fix: Xonsh integration #5557

jfmontanaro · 2025-07-10T10:36:01Z

The Xonsh integration is currently broken. It doesn't output any errors when running execx($(mise activate -s xonsh)), but calling mise after doing so will raise an error:

joe@vingilot ~/Documents/code/mise main @ execx($(mise activate xonsh))
joe@vingilot ~/Documents/code/mise main @ mise
xonsh: For full traceback set: $XONSH_SHOW_TRACEBACK = True
Exception in thread {'cls': 'ProcProxyThread', 'name': 'Thread-33', 'func': FuncAlias({'name': 'mise', 'func': '_mise', 'return_what': 'result'}), 'alias': 'mise', 'pid': None}
FileNotFoundError: [Errno 2] No such file or directory: 'command'

Ultimately this error is due to the activating script trying to execute command mise ..., and command isn't a proper executable. command is a Bash builtin (and maybe exists in other more bash-like shells as well?), so I'm guessing what happened was that some logic was ported over from other shells and doesn't work here.

Fixing this issue is straightforward, but doing so reveals a second issue. The pre-prompt hook attempts to capture the output of mise hook-env via $(...), but this doesn't work because mise has been replaced with an alias that runs it using subprocess.run(), which bypasses Xonsh's output-capturing mechanics.

To fix these issues I suggest the following changes:

Use normal xonsh subprocess semantics in the main mise alias, which fixes output capturing
Since the original motivation for using subprocess.run() was to speed up execution, but we really only care about this in the pre-prompt hook, we will use subprocess.run() only in the pre-prompt hook.
Switch to passing in the Xonsh environment via XSH.env.detype(). This avoids the added complexity of having to set env vars in both XSH.env and os.environ, which significantly cleans up the implementation.
Add an e2e test for Xonsh, at least for the basic behavior. I modeled this one mostly after the e2e test for Zsh.

If that seems reasonable, I have a couple of additional questions:

There's a section in the docs that talks about hooking into cd, rather than just running every time the prompt is displayed. This makes sense to me - the PATH manipulation that mise does should only need to be updated when the working directory changes - but I'm not sure if it means what I think it means. At least, the docs claim that this happens in Bash and Zsh, but looking at those implementations it appears that they are still running on prompt as well as on cd, so I'm not sure what's going on. If my original intuition is right and the hook only really needs to fire when the directory is changed, this would be easy to do in Xonsh as well. We'd just need to hook into the on_chdir event instead of on_pre_prompt.
shfmt doesn't like the Xonsh test script, which is understandable since Xonsh syntax can get pretty far from regular shell (all valid Python is also valid Xonsh.) Unfortunately it's causing some checks to fail in CI, and I can't find a way to tell it to ignore this file, or just mark it as an expected fail. Is that possible?

jdx · 2025-07-10T13:08:26Z

There's a section in the docs that talks about hooking into cd, rather than just running every time the prompt is displayed. This makes sense to me - the PATH manipulation that mise does should only need to be updated when the working directory changes - but I'm not sure if it means what I think it means. At least, the docs claim that this happens in Bash and Zsh, but looking at those implementations it appears that they are still running on prompt as well as on cd, so I'm not sure what's going on. If my original intuition is right and the hook only really needs to fire when the directory is changed, this would be easy to do in Xonsh as well. We'd just need to hook into the on_chdir event instead of on_pre_prompt.

both are important. cd is useful when doing something like cd foo && node -v and prompt is useful when editing config files and not leaving the directory.

I think shfmt is configured here:

mise/hk.pkl

Line 21 in c008173

["shfmt"] = (Builtins.shfmt) {

but you may also be able to add an ignore rule for it in .editorconfig

jfmontanaro · 2025-07-10T14:59:19Z

Got it, thanks!

I've added the mise hook to the on_chdir event in Xonsh, updated the docs to reflect that, and ignored the test script in the linter, so as long as you're ok with it then I'm good to go.

Copilot

Pull Request Overview

This PR fixes the broken Xonsh integration in mise by switching to Xonsh-native subprocess semantics, cleaning up environment variable handling, and adding a proper pre-prompt + on-chdir hook. It also adds an end-to-end test for Xonsh, updates snapshots, updates docs to mention the new on_chdir hook, and ensures Xonsh is installed in CI.

Use Xonsh’s execx and XSH.env.detype() for environment updates and limit subprocess.run() to the hook
Register both on_pre_prompt and on_chdir hooks and update snapshots accordingly
Add an e2e Xonsh test script, update docs, and install Xonsh in CI

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/shell/xonsh.rs	Refactor alias to use Xonsh API, add on_chdir hook
src/shell/snapshots/*	Update snapshots to reflect new hook names
e2e/shell/xonsh_script, e2e/shell/test_xonsh	Add Xonsh integration end-to-end test
docs/dev-tools/shims.md	Document Xonsh’s `on_chdir` hook usage
.github/workflows/test.yml	Install Xonsh in CI
hk.pkl	Exclude the Xonsh test script from bash linter

Comments suppressed due to low confidence (1)

src/shell/xonsh.rs:64

There’s no test covering the no_hook_env path. Adding a unit or integration test for when opts.no_hook_env is true would help ensure hooks aren’t registered unexpectedly.

        if !opts.no_hook_env {

Copilot · 2025-07-10T18:01:22Z

src/shell/xonsh.rs

+                import shlex
+                import subprocess
+
+                extra_args = shlex.split('{flags}')


Embedding raw {flags} into a shell split call can lead to code-injection risks. Consider constructing the flags list directly in Rust and serializing it to a Python list literal, or otherwise ensure that {flags} is properly escaped before splitting.

Suggested change

extra_args = shlex.split('{flags}')

escaped_flags = xonsh_escape_sq('{flags}')

extra_args = shlex.split(escaped_flags)

This was already the case before the PR. I wouldn't mind escaping, but my feeling is that because the flags can only ever be a known set of values it's not a problem. Most likely that's why it was never escaped to begin with.

yeah I was going to verify that myself because I thought that was the case but thanks for checking!

Copilot · 2025-07-10T18:01:22Z

hk.pkl

@@ -2,7 +2,7 @@ amends "package://github.com/jdx/hk/releases/download/v1.0.0/hk@1.0.0#/Config.pk
 import "package://github.com/jdx/hk/releases/download/v1.0.0/hk@1.0.0#/Builtins.pkl"

 local bash_glob = List("*.sh", "xtasks/**", "scripts/**", "e2e/**")
-local bash_exclude = List("*.ps1", "*.fish", "*.ts", "*.js", "*.json", "*.bat", "**/.*", "src/assets/bash_zsh_support/**")
+local bash_exclude = List("*.ps1", "*.fish", "*.ts", "*.js", "*.json", "*.bat", "**/.*", "src/assets/bash_zsh_support/**", "e2e/shell/xonsh_script")


[nitpick] The exclude pattern is very specific; consider using a wildcard (e.g., "e2e/shell/xonsh_script*") or including an extension to ensure all related scripts are excluded from bash linters.

Suggested change

local bash_exclude = List("*.ps1", "*.fish", "*.ts", "*.js", "*.json", "*.bat", "**/.*", "src/assets/bash_zsh_support/**", "e2e/shell/xonsh_script")

local bash_exclude = List("*.ps1", "*.fish", "*.ts", "*.js", "*.json", "*.bat", "**/.*", "src/assets/bash_zsh_support/**", "e2e/shell/xonsh_script*", "*.xonsh")

@risu729

### 🐛 Bug Fixes - **(aqua)** align version resolution logic in list_bin_paths by [@risu729](https://github.com/risu729) in [#5562](#5562) - Xonsh integration by [@jfmontanaro](https://github.com/jfmontanaro) in [#5557](#5557) ### 📚 Documentation - create comprehensive architecture documentation suite and enhance development guides by [@jdx](https://github.com/jdx) in [d2b4a05](d2b4a05) ### 📦️ Dependency Updates - update rust crate bzip2 to 0.6 by [@renovate[bot]](https://github.com/renovate[bot]) in [#5568](#5568) - update rust crate clap_mangen to v0.2.28 by [@renovate[bot]](https://github.com/renovate[bot]) in [#5566](#5566) - update rust crate clap to v4.5.41 by [@renovate[bot]](https://github.com/renovate[bot]) in [#5565](#5565) - update rust crate taplo to 0.14 by [@renovate[bot]](https://github.com/renovate[bot]) in [#5158](#5158) ### Chore - added xonsh for release builds by [@jdx](https://github.com/jdx) in [#5561](#5561) - enable backtrace lines on panic by [@jdx](https://github.com/jdx) in [#5571](#5571) - shfmt update by [@jdx](https://github.com/jdx) in [67ee245](67ee245) ### New Contributors - @jfmontanaro made their first contribution in [#5557](#5557)

@yjoer

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@matracey made their first contribution in [#5487](jdx/mise#5487) - @andreabedini made their first contribution in [#5495](jdx/mise#5495) ## [2025.7.0](https://github.com/jdx/mise/compare/v2025.6.8..v2025.7.0) - 2025-07-01 ### 🚀 Features - **(registry)** adds gemini-cli by [@risu729](https://github.com/risu729) in [#5447](jdx/mise#5447) - **(registry)** adds npm backended tools by [@risu729](https://github.com/risu729) in [#5446](jdx/mise#5446) - **(registry)** add powershell alias by [@risu729](https://github.com/risu729) in [#5449](jdx/mise#5449) - **(registry)** add dagu by [@yottahmd](https://github.com/yottahmd) in [#5476](jdx/mise#5476) - **(registry)** update aws-sam backends to include aqua source by [@yashikota](https://github.com/yashikota) in [#5461](jdx/mise#5461) - **(registry)** use ubi backend for youtube-dl nightly releases by [@risu729](https://github.com/risu729) in [#5466](jdx/mise#5466) ### 🐛 Bug Fixes - **(aqua)** update victoria-metrics package name casing by [@shikharbhardwaj](https://github.com/shikharbhardwaj) in [#5483](jdx/mise#5483) - **(aqua)** handle hard links in aqua packages by [@risu729](https://github.com/risu729) in [#5463](jdx/mise#5463) - **(bun)** enhance architecture detection for musl targets by [@roele](https://github.com/roele) in [#5450](jdx/mise#5450) - **(erlang)** use precompiled ubuntu binaries on GHA by [@paradox460](https://github.com/paradox460) in [#5439](jdx/mise#5439) - **(erlang)** add `install_precompiled` for unsupported os by [@risu729](https://github.com/risu729) in [#5479](jdx/mise#5479) - **(registry)** use aqua backend for cargo-make by [@risu729](https://github.com/risu729) in [#5465](jdx/mise#5465) - **(registry)** use aqua backends for all available tools by [@risu729](https://github.com/risu729) in [#5467](jdx/mise#5467) - `parse_command` passing `-c` flag to cmd.exe by [@IMXEren](https://github.com/IMXEren) in [#5441](jdx/mise#5441) ### 🧪 Testing - **(registry)** disable bitwarden test by [@risu729](https://github.com/risu729) in [#5468](jdx/mise#5468) ### ◀️ Revert - Revert "chore(deps): pin dependencies" by [@jdx](https://github.com/jdx) in [#5453](jdx/mise#5453) - Revert "fix(aqua): handle hard links in aqua packages" by [@jdx](https://github.com/jdx) in [#5485](jdx/mise#5485) ### 📦️ Dependency Updates - pin dependencies by [@renovate[bot]](https://github.com/renovate[bot]) in [#5443](jdx/mise#5443) - update jdx/mise-action digest to 5cb1df6 by [@renovate[bot]](https://github.com/renovate[bot]) in [#5444](jdx/mise#5444) ### Chore - disable automatic cargo up due to windows build failure in homedir crate by [@jdx](https://github.com/jdx) in [7570d0a](jdx/mise@7570d0a) ### Ci - **(test)** run `apt-get update` before `apt-get install` by [@risu729](https://github.com/risu729) in [#5448](jdx/mise#5448) ### New Contributors - @yashikota made their first contribution in [#5461](jdx/mise#5461) - @yottahmd made their first contribution in [#5476](jdx/mise#5476) - @IMXEren made their first contribution in [#5441](jdx/mise#5441) ## [2025.6.8](https://github.com/jdx/mise/compare/v2025.6.7..v2025.6.8) - 2025-06-26 ### 🚀 Features - **(java)** add support for tar.xz in Java core plugin to support RedHat JDKs by [@roele](https://github.com/roele) in [#5354](jdx/mise#5354) - **(registry)** add osv-scanner by [@scop](https://github.com/scop) in [#5413](jdx/mise#5413) - **(registry)** add scorecard by [@scop](https://github.com/scop) in [#5410](jdx/mise#5410) - **(registry)** add docker cli by [@acesyde](https://github.com/acesyde) in [#5344](jdx/mise#5344) - **(registry)** add claude code by [@lelouvincx](https://github.com/lelouvincx) in [#5420](jdx/mise#5420) - **(registry)** add aws `cfn-lint` by [@garysassano](https://github.com/garysassano) in [#5434](jdx/mise#5434) - added graphite by [@jdx](https://github.com/jdx) in [#5429](jdx/mise#5429) ### 🐛 Bug Fixes - **(erlang)** use precompiled binaries for linux ubuntu by [@paradox460](https://github.com/paradox460) in [#5402](jdx/mise#5402) - **(ubi)** checksum generation might fail if extract_all option is used by [@roele](https://github.com/roele) in [#5394](jdx/mise#5394) - `self-update` on MITM firewall by [@joehorsnell](https://github.com/joehorsnell) in [#5387](jdx/mise#5387) - lint warning by [@jdx](https://github.com/jdx) in [#5425](jdx/mise#5425) - only warn on toolset resolve errors by [@jdx](https://github.com/jdx) in [#5435](jdx/mise#5435) ### 🚜 Refactor - **(registry)** use pipx for semgrep by [@scop](https://github.com/scop) in [#5423](jdx/mise#5423) - **(registry)** add backends and tests by [@risu729](https://github.com/risu729) in [#5388](jdx/mise#5388) ### ◀️ Revert - Revert "fix: `self-update` on MITM firewall" by [@jdx](https://github.com/jdx) in [#5427](jdx/mise#5427) ### Ci - unpin hyperfine by [@risu729](https://github.com/risu729) in [#5411](jdx/mise#5411) ### New Contributors - @paradox460 made their first contribution in [#5402](jdx/mise#5402) - @lelouvincx made their first contribution in [#5420](jdx/mise#5420) ## [2025.6.7](https://github.com/jdx/mise/compare/v2025.6.6..v2025.6.7) - 2025-06-23 ### 🐛 Bug Fixes - **(aqua)** fix versions order by [@risu729](https://github.com/risu729) in [#5406](jdx/mise#5406) ### Ci - use pinnable tag of taiki-e/install-action by [@risu729](https://github.com/risu729) in [#5405](jdx/mise#5405)

jfmontanaro added 6 commits July 10, 2025 06:07

rework xonsh integration scripts

df86c3a

add beginnings of xonsh e2e test

3c883bd

update xonsh test snapshots and install xonsh in CI

ea2bb02

fix xonsh command in test

5ac61a1

pre-install required node versions in xonsh test script

d36a206

ignore shellcheck errors in xonsh test script

c38e846

jfmontanaro changed the title ~~Fix Xonsh integration~~ fix: Xonsh integration Jul 10, 2025

add tests for moving up directory and deactivating to xonsh script

5956bd3

jfmontanaro force-pushed the main branch from ba21548 to 5956bd3 Compare July 10, 2025 10:41

fire mise hook on chdir in xonsh, and mention in docs

dd040d3

jfmontanaro force-pushed the main branch from a2330bc to dd040d3 Compare July 10, 2025 14:27

ignore xonsh test script when linting

c193390

jdx requested a review from Copilot July 10, 2025 16:17

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make env var escaping consistent in xonsh integration

f3eacb1

jdx requested a review from Copilot July 10, 2025 18:00

Copilot AI reviewed Jul 10, 2025

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jdx merged commit f54fb4c into jdx:main Jul 10, 2025
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mise-en-dev mentioned this pull request Jul 10, 2025

chore: release 2025.7.4 #5560

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BrewTestBot mentioned this pull request Jul 12, 2025

mise 2025.7.4 Homebrew/homebrew-core#229839

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fix: Xonsh integration #5557

fix: Xonsh integration #5557

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jfmontanaro commented Jul 10, 2025 •

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jfmontanaro Jul 10, 2025 •

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	extra_args = shlex.split('{flags}')
	escaped_flags = xonsh_escape_sq('{flags}')
	extra_args = shlex.split(escaped_flags)

	local bash_exclude = List(".ps1", ".fish", ".ts", ".js", ".json", ".bat", "*/.", "src/assets/bash_zsh_support/**", "e2e/shell/xonsh_script")
	local bash_exclude = List(".ps1", ".fish", ".ts", ".js", ".json", ".bat", "*/.", "src/assets/bash_zsh_support/*", "e2e/shell/xonsh_script", "*.xonsh")

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fix: Xonsh integration #5557

fix: Xonsh integration #5557

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jfmontanaro commented Jul 10, 2025 •

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