Use explicit --manifest-path for pixi jobs instead of unsetting PIXI_PROJECT_MANIFEST by mkitti · Pull Request #406 · JaneliaSciComp/fileglancer

mkitti · 2026-07-08T01:24:30Z

Summary

pixi's --manifest-path flag always overrides the PIXI_PROJECT_MANIFEST env var (verified against pixi 0.70.2), so this switches the generated pixi command to pixi run --manifest-path "$FG_MANIFEST_DIR" <task> instead of unsetting PIXI_PROJECT_MANIFEST and relying on cwd-based manifest discovery.
Introduces FG_MANIFEST_DIR, exported alongside FG_WORK_DIR in every generated job script (all app types, not just pixi), pointing at the directory containing the app's manifest.
Updates tests/test_apps.py to assert on the new preamble.

Supersedes #405 (moved from a fork branch to a branch within this repo).

Test plan

pixi run -e test test-backend — all 723 tests pass

🤖 Generated with Claude Code

…PROJECT_MANIFEST pixi's --manifest-path flag always overrides the PIXI_PROJECT_MANIFEST env var, so pointing pixi run at the manifest directory explicitly is more robust than unsetting the env var and relying on cwd-based discovery. Introduces FG_MANIFEST_DIR, exported alongside FG_WORK_DIR for all job types. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

krokicki · 2026-07-08T20:45:36Z

Nice, I like it!

krokicki · 2026-07-08T21:03:51Z

But I think we still need the unset PIXI_PROJECT_MANIFEST in there for now, because we don't want Fileglancer's manifest leaking into the cluster jobs.

I'm going to fix the ENV leakage on a separate PR.

mkitti · 2026-07-17T17:42:41Z

Does pixi set that environment variable? Did you want me to revert that here?

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Pull request overview

This PR updates Fileglancer’s generated job scripts so Pixi-based app entry points run with an explicit manifest location via pixi run --manifest-path "$FG_MANIFEST_DIR" ..., and introduces a new FG_MANIFEST_DIR environment variable (alongside FG_WORK_DIR) for generated scripts.

Changes:

Add FG_MANIFEST_DIR export to the job-script preamble to point at the app manifest directory inside the job workdir snapshot.
Update Pixi app entry points to run via pixi run --manifest-path "$FG_MANIFEST_DIR" <task>.
Update tests/test_apps.py assertions to match the new script preamble and manifest-path behavior.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
`fileglancer/apps/jobs.py`	Adds `FG_MANIFEST_DIR` export to the generated script preamble (but currently still unsets `PIXI_PROJECT_MANIFEST`, causing mismatch with updated test/intent).
`fileglancer/apps/pixi.py`	Switches generated Pixi commands to use `--manifest-path "$FG_MANIFEST_DIR"`.
`tests/test_apps.py`	Updates job-script assertions to validate `FG_WORK_DIR`/`FG_MANIFEST_DIR` preamble and expected working directory.

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        preamble_lines = [
            "unset PIXI_PROJECT_MANIFEST",
            f"export FG_WORK_DIR={shlex.quote(str(work_dir))}",
+            f'export FG_MANIFEST_DIR="$FG_WORK_DIR"/{shlex.quote(cd_suffix)}',
            # Where the script reports its startup phase (e.g. pulling a container


mkitti · 2026-07-17T19:25:25Z

I recommend squashing this merge.

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Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

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Copilot

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.


    # Build the pixi run command
-    command = f"pixi run {name}"
+    command = f'pixi run --manifest-path "$FG_MANIFEST_DIR" {name}'


+        # FG_MANIFEST_DIR always points at the manifest's directory, so
+        # pixi-style commands can pass --manifest-path explicitly.


mkitti · 2026-07-20T19:27:02Z

But I think we still need the unset PIXI_PROJECT_MANIFEST in there for now, because we don't want Fileglancer's manifest leaking into the cluster jobs.

I'm going to fix the ENV leakage on a separate PR.

@krokicki Do we still need to unset the environment variable here or does #408 now address that?

As suggested by Github Copilot

krokicki · 2026-07-20T19:46:33Z

But I think we still need the unset PIXI_PROJECT_MANIFEST in there for now, because we don't want Fileglancer's manifest leaking into the cluster jobs.
I'm going to fix the ENV leakage on a separate PR.

@krokicki Do we still need to unset the environment variable here or does #408 now address that?

It should be fixed in #408

mkitti · 2026-07-20T20:02:24Z

I think this is ready to merge then.

krokicki

Tested on my Pixi project. LGTM.

mkitti · 2026-07-21T19:31:54Z

I'll merge this then.

mkitti mentioned this pull request Jul 8, 2026

Use explicit --manifest-path for pixi jobs instead of unsetting PIXI_PROJECT_MANIFEST #405

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mkitti commented Jul 17, 2026

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mkitti added 2 commits July 17, 2026 13:46

Update fileglancer/apps/jobs.py

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Update fileglancer/apps/jobs.py

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Update fileglancer/apps/jobs.py

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Merge branch 'main' into mkitti-pixi-manifest-path

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mkitti requested a review from Copilot July 20, 2026 19:15

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Shell quote name when providing it to pixi.

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mkitti added 2 commits July 20, 2026 15:57

test: add unit test for task-name shell quoting

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docs: address minor comment findings from GitHub Copilot review

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mkitti self-assigned this Jul 20, 2026

mkitti requested a review from krokicki July 20, 2026 20:01

updated code comments

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krokicki approved these changes Jul 21, 2026

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mkitti merged commit 815f8d3 into main Jul 21, 2026
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mkitti deleted the mkitti-pixi-manifest-path branch July 21, 2026 19:47

		# FG_MANIFEST_DIR always points at the manifest's directory, so
		# pixi-style commands can pass --manifest-path explicitly.

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mkitti commented Jul 8, 2026

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mkitti commented Jul 20, 2026

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