Incomplete DAG with checkpoints

[fgvieira]

Snakemake version

v8.10.7

Describe the bug

DAG is incomplete when there are checkpoints, since it only plots the DAG for the rules upstream of the checkpoint.

Minimal example

On test snakemake/tests/test_checkpoint_allowed_rules, if we run snakemake c --dag | dot -Tsvg > dag.svg, we get the DAG:

Where I think we would also expect rule b going into rule c.

[cademirch]

Seems slightly related to #2824. I think this makes sense since B doesn't exist in the DAG until after A has been run.

[fgvieira]

Yes, but then it should work if a has been run, but it does not. As it is now:

• if a has not been run: a -> c
• if a has bee run: b -> c

So it is never possible to get the full DAG.

[cademirch]

Ah. I see what you're saying. I agree you should get the full dag.