+            str(module_root),
+            "--execute-install",
+        ],
+    )
+
+    install_root = prefix / "module-manager" / "0.5.0"
+    assert result.exit_code == 0, result.output
+    assert (install_root / "bin" / "module-manager").exists()
+    assert (install_root / "uv-tools" / "env-module-manager" / "uv-receipt.toml").exists()
+    assert (module_root / "module-manager" / "0.5.0").is_file()
+    assert not inherited_tool_dir.exists()
+    assert not inherited_bin_dir.exists()

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/tests/test_modulefile.py

@@ -14,6 +14,7 @@ from module_manager.deploy import (
     require_executable,
     uninstall_tool,
     uv_install_command,
+    uv_install_environment,
 )
 from module_manager.modulefile import (
     ModuleSpec,
@@ -109,6 +110,40 @@ def test_python_tool_install_command_accepts_python() -> None:
     ]
 
 
+def test_python_tool_install_command_accepts_uv_config_file() -> None:
+    """Uv install commands should include a requested uv config file."""
+    assert uv_install_command("ruff==0.8.0", uv_config_file=Path("/prod/uv.toml")) == [
+        "uv",
+        "tool",
+        "--config-file",
+        "/prod/uv.toml",
+        "install",
+        "ruff==0.8.0",
+    ]
+
+
+def test_uv_install_environment_ignores_inherited_uv_tool_settings(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    """Managed uv installs should ignore inherited tool-specific settings.
+
+    Args:
+        tmp_path: Temporary deployment root.
+        monkeypatch: Pytest helper used to control the process environment.
+    """
+    monkeypatch.setenv("UV_TOOL_DIR", "/inherited/tools")
+    monkeypatch.setenv("UV_TOOL_BIN_DIR", "/inherited/bin")
+    monkeypatch.setenv("UV_TOOL_UPGRADE", "1")
+    monkeypatch.setenv("UV_CONFIG_FILE", "/prod/uv.toml")
+
+    env = uv_install_environment(tmp_path / "tools", tmp_path / "bin")
+
+    assert env["UV_TOOL_DIR"] == str(tmp_path / "tools")
+    assert env["UV_TOOL_BIN_DIR"] == str(tmp_path / "bin")
+    assert "UV_TOOL_UPGRADE" not in env
+    assert env["UV_CONFIG_FILE"] == "/prod/uv.toml"
+
+
 def test_deploy_python_tool_writes_package_sources_to_install_hint(tmp_path: Path) -> None:
     """Generated module help should show the package source options.
 
@@ -123,9 +158,11 @@ def test_deploy_python_tool_writes_package_sources_to_install_hint(tmp_path: Pat
         prefix=tmp_path / "tools",
         indexes=("https://packages.example/simple",),
         find_links=("/prod/wheels",),
+        uv_config_file=Path("/prod/uv.toml"),
     )
 
     modulefile = paths.modulefile.read_text(encoding="utf-8")
+    assert "--config-file /prod/uv.toml" in modulefile
     assert "--index https://packages.example/simple" in modulefile
     assert "--find-links /prod/wheels" in modulefile
 
@@ -366,6 +403,7 @@ package = "ruff==0.8.0"
 python = "3.12"
 indexes = ["https://packages.example/simple"]
 find_links = ["/prod/wheels"]
+uv_config_file = "uv.toml"
 
 [[tools]]
 type = "script"
@@ -384,6 +422,7 @@ script = "scripts/helper"
     assert not spec.make_default
     assert spec.tools[0].package == "ruff==0.8.0"
     assert spec.tools[0].indexes == ("https://packages.example/simple",)
+    assert spec.tools[0].uv_config_file == tmp_path / "uv.toml"
     assert spec.tools[1].script == tmp_path / "scripts/helper"
 
 
@@ -491,6 +530,7 @@ type = "python"
 name = "ruff"
 package = "ruff==0.8.0"
 python = "3.12"
+uv_config_file = "uv.toml"
 """.strip(),
         encoding="utf-8",
     )
@@ -502,7 +542,16 @@ python = "3.12"
         prefix=tmp_path / "tools",
     )
 
-    assert calls[0][0] == ["uv", "tool", "install", "--python", "3.12", "ruff==0.8.0"]
+    assert calls[0][0] == [
+        "uv",
+        "tool",
+        "--config-file",
+        str(tmp_path / "uv.toml"),
+        "install",
+        "--python",
+        "3.12",
+        "ruff==0.8.0",
+    ]
     assert calls[0][1]["UV_TOOL_DIR"] == str(result.paths.install_root / "uv-tools")
     assert calls[0][1]["UV_TOOL_BIN_DIR"] == str(result.paths.bin_dir)
     assert result.paths.modulefile.exists()

{env_module_manager-0.3.0 → env_module_manager-0.5.0}/uv.lock

@@ -344,7 +344,7 @@ wheels = [
 
 [[package]]
 name = "env-module-manager"
-version = "0.3.0"
+version = "0.5.0"
 source = { editable = "." }
 dependencies = [
     { name = "click" },