Aluriak / Aluriak/PowerGrASP

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

Đang mở
#1 1 bình luận 0 reaction 0 người được giao Xem trên GitHub
Ngôn ngữ chính
Answer Set Programming
Star
12
Fork
2
Chỉ số merge pull request
Không có pull request nào được merge trong 30 ngày

Mô tả

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.

Hướng dẫn đóng góp

Chưa lập chỉ mục được hướng dẫn đóng góp cho kho mã nguồn này

Đánh giá

Issue này chưa được đánh giá.

Nhận issue mới trong hộp thư của bạn

Bản tóm tắt ngắn những issue GitHub phù hợp với người mới.