Job progress not recorded when using Snakemake version 7.32.0 and above

[matinnuhamunada]

Describe the bug
When upgrading snakemake from version 7.31.1 to 7.32.0, workflow run is recorded, but does not show any progress even though the job is complete. In the example workflow, there should be 14/14 jobs in the workflow, but in snakemake version 7.32.0 it will only shows 0/1

To Reproduce
Steps to reproduce the behavior:

1. Create conda environment with:

mamba create -c conda-forge -c bioconda -n panoptes_test snakemake==7.32.0 python=3.11 panoptes-ui==0.2.3
mamba activate panoptes_test

2. Start panoptes

panoptes

3. Open a new terminal, grab the example workflow

# clone snakemake example workflow
git clone https://github.com/panoptes-organization/snakemake_example_workflow.git
cd snakemake_example_workflow

4. Run snakemake

mamba activate panoptes_test
bash run_local.sh

5. See workflow monitor in http://localhost:5000/workflows/ , no jobs were recorded (0/1)
   

6. Downgrade snakemake

mamba install snakemake==7.31.1

7. Run snakemake again

rm -rf results/
bash run_local.sh

8. See workflow monitor in http://localhost:5000/workflows/ , now 14/14 jobs are recorded
   

Desktop (please complete the following information):

• OS: Linux / Ubuntu 22 running on Microsoft Azure VM
• Browser Chrome

[fgvieira]

I think the only change between those two versions that seems to might have caused this would be snakemake/snakemake#2347.

Could this be related to snakemake/snakemake#2390? Did you try providing --snakefile?

[odcambc]

This is fixed in main currently.

Can confirm that snakemake/snakemake#2347 (7fafa7a) breaks job progress - bc854a7 works for me.

It seems like this is working properly as of 0d34be9, but 98d2bdf is the commit that fixes logging.py.

[fgypas]

I opened a PR that eliminates the need of passing the snakefile as metadata when the wms-monitor is used: snakemake/snakemake#2573
I tested it with 8.0.1