Improve kernel supervisor wrapper to make environment more predictable and configurable #7797

jmcphers · 2025-05-21T18:32:09Z

This change updates the kernel supervisor to 0.1.40, which, together with the Positron changes in this PR, addresses a number of related issues around the supervisor's lifecycle and environment.

The changes are as follows:

The supervisor is itself run in a login shell, and it can start kernels in login shells too, so that each kernel start (or restart) runs login scripts and picks up changes to e.g. .bash_profile. This behavior does have a minor impact on startup time, so I've made it optional.
The supervisor wrapper script now invokes nohup instead of the other way around. This inversion allows us to better control the behavior of nohup and prevent it from littering the project with nohup.out files.
The supervisor can now adjust its shutdown timeout on the fly. This allows the shutdown timeout setting to work correctly in the Remote SSH environment, and also makes this setting take effect immediately instead of requiring a restart.
The supervisor is now smarter about environment variables on Windows, addressing an issue that caused PATH to (non deterministically) be incorrect in R and Python sessions.

Addresses #6757
Addresses #7215
Addresses #7274
Addresses #7537

Release Notes

New Features

Shell login scripts (e.g. .bash_profile, .zprofile) are now run when starting Python and R sessions (Supervisor: Run kernels in a login shell, or otherwise run startup scripts #6757)

Bug Fixes

Fixed nohup.out file littering projects when kernel supervisor is set to run after Positron exits (File nohup.out generated by Positron Supervisor #7215)
Shutdown idle timeout now respected in Remote SSH sessions (Supervisor: Shutdown Timeout not respected for Remote SSH #7537)
On Windows, user and system environment variables now appear correctly inside R and Python sessions ([Bug] Positron console fails to inherit PATH "User Variables" on Windows #7274)

QA Notes

Note that the supervisor and kernels are run in login shells, not interactive shells. This means that variables from .bashrc may not be visible; use e.g. .bash_profile instead. The system will attempt to use your default shell, which is zsh on recent macOS, so make sure you edit the profile script that matches your $SHELL.

…vironment

github-actions · 2025-05-21T18:32:25Z

E2E Tests 🚀
This PR will run tests tagged with: @:critical

^readme ^{valid tags}

Copilot

Pull Request Overview

This PR upgrades the kernel supervisor to v0.1.40 and makes its environment and lifecycle more configurable and predictable.

Introduces a runInShell flag to optionally start supervisor and kernels in login shells
Refactors the wrapper script to invoke nohup internally and avoid stray nohup.out files
Adds API endpoints to get/set server configuration (e.g. idle shutdown hours) and dynamic timeout updates

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
extensions/positron-supervisor/src/kcclient/model/serverStatus.ts	Add `version` and `processId` fields to the server status model
extensions/positron-supervisor/src/kcclient/model/serverConfiguration.ts	Introduce the `ServerConfiguration` model
extensions/positron-supervisor/src/kcclient/model/newSession.ts	Add `runInShell` flag to session creation
extensions/positron-supervisor/src/kcclient/model/models.ts & .openapi-generator/FILES	Export the new configuration model
extensions/positron-supervisor/src/kcclient/api/defaultApi.ts	Add `getServerConfiguration` and `setServerConfiguration` methods
extensions/positron-supervisor/src/KallichoreSession.ts	Pass `runInShell` from settings into new sessions
extensions/positron-supervisor/src/KallichoreAdapterApi.ts	Hook config changes for idle shutdown, refactor `nohup` logic, track real PID
extensions/positron-supervisor/resources/supervisor-wrapper.sh	Support optional `nohup`, run in login shell, and cleaned redirection
extensions/positron-supervisor/package.json & package.nls.json	Add `kernelSupervisor.runInShell` setting and bump `kallichore` version

Comments suppressed due to low confidence (1)

extensions/positron-supervisor/src/kcclient/api/defaultApi.ts:452

New methods getServerConfiguration and setServerConfiguration are added but there are no corresponding unit or integration tests. Adding tests will ensure these endpoints work as expected.

public async getServerConfiguration (options: {headers: {[name: string]: string}} = {headers: {}}) : Promise<{ response: http.IncomingMessage; body: ServerConfiguration;  }> {

extensions/positron-supervisor/src/KallichoreAdapterApi.ts

extensions/positron-supervisor/resources/supervisor-wrapper.sh

extensions/positron-supervisor/src/kcclient/model/newSession.ts

Co-authored-by: Copilot <[email protected]> Signed-off-by: Jonathan <[email protected]>

sharon-wang

Updating idle timeout

I didn't test this using Remote SSH, but I confirmed that changing the timeout is reflected in the Kernel Supervisor output -- some sample output:

Updating server configuration with new shutdown timeout: 0
18:22:05 [INFO] Updating idle shutdown hours to None
Updating server configuration with new shutdown timeout: 4
18:22:07 [INFO] Updating idle shutdown hours to Some(4)
Updating server configuration with new shutdown timeout: -1
Failed to update idle timeout: HTTP 400. idle_shutdown_hours must be a non-negative integer
Updating server configuration with new shutdown timeout: 1
18:22:17 [INFO] Updating idle shutdown hours to Some(1)

there seems to be an error when setting the timeout to indefinitely though -- I left a comment in the code where the error is caught

Windows PATH

I did not test this 🤠

login shell change ✅

MY_ZPROFILE_VAR is in my .zprofile

nohup no longer generated ✅

on Mac, I set "kernelSupervisor.shutdownTimeout": "4" and restarted Positron

created a Python console session and ran the following code:

import time
x = 10000
while x > 0:
    print(x)
    x-=1
    time.sleep(2)

quit Positron
opened Activity Monitor, searched for kcserver and quit the process
opened Positron again
no nohup.out in workspace (in 2025.06.0-107 I do get a nohup.out)

sharon-wang · 2025-05-23T18:34:56Z

extensions/positron-supervisor/src/KallichoreAdapterApi.ts

+		try {
+			await this._api.setServerConfiguration({
+				idleShutdownHours: timeout
+			});
+		} catch (err) {
+			this._log.appendLine(`Failed to update idle timeout: ${summarizeError(err)}`);
+		}


We're hitting the error case when the idle timeout is set to "indefinitely" -1 -- is it intentional to error?

No, I forgot to update the supervisor side of this value! Thanks for catching that.

sharon-wang · 2025-05-23T18:36:35Z

extensions/positron-supervisor/src/KallichoreAdapterApi.ts

+	/**
+	 * Update the idle timeout on the server. This is used to set the idle
+	 * timeout on a server that has already started.
+	 */
+	async updateIdleTimeout() {


Shall we remove the "Restart Positron to apply" guidance for the setting?

This needs to stay because there are certain transitions that do require a restart. In particular we store sessions differently when you are in "immediate" mode (ephemeral storage) vs. one of the other modes (durable storage), and there is no logic to move sessions between these storage classes. So you could change from e.g. 4 to 8 hours w/o a restart, but going from immediate to 4 does require a restart. I think this is probably too difficult to explain and we should just tell folks they always need to restart.

…vironment

jmcphers · 2025-05-23T20:24:56Z

@sharon-wang this should be ready for you to check again -- I've updated the supervisor with a new version that correctly supports the client side.

sharon-wang

LGTM!

Output looks happy now 😄

21:34:54 [DEBUG] (3) kcserver::kernel_session: [session python-1c3a9172] Running kernel in login shell: /bin/zsh
Updating server configuration with new shutdown timeout: -1
21:35:12 [INFO] set_server_configuration - X-Span-ID: "f3a721d3-4ff2-4e19-8092-823c8ef79fb1"
21:35:12 [INFO] Updating idle shutdown hours to None
21:35:14 [INFO] client_heartbeat - X-Span-ID: "2165fdb8-eb25-4e50-a7cf-a95fd0017ee9"

jmcphers · 2025-05-24T00:48:33Z

Full test suite results - https://github.com/posit-dev/positron/actions/runs/15220852088

jmcphers added 11 commits May 19, 2025 16:43

run under a login shell

43f2204

regenerate api

5736352

update idle timeout after reconnect

f9b025b

Merge remote-tracking branch 'origin/main' into feature/kallichore-en…

5f6de89

…vironment

add runInShell arg

c40c51a

pass run in shell option to kallichore

8b92597

forward new idle timeout hours to server immediately

7f1921f

add pid to server response

3e8ffb5

use self reported pid from kallichore

2bda0d3

clarify comments in wrapper script

3d3fdec

bump kallichore version

f86ecb7

jmcphers requested a review from Copilot May 21, 2025 18:32

Copilot AI reviewed May 21, 2025

View reviewed changes

jmcphers mentioned this pull request May 21, 2025

[Bug] Positron console fails to inherit PATH "User Variables" on Windows #7274

Closed

Update extensions/positron-supervisor/resources/supervisor-wrapper.sh

1f518fc

Co-authored-by: Copilot <[email protected]> Signed-off-by: Jonathan <[email protected]>

jmcphers requested a review from sharon-wang May 21, 2025 22:58

sharon-wang reviewed May 23, 2025

View reviewed changes

jmcphers added 2 commits May 23, 2025 12:53

Merge remote-tracking branch 'origin/main' into feature/kallichore-en…

d0bcc0d

…vironment

bump supervisor version

73dcc2f

jmcphers requested a review from sharon-wang May 23, 2025 20:20

sharon-wang approved these changes May 23, 2025

View reviewed changes

jmcphers merged commit f8d54a3 into main May 24, 2025
14 checks passed

jmcphers deleted the feature/kallichore-environment branch May 24, 2025 00:48

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Improve kernel supervisor wrapper to make environment more predictable and configurable #7797

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jmcphers commented May 21, 2025

Release Notes

New Features

Bug Fixes

QA Notes

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Pull Request Overview

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Updating idle timeout

Windows PATH

login shell change ✅

nohup no longer generated ✅

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