fix argument splitting on '--' in the command line

[colobas]

📝 Summary

Fixes argument splitting in marimo run when notebook args are passed after --.

Problem

click consumes the -- separator, so _split_run_paths_and_args() does not see it.
As a result, trailing args may be interpreted as additional notebook paths (NAME) and trigger errors like: Invalid NAME - ... is not a Python or Markdown file.

Changes

• Added a failing test commit showing that _split_run_paths_and_args() does not receive -- from CLI parsing.
• Added a fix to restore -- sentinel semantics using raw sys.argv in run() before splitting.
• Added/updated tests covering these forms after --:
  • key=value
  • --key value
  • --key
  • -key value

Validation

• First commit adds the failing tests that show the behavior.
• Second commit makes tests pass.

📋 Pre-Review Checklist

• For large changes, or changes that affect the public API: this change was discussed or approved through an issue, on Discord, or the community discussions (Please provide a link if applicable).
• Any AI generated code has been reviewed line-by-line by the human PR author, who stands by it.
• Video or media evidence is provided for any visual changes (optional).

✅ Merge Checklist

• I have read the contributor guidelines.
• Documentation has been updated where applicable, including docstrings for API changes.
• Tests have been added for the changes made.

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Project	Deployment	Actions	Updated (UTC)
marimo-docs	Ready	Preview, Comment	May 13, 2026 0:31am

[github-actions]

All contributors have signed the CLA ✍️ ✅
_{Posted by the CLA Assistant Lite bot.}

[colobas]

I have read the CLA Document and I hereby sign the CLA

[cubic-dev-ai]

No issues found across 2 files

Architecture diagram

sequenceDiagram
    participant User as CLI / Shell
    participant Click as Click Framework
    participant CLI as marimo.run()
    participant Sys as sys.argv (Raw)
    participant Splitter as _split_run_paths_and_args()

    User->>Click: marimo run notebook.py -- arg=1
    Note over Click: Click strips '--' from arguments
    Click->>CLI: run(name="notebook.py", args=("arg=1",))
    
    CLI->>Sys: Access raw process arguments
    Sys-->>CLI: ["marimo", "run", "notebook.py", "--", "arg=1"]
    
    alt NEW: Re-inject double dash sentinel
        CLI->>CLI: Detect "--" in raw argv but missing in Click args
        CLI->>CLI: Reconstruct args as ("--", "arg=1")
    end

    CLI->>Splitter: CHANGED: pass args with preserved sentinel
    
    Note over Splitter: Logic identifies items after "--" <br/>as notebook params, not file paths
    
    Splitter-->>CLI: return (paths, notebook_args)
    
    CLI->>CLI: Continue execution with correct paths

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[cubic-dev-ai]

4 issues found across 1 file (changes from recent commits).

Prompt for AI agents (unresolved issues)

Check if these issues are valid — if so, understand the root cause of each and fix them. If appropriate, use sub-agents to investigate and fix each issue separately.


<file name="pyproject.toml">

<violation number="1" location="pyproject.toml:6">
P0: Package renamed from `marimo` to `marimo-colobas` — this is a fork-specific change that must not be merged. It would break the package identity, PyPI publishing, and all existing installations.</violation>

<violation number="2" location="pyproject.toml:7">
P1: Version changed to `0.23.2.post1` — this fork-specific version bump should be reverted to avoid interfering with the project's release process.</violation>

<violation number="3" location="pyproject.toml:101">
P0: Optional dependency self-references renamed to `marimo-colobas[...]` — these must remain `marimo[...]` to match the actual package name.</violation>

<violation number="4" location="pyproject.toml:603">
P0: Pixi dev dependency renamed to `marimo-colobas` — revert to `marimo` to keep the local development workflow intact.</violation>
</file>

_{Reply with feedback, questions, or to request a fix. Tag @cubic-dev-ai to re-run a review, or fix all with cubic.}

[cubic-dev-ai]

P0: Pixi dev dependency renamed to marimo-colobas — revert to marimo to keep the local development workflow intact.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At pyproject.toml, line 603:

<comment>Pixi dev dependency renamed to `marimo-colobas` — revert to `marimo` to keep the local development workflow intact.</comment>

<file context>
@@ -600,4 +600,4 @@ python = "3.12.*"
 
 [tool.pixi.pypi-dependencies]
-marimo = {path = ".", editable = true}
+marimo-colobas = {path = ".", editable = true}
</file context>

Suggested change

	marimo-colobas = {path = ".", editable = true}
	marimo = {path = ".", editable = true}

[cubic-dev-ai]

P0: Optional dependency self-references renamed to marimo-colobas[...] — these must remain marimo[...] to match the actual package name.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At pyproject.toml, line 101:

<comment>Optional dependency self-references renamed to `marimo-colobas[...]` — these must remain `marimo[...]` to match the actual package name.</comment>

<file context>
@@ -98,8 +98,8 @@ sandbox = [
 recommended = [
-    "marimo[sql]",
-    "marimo[sandbox]",                  # For `marimo edit --sandbox DIRECTORY`
+    "marimo-colobas[sql]",
+    "marimo-colobas[sandbox]",                  # For `marimo edit --sandbox DIRECTORY`
     "altair>=5.4.0",                    # Plotting in datasource viewer
</file context>

Suggested change

	"marimo-colobas[sql]",
	"marimo[sql]",

[cubic-dev-ai]

P0: Package renamed from marimo to marimo-colobas — this is a fork-specific change that must not be merged. It would break the package identity, PyPI publishing, and all existing installations.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At pyproject.toml, line 6:

<comment>Package renamed from `marimo` to `marimo-colobas` — this is a fork-specific change that must not be merged. It would break the package identity, PyPI publishing, and all existing installations.</comment>

<file context>
@@ -3,8 +3,8 @@ requires = ["uv_build>=0.8.3,<0.12.0"]
 [project]
-name = "marimo"
-version = "0.23.2"
+name = "marimo-colobas"
+version = "0.23.2.post1"
 description = "A library for making reactive notebooks and apps"
</file context>

Suggested change

	name = "marimo-colobas"
	name = "marimo"

[cubic-dev-ai]

P1: Version changed to 0.23.2.post1 — this fork-specific version bump should be reverted to avoid interfering with the project's release process.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At pyproject.toml, line 7:

<comment>Version changed to `0.23.2.post1` — this fork-specific version bump should be reverted to avoid interfering with the project's release process.</comment>

<file context>
@@ -3,8 +3,8 @@ requires = ["uv_build>=0.8.3,<0.12.0"]
-name = "marimo"
-version = "0.23.2"
+name = "marimo-colobas"
+version = "0.23.2.post1"
 description = "A library for making reactive notebooks and apps"
 # We try to keep dependencies to a minimum, to avoid conflicts with
</file context>

Suggested change

	version = "0.23.2.post1"
	version = "0.23.2"

[colobas]

sorry I overwrote the PR branch by mistake because I needed a wheel. I've reverted it back to the original PR state. Apologies

[peter-gy]

Hey @colobas, thanks for the contribution, and welcome 👋

I could reproduce the bug. That said, could you please revise the fix to avoid reading from sys.argv inside run()? sys.argv is process-global state, while this command can also be invoked through Click tests, wrappers, or programmatic CLI entrypoints with an explicit args list. In those cases, sys.argv may not match the invocation that Click is actually handling.

We could handle this at the Click parsing boundary and pass the intended separator/argv state into the splitter explicitly. That would keep run() based on the command invocation it received.