fix(prepare): install config tools before running prepare steps by jdx · Pull Request #8582 · jdx/mise

jdx · 2026-03-13T13:22:55Z

Summary

InstallOptions::default() sets missing_args_only: true, which only installs tools passed as CLI arguments — not tools from [tools] in config files
This caused prepare steps to run before their required tools were installed, failing on clean machines where tools like uv aren't available system-wide
Set missing_args_only: false in both mise run and mise prepare so config tools are installed before prepare steps execute

Test plan

Verified with a test project using [tools] uv = "0.9.25" and a custom prepare step that runs uv pip install
Before fix: prepare runs before uv is installed (uses system uv if available, fails on clean machines)
After fix: uv is installed first, then prepare runs successfully
CI passes

🤖 Generated with Claude Code

Note

Medium Risk
Changes tool auto-install behavior for mise prepare/mise run and alters how prepare commands are executed (now via an inline shell), which could affect projects relying on previous argument parsing or auto-install settings.

Overview
Ensures mise prepare installs all configured [tools] before executing prepare rules by setting InstallOptions.missing_args_only to false, preventing prepare steps from failing on clean machines.

Aligns prepare command execution with task behavior by wrapping PrepareCommand::from_string in the configured inline shell (enabling pipes/redirects/&&) and updates --explain output to show the command description. Adds an e2e regression test (test_prepare_tool_install) that verifies tool installation occurs before the prepare step runs.

^{Written by Cursor Bugbot for commit 288b0c4. This will update automatically on new commits. Configure here.}

`InstallOptions::default()` sets `missing_args_only: true`, which skips tools from `[tools]` config and only installs CLI-argument tools. This caused prepare steps to run before their required tools were installed, failing on clean machines where tools like `uv` aren't available system-wide. Fixes #8567 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

gemini-code-assist · 2026-03-13T13:23:08Z

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses a critical issue where mise's prepare steps could fail on environments without pre-installed tools. By modifying the tool installation logic, it ensures that all necessary tools specified in configuration files are installed before any prepare steps are executed, preventing failures and improving the reliability of mise in new or clean development environments.

Highlights

InstallOptions::default() behavior: InstallOptions::default() previously set missing_args_only: true, which meant only tools explicitly passed as CLI arguments were installed, not those specified in [tools] in config files.
Impact on prepare steps: This behavior caused prepare steps to fail on clean machines because required tools from config files were not installed before the prepare steps attempted to use them.
Solution implemented: The missing_args_only flag is now explicitly set to false in both mise run and mise prepare commands, ensuring that all tools defined in config files are installed before any prepare steps are executed.

Activity

Verified the fix with a test project using [tools] uv = "0.9.25" and a custom prepare step that runs uv pip install.
Confirmed that before the fix, prepare steps would run before uv was installed, potentially using a system uv or failing on clean machines.
Confirmed that after the fix, uv is installed first, and then the prepare steps run successfully.
CI passes.

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greptile-apps · 2026-03-13T13:26:28Z

Greptile Summary

This PR fixes a race condition where mise prepare and mise run would execute prepare steps before installing tools declared in [tools] config, causing failures on clean machines where tools like uv or tiny aren't available system-wide.

Key changes:

src/cli/prepare.rs: Sets missing_args_only: false in InstallOptions so all [tools] entries are installed before prepare providers execute. Note: skip_auto_install is still not set here (see discussion in previous review threads about auto_install = false not being respected).
src/cli/run.rs: Adds missing_args_only and skip_auto_install fields driven by Settings::get().task.run_auto_install and Settings::get().auto_install, matching the established pattern in task_tool_installer.rs.
src/prepare/mod.rs: PrepareCommand::from_string now wraps the run string with the platform default inline shell (sh -c on Unix), enabling shell features like pipes, redirects, and && in custom prepare commands. The empty-shell edge case is now handled with a proper error (ok_or_else) instead of a panic.
e2e/cli/test_prepare_tool_install: Adds a regression test that removes the tiny installation and then calls mise prepare, verifying that the tool is installed before the prepare step runs.

The --explain output in prepare.rs now uses cmd.description (the human-readable run string or explicit description) instead of cmd.program + " " + cmd.args.join(" ") which would have emitted the raw sh -c <run> form after the shell-wrapping change.

Confidence Score: 3/5

Mostly safe to merge — the core bug fix is correct and well-tested, but prepare.rs still does not respect auto_install = false (an outstanding concern from previous review threads).
The fix correctly addresses the root cause (missing_args_only: true skipping config tools) and the run.rs change properly mirrors the task_tool_installer.rs pattern including skip_auto_install. The shell-wrapping change in mod.rs is intentional and safe. Score is 3 rather than 4 because prepare.rs still omits skip_auto_install, silently ignoring users' auto_install = false global setting — an issue raised in prior review threads that remains unresolved in this PR.
Pay close attention to src/cli/prepare.rs — the skip_auto_install field should be set consistently with exec.rs and task_tool_installer.rs to honor the global auto_install setting.

Important Files Changed

Filename	Overview
src/cli/prepare.rs	Core fix: sets `missing_args_only: false` so config tools are installed before prepare runs. However, `skip_auto_install` is still not set, meaning `auto_install = false` in global settings is silently ignored for `mise prepare`. The `--explain` output now correctly uses `cmd.description` instead of reconstructing the shell-wrapped command.
src/cli/run.rs	Correctly mirrors the `task_tool_installer.rs` pattern by adding `missing_args_only` and `skip_auto_install` based on `task.run_auto_install` and `auto_install` settings, ensuring config tools are installed before prepare steps run in `mise run`.
src/prepare/mod.rs	Changes `PrepareCommand::from_string` to shell-wrap custom `run` commands using `default_inline_shell()`, enabling shell features like pipes and redirects. Correctly handles empty shell configuration with an error instead of a panic (`ok_or_else` instead of `unwrap`).
e2e/cli/test_prepare_tool_install	New regression test that installs `tiny = "1"` via `[tools]` and uses it in a prepare step, verifying the install-before-prepare ordering. Properly removes the `tiny` installation before running to exercise the install path. Uses an isolated temp directory via the test framework, so state from previous runs doesn't interfere.

Sequence Diagram

sequenceDiagram
    participant User
    participant prepare_rs as mise prepare / mise run
    participant Toolset
    participant PrepareEngine
    participant PrepareCommand

    User->>prepare_rs: invoke command
    prepare_rs->>Toolset: build toolset (ToolsetBuilder)
    prepare_rs->>Toolset: install_missing_versions(missing_args_only: false)
    Note over Toolset: Installs ALL config [tools] (e.g. uv, tiny)<br/>Before fix: missing_args_only was true,<br/>skipping config tools
    Toolset-->>prepare_rs: tools installed, shims rebuilt
    prepare_rs->>Toolset: env_with_path() → PATH includes new tools
    prepare_rs->>PrepareEngine: run(PrepareOptions { env: toolset_env })
    PrepareEngine->>PrepareCommand: from_string(run, config)
    Note over PrepareCommand: Wraps in default_inline_shell()<br/>(sh -c) to support pipes/redirects
    PrepareCommand-->>PrepareEngine: PrepareCommand { program: "sh", args: ["-c", run] }
    PrepareEngine->>PrepareEngine: execute_prepare_static(cmd, toolset_env)
    Note over PrepareEngine: Runs with PATH containing installed tools
    PrepareEngine-->>prepare_rs: PrepareStepResult::Ran(id)
    prepare_rs-->>User: "Prepared: {id}"

_{Last reviewed commit: 288b0c4}

src/cli/prepare.rs

gemini-code-assist

Code Review

This pull request correctly fixes an issue where tools from config files were not installed before prepare steps in mise run and mise prepare. The change involves setting missing_args_only: false when installing tools. My review includes a couple of minor suggestions to improve code conciseness by inlining the InstallOptions struct where it's used only once.

gemini-code-assist · 2026-03-13T13:28:09Z

src/cli/prepare.rs

+        let install_opts = InstallOptions {
+            missing_args_only: false,
+            ..Default::default()
+        };
+        ts.install_missing_versions(&mut config, &install_opts)
            .await?;


For conciseness, you can construct InstallOptions inline within the install_missing_versions call, since the install_opts variable is not used elsewhere.

Suggested change

let install_opts = InstallOptions {

missing_args_only: false,

..Default::default()

};

ts.install_missing_versions(&mut config, &install_opts)

.await?;

ts.install_missing_versions(&mut config, &InstallOptions {

missing_args_only: false,

..Default::default()

})

.await?;

gemini-code-assist · 2026-03-13T13:28:09Z

src/cli/run.rs

        let opts = InstallOptions {
            jobs: self.jobs,
            raw: self.raw,
+            missing_args_only: false,
            ..Default::default()
        };
        let _ = ts.install_missing_versions(&mut config, &opts).await?;


For conciseness, you can construct InstallOptions inline within the install_missing_versions call, since the opts variable is not used elsewhere.

Suggested change

let opts = InstallOptions {

jobs: self.jobs,

raw: self.raw,

missing_args_only: false,

..Default::default()

};

let _ = ts.install_missing_versions(&mut config, &opts).await?;

let _ = ts.install_missing_versions(&mut config, &InstallOptions {

jobs: self.jobs,

raw: self.raw,

missing_args_only: false,

..Default::default()

}).await?;

Ensures tools from [tools] config are installed before prepare steps that depend on them, preventing regression of the ordering fix. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/cli/run.rs

Custom prepare commands were executed directly (splitting into program + args) which meant shell features like pipes, redirects, and && didn't work. Now wraps commands with the default inline shell (sh -c) to match task execution behavior. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Match the pattern from task_tool_installer.rs: honor task.run_auto_install and auto_install settings so users who set auto_install = false don't get config tools force-installed. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

e2e/cli/test_prepare

Use cmd.description (the original run string) instead of the shell-wrapped program+args in --explain output. Restores precise assertion in e2e test. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

cursor

Cursor Bugbot has reviewed your changes and found 1 potential issue.

^{Bugbot Autofix is OFF. To automatically fix reported issues with cloud agents, enable autofix in the Cursor dashboard.}

src/cli/prepare.rs

mise prepare is an explicit user command like mise install, so it should always install config tools regardless of auto_install setting. The auto_install guard is only appropriate for implicit installs (shims, mise x, mise run). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/prepare/mod.rs

Replace unwrap() with a proper error message if the user has configured an empty shell string. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

github-actions · 2026-03-13T14:27:21Z

Hyperfine Performance

`mise x -- echo`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`mise-2026.3.8 x -- echo`	23.7 ± 0.4	22.9	28.9	1.00
`mise x -- echo`	23.7 ± 0.6	22.8	29.2	1.00 ± 0.03

`mise env`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`mise-2026.3.8 env`	23.8 ± 0.6	22.5	25.3	1.00
`mise env`	24.3 ± 0.5	23.0	26.6	1.02 ± 0.03

`mise hook-env`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`mise-2026.3.8 hook-env`	24.9 ± 0.6	23.7	32.2	1.00
`mise hook-env`	25.0 ± 0.8	23.2	27.6	1.00 ± 0.04

`mise ls`

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
`mise-2026.3.8 ls`	24.4 ± 0.7	22.9	29.9	1.00 ± 0.04
`mise ls`	24.3 ± 0.7	22.5	27.2	1.00

`xtasks/test/perf`

Command	mise-2026.3.8	mise	Variance
install (cached)	152ms	153ms	+0%
ls (cached)	84ms	84ms	+0%
bin-paths (cached)	86ms	86ms	+0%
task-ls (cached)	849ms	824ms	+3%

@roele

### 🚀 Features - **(github)** use release latest endpoint to get latest release by @roele in [#8516](#8516) - **(install)** add shared and system install directories by @jdx in [#8581](#8581) - **(vfox)** add provenance metadata to lockfile for tool plugins by @malept in [#8544](#8544) ### 🐛 Bug Fixes - **(aqua)** expose main binary when files field is empty and symlink_bins is enabled by @AlexanderTheGrey in [#8550](#8550) - **(env)** redact secrets in `mise set` listing and task-specific env by @jdx in [#8583](#8583) - **(prepare)** install config tools before running prepare steps by @jdx in [#8582](#8582) - **(task)** allow ctrl-c to interrupt tool downloads during `mise run` by @jdx in [#8571](#8571) - **(tasks)** add file task header parser support for spaces around = by @roele in [#8574](#8574) ### 📚 Documentation - **(task)** add property description for interactive by @roele in [#8562](#8562) - add missing `</bold>` closing tag by @muzimuzhi in [#8564](#8564) - rebrand site with new chef logo and warm culinary palette by @jdx in [#8587](#8587) ### 📦️ Dependency Updates - update ghcr.io/jdx/mise:alpine docker digest to de4657e by @renovate[bot] in [#8577](#8577) - update ghcr.io/jdx/mise:copr docker digest to eef29a2 by @renovate[bot] in [#8578](#8578) - update ghcr.io/jdx/mise:rpm docker digest to 5a96587 by @renovate[bot] in [#8580](#8580) - update ghcr.io/jdx/mise:deb docker digest to 464cf7c by @renovate[bot] in [#8579](#8579) ### 📦 Registry - fix flatc version test mismatch by @jdx in [#8588](#8588) ### Chore - **(registry)** skip spark test-tool by @jdx in [#8572](#8572) ### New Contributors - @AlexanderTheGrey made their first contribution in [#8550](#8550) ## 📦 Aqua Registry Updates #### New Packages (6) - [`bahdotsh/mdterm`](https://github.com/bahdotsh/mdterm) - [`callumalpass/mdbase-lsp`](https://github.com/callumalpass/mdbase-lsp) - [`facebook/ktfmt`](https://github.com/facebook/ktfmt) - [`gurgeous/tennis`](https://github.com/gurgeous/tennis) - [`tektoncd/pipelines-as-code`](https://github.com/tektoncd/pipelines-as-code) - [`weedonandscott/trolley`](https://github.com/weedonandscott/trolley) #### Updated Packages (2) - [`apple/container`](https://github.com/apple/container) - [`cocogitto/cocogitto`](https://github.com/cocogitto/cocogitto)

…8582) ## Summary - `InstallOptions::default()` sets `missing_args_only: true`, which only installs tools passed as CLI arguments — not tools from `[tools]` in config files - This caused prepare steps to run before their required tools were installed, failing on clean machines where tools like `uv` aren't available system-wide - Set `missing_args_only: false` in both `mise run` and `mise prepare` so config tools are installed before prepare steps execute Fixes jdx#8567 ## Test plan - [x] Verified with a test project using `[tools] uv = "0.9.25"` and a custom prepare step that runs `uv pip install` - [x] Before fix: prepare runs before uv is installed (uses system uv if available, fails on clean machines) - [x] After fix: uv is installed first, then prepare runs successfully - [ ] CI passes 🤖 Generated with [Claude Code](https://claude.com/claude-code)  --- > [!NOTE] > **Medium Risk** > Changes tool auto-install behavior for `mise prepare`/`mise run` and alters how prepare commands are executed (now via an inline shell), which could affect projects relying on previous argument parsing or auto-install settings. > > **Overview** > Ensures `mise prepare` installs all configured `[tools]` before executing prepare rules by setting `InstallOptions.missing_args_only` to `false`, preventing prepare steps from failing on clean machines. > > Aligns prepare command execution with task behavior by wrapping `PrepareCommand::from_string` in the configured inline shell (enabling pipes/redirects/`&&`) and updates `--explain` output to show the command description. Adds an e2e regression test (`test_prepare_tool_install`) that verifies tool installation occurs before the prepare step runs. > > <sup>Written by [Cursor Bugbot](https://cursor.com/dashboard?tab=bugbot) for commit 288b0c4. This will update automatically on new commits. Configure [here](https://cursor.com/dashboard?tab=bugbot).</sup>  --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

@roele

### 🚀 Features - **(github)** use release latest endpoint to get latest release by @roele in [jdx#8516](jdx#8516) - **(install)** add shared and system install directories by @jdx in [jdx#8581](jdx#8581) - **(vfox)** add provenance metadata to lockfile for tool plugins by @malept in [jdx#8544](jdx#8544) ### 🐛 Bug Fixes - **(aqua)** expose main binary when files field is empty and symlink_bins is enabled by @AlexanderTheGrey in [jdx#8550](jdx#8550) - **(env)** redact secrets in `mise set` listing and task-specific env by @jdx in [jdx#8583](jdx#8583) - **(prepare)** install config tools before running prepare steps by @jdx in [jdx#8582](jdx#8582) - **(task)** allow ctrl-c to interrupt tool downloads during `mise run` by @jdx in [jdx#8571](jdx#8571) - **(tasks)** add file task header parser support for spaces around = by @roele in [jdx#8574](jdx#8574) ### 📚 Documentation - **(task)** add property description for interactive by @roele in [jdx#8562](jdx#8562) - add missing `</bold>` closing tag by @muzimuzhi in [jdx#8564](jdx#8564) - rebrand site with new chef logo and warm culinary palette by @jdx in [jdx#8587](jdx#8587) ### 📦️ Dependency Updates - update ghcr.io/jdx/mise:alpine docker digest to de4657e by @renovate[bot] in [jdx#8577](jdx#8577) - update ghcr.io/jdx/mise:copr docker digest to eef29a2 by @renovate[bot] in [jdx#8578](jdx#8578) - update ghcr.io/jdx/mise:rpm docker digest to 5a96587 by @renovate[bot] in [jdx#8580](jdx#8580) - update ghcr.io/jdx/mise:deb docker digest to 464cf7c by @renovate[bot] in [jdx#8579](jdx#8579) ### 📦 Registry - fix flatc version test mismatch by @jdx in [jdx#8588](jdx#8588) ### Chore - **(registry)** skip spark test-tool by @jdx in [jdx#8572](jdx#8572) ### New Contributors - @AlexanderTheGrey made their first contribution in [jdx#8550](jdx#8550) ## 📦 Aqua Registry Updates #### New Packages (6) - [`bahdotsh/mdterm`](https://github.com/bahdotsh/mdterm) - [`callumalpass/mdbase-lsp`](https://github.com/callumalpass/mdbase-lsp) - [`facebook/ktfmt`](https://github.com/facebook/ktfmt) - [`gurgeous/tennis`](https://github.com/gurgeous/tennis) - [`tektoncd/pipelines-as-code`](https://github.com/tektoncd/pipelines-as-code) - [`weedonandscott/trolley`](https://github.com/weedonandscott/trolley) #### Updated Packages (2) - [`apple/container`](https://github.com/apple/container) - [`cocogitto/cocogitto`](https://github.com/cocogitto/cocogitto)

greptile-apps bot reviewed Mar 13, 2026

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test(prepare): add e2e test for tool install before prepare

cab6bbc

Ensures tools from [tools] config are installed before prepare steps that depend on them, preventing regression of the ordering fix. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

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jdx and others added 2 commits March 13, 2026 14:40

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e2e/cli/test_prepare Outdated Show resolved Hide resolved

fix(prepare): show user command in --explain output, not shell wrapper

ff09e7c

Use cmd.description (the original run string) instead of the shell-wrapped program+args in --explain output. Restores precise assertion in e2e test. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

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fix(prepare): handle empty default_inline_shell without panicking

288b0c4

Replace unwrap() with a proper error message if the user has configured an empty shell string. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

jdx enabled auto-merge (squash) March 13, 2026 14:17

jdx merged commit 1cda78e into main Mar 13, 2026
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jdx deleted the fix/prepare-install-tools-first branch March 13, 2026 14:20

mise-en-dev mentioned this pull request Mar 13, 2026

chore: release 2026.3.9 #8563

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BrewTestBot mentioned this pull request Mar 13, 2026

mise 2026.3.9 Homebrew/homebrew-core#272196

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fix(prepare): install config tools before running prepare steps#8582

fix(prepare): install config tools before running prepare steps#8582
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Confidence Score: 3/5

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Hyperfine Performance

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`mise x -- echo`

`mise env`

`mise hook-env`

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`xtasks/test/perf`