KeyError and CreateRuleException while using modifying use statement

[ashwinvis]

Snakemake version 6.1.1 and git version 6.1.1+7.g5349f2a4

Describe the bug

Errors are thrown if we have modified rules made using the use rule ... as ... with: syntax in a Snakemake module while snakemake --list.

Minimal example

Assume there are two rules defined in a module other_workflow.smk. There is one scenario in which everything works as expected and 2 in which errors are thrown.

rule some_task:
    output: "output.txt"
    shell: "cat hello >> {output}"

use rule some_task as another_task with:
    output: "another.txt"

1. Working Snakefile

module other_workflow:
    snakefile: "other_workflow.smk"

use rule * from other_workflow

❯ snakemake -l          
some_task
another_task

2. Buggy Snakefile

module other_workflow:
    snakefile: "other_workflow.smk"

use rule * from other_workflow as other_*

❯ snakemake -l 
KeyError in line 7 of /home/avmo/src/sandbox/snakemake-module-issue/other_workflow.smk:
'some_task'
  File "/home/avmo/src/sandbox/snakemake-module-issue/Snakefile", line 5, in <module>
  File "/home/avmo/src/sandbox/snakemake-module-issue/other_workflow.smk", line 7, in <module>

It seems like an issue with the scope of the modules.

3. Buggy Snakefile

module other_workflow:
    snakefile: "other_workflow.smk"

use rule * from other_workflow

use rule some_task from other_workflow as other_some_task with:
    output:  "some-result.txt"

❯ snakemake -l
CreateRuleException in line 7 of /home/avmo/src/sandbox/snakemake-module-issue/other_workflow.smk:
The name another_task is already used by another rule
  File "/home/avmo/src/sandbox/snakemake-module-issue/Snakefile", line 9, in <module>
  File "/home/avmo/src/sandbox/snakemake-module-issue/other_workflow.smk", line 7, in <module>

It seems like an issue with importing rules multiple times

[ashwinvis]

Really bad workaround for case 2. Buggy Snakefile

If other_workflow.smk is re-written as

rule some_task:
    output: "output.txt"
    shell: "cat hello >> {output}"

use rule other_some_task as another_task with:
    output: "another.txt"

the 2. Buggy snakefile case works where it shouldn't have!

❯ snakemake -l                                                                                                                                                                
other_some_task
another_task

[ashwinvis]

• KeyError in case 2 fixed in fix: rule inheritance within modules (did previously lead to key errors) #1292
• CreateRuleException still persists, and cannot modify rules after inheriting.