Submit with --ignore-conditions not reflected in output job script

[rayasare]

Description

python project.py submit --ignore-conditions all --pretend output does not include the --ignore-conditions all flag in the output job script.

To reproduce

#!/bin/bash
#SBATCH --job-name=job name
#SBATCH --partition=partition
#SBATCH -t 05:00:00
#SBATCH -N 1
#SBATCH --ntasks=1
#SBATCH -A account
#SBATCH --output=output

set -e
set -u

cd path-to-project


# operation_name(141eae18cc920ad67709909534e776e3)
path_to:project.py run -o operation_name -j 141eae18cc920ad67709909534e776e3 
# Operations with all postconditions met:
# path_to:project.py run exec operation_name 141eae18cc920ad67709909534e776e3

Error output

Slurm file is generated but operation is not run (because postconditions were already met, as shown in output script).

System configuration

Please complete the following information:

• Operating System [e.g. macOS]: Linux-4.18.0-477.27.1.el8_8.x86_64-x86_64-with-glibc2.28
• Version of Python [e.g. 3.7]: 3.10.4 (main, Mar 31 2022, 08:41:55) [GCC 7.5.0]
• Version of signac [e.g. 1.0]: 1.8.0
• Version of signac-flow: 0.24.0

[b-butler]

@rayasare, this is caused by the switch a few years back to call run from submit. Could you work on the fix? It would involve adding the flag to the end of the command in submit_operations (I think that is the function).

Also, in the meantime you can use groups with submit_options set to the string flag and submit that.

[rayasare]

I can take a shot at fixing this.