Aluriak / Aluriak/PowerGrASP

Options not handled with new version of clyngor having clingo as dependency.

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Answer Set Programming
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Descripción

Hi,

While using powergrasp in metage2metabo, I encountered the following error:

```
Traceback (most recent call last):
File "/usr/local/bin/m2m_analysis", line 33, in
sys.exit(load_entry_point('Metage2Metabo', 'console_scripts', 'm2m_analysis')())
File "/shared/programs/metage2metabo/metage2metabo/__main_analysis__.py", line 292, in main
main_analysis_workflow(network_dir, args.targets, args.seeds, args.out, args.taxon,
File "/shared/programs/metage2metabo/metage2metabo/__main_analysis__.py", line 307, in main_analysis_workflow
run_analysis_workflow(*allargs)
File "/shared/programs/metage2metabo/metage2metabo/m2m_analysis/m2m_analysis_workflow.py", line 48, in run_analysis_workflow
powergraph_analysis(gml_output, output_dir, oog_jar, taxon_file, taxonomy_level)
File "/shared/programs/metage2metabo/metage2metabo/m2m_analysis/graph_compression.py", line 153, in powergraph_analysis
compression(gml_input_path, bbl_output)
File "/shared/programs/metage2metabo/metage2metabo/m2m_analysis/graph_compression.py", line 213, in compression
for line in powergrasp.compress_by_cc(gml_input):
File "/shared/programs/PowerGrASP/powergrasp/routines.py", line 201, in compress_by_cc
yield from compress(graph, cc_idx=idx, recipe=recipe_for(graph))
File "/shared/programs/PowerGrASP/powergrasp/routines.py", line 96, in compress
best_motifs = search_best_motifs(searchers, step, recipe=recipe_line)
File "/shared/programs/PowerGrASP/powergrasp/routines.py", line 35, in search_best_motifs_sequentially
motifs = MotifBatch(searcher.search(step, score_to_beat, recipe=recipe))
File "/shared/programs/PowerGrASP/powergrasp/motif_batch.py", line 18, in __init__
self.motifs = tuple(motifs)
File "/shared/programs/PowerGrASP/powergrasp/searchers.py", line 123, in search
yield from (
File "/shared/programs/PowerGrASP/powergrasp/searchers.py", line 123, in
yield from (
File "/shared/programs/PowerGrASP/powergrasp/searchers.py", line 278, in _search
yield from asp.solve_motif_search(step, lowerbound, upperbound,
File "/shared/programs/PowerGrASP/powergrasp/asp.py", line 37, in multishot_motif_search
all_models = _build_solver(step, lowerbound, upperbound, files, graph, options='--opt-mode=optN ' + options)
File "/shared/programs/PowerGrASP/powergrasp/asp.py", line 19, in _build_solver
models = clyngor.solve(files=tuple(files), inline=str(graph), constants=constants, stats=False, options=options)
File "/shared/programs/clyngor/clyngor/solving.py", line 92, in solve
raise ValueError("Options 'time_limit' and 'constants' are not "
ValueError: Options 'time_limit' and 'constants' are not handled when used with python clingo module.
```

This issue occurs recently (with Python `3.8.10` and the github version of powergrasp `0.8.19.dev0`) and I think it is linked to the release of clyngor `0.4.1` and especially the fact the clingo python package is now a dependency of clyngor. Due to this, the clingo package is always available so the variable `use_clingo_module` is always set to `True` and leads to this error.

Putting a `use_clingo_module=False` in [clyngor call](https://github.com/Aluriak/PowerGrASP/blob/master/powergrasp/asp.py#L19) solves the issue for me. But maybe there is a better way to handle this.

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