Sketch Gagolewski's reuse

[imallona]

Attempting to reuse Gagolewski's clustering-data-v1 encoding the files as data-specific params.

Works on snakemake 8.24.1 and omnibenchmark v0.1.0-rc.2

It currently fails on snakemake 8.25.5 and omnibenchmark v0.1.0-rc.2 with:

(omnibenchmark) [imallona@MLS-L-IZMA clustering_example]$ ob run benchmark  -b Clustering.yaml --local
Benchmark YAML file integrity check passed.
Running benchmark...
Assuming unrestricted shared filesystem usage.
host: MLS-L-IZMA
Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however important for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job                        count
-----------------------  -------
all                            1
data_clustbench_param_0        1
data_clustbench_param_1        1
data_clustbench_param_2        1
total                          4

Select jobs to execute...
Execute 1 jobs...

[Mon Dec 16 11:14:55 2024]
localrule data_clustbench_param_2:
    output: out/data/clustbench/param_2/clustbench.data.gz, out/data/clustbench/param_2/clustbench.labels0.gz
    jobid: 3
    reason: Missing output files: out/data/clustbench/param_2/clustbench.labels0.gz, out/data/clustbench/param_2/clustbench.data.gz
    wildcards: stage=data, module=clustbench, params=param_2, dataset=clustbench
    resources: tmpdir=/home/imallona/tmp

Activating conda environment: .snakemake/conda/19d5081c77a4cb3f39a74cad33393bb9_
Activating conda environment: .snakemake/conda/19d5081c77a4cb3f39a74cad33393bb9_
Traceback (most recent call last):

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/cli.py", line 2156, in args_to_api
    dag_api.execute_workflow(

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/api.py", line 595, in execute_workflow
    workflow.execute(

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/workflow.py", line 1264, in execute
    raise e

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/workflow.py", line 1260, in execute
    success = self.scheduler.schedule()
              ^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/scheduler.py", line 194, in schedule
    self._finish_jobs()

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/scheduler.py", line 401, in _finish_jobs
    async_run(postprocess())

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/common/__init__.py", line 90, in async_run
    return asyncio.run(coroutine)
           ^^^^^^^^^^^^^^^^^^^^^^

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/asyncio/runners.py", line 194, in run
    return runner.run(main)
           ^^^^^^^^^^^^^^^^

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/asyncio/runners.py", line 118, in run
    return self._loop.run_until_complete(task)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/asyncio/base_events.py", line 687, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/scheduler.py", line 350, in postprocess
    await job.postprocess(

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/jobs.py", line 1194, in postprocess
    await self.dag.workflow.persistence.finished(self)

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/persistence.py", line 312, in finished
    software_stack_hash = self._software_stack_hash(job)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/persistence.py", line 525, in _software_stack_hash
    md5hash.update(job.env_modules.hash.encode())
                   ^^^^^^^^^^^^^^^^^^^^

  File "/home/imallona/miniconda3/envs/omnibenchmark/lib/python3.12/site-packages/snakemake/deployment/env_modules.py", line 27, in hash
    md5hash.update(name.encode())
                   ^^^^^^^^^^^

AttributeError: 'NoneType' object has no attribute 'encode'

Benchmark run has failed.

[csoneson]

As discussed also in the meeting this morning, I think this looks good!