✨ Add clp guidance megacomplex #1029
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Benchmark is done. Checkout the benchmark result page. Benchmark diff v0.5.1 vs. mainParametrized benchmark signatures: BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)Benchmark diff main vs. PRParametrized benchmark signatures: BenchmarkOptimize.time_optimize(index_dependent, grouped, weight) |
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Just some minor nitpicks about error messages and backward compatibility with the ascii format.
Might also be nice to factor the creation out in a separate function so we can use it on a dataset from file basis (e.g. reading legacy project ascii files from TMP and TIMP) 🤔
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Sourcery Code Quality Report❌ Merging this PR will decrease code quality in the affected files by 0.78%.
Here are some functions in these files that still need a tune-up:
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This is what the model would look like as dataset:
dataset1:
megacomplex:
- mc1
dataset2:
megacomplex:
- mc2
dataset_groups:
default:
link_clp: true
megacomplex:
mc1:
compartments:
- s1
- s2
rates:
- '1'
- '2'
type: decay-sequential
mc2:
dimension: time
target: s1
type: clp-guide |
Co-authored-by: Jörn Weißenborn <[email protected]>
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clp_label coordinate
The function can also be used for loaded result datasets
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Should be ready to merge now (reviewing my own changes 😝 )
@jsnel @ism200 For the usage guide of create_clp_guide_dataset see the docs generated from the docstrings you can try it on binder (also works with ascii just change the file extension)
Minor improvements to documentation following code review on glotaran#1029. Fixed interrogate issues with invalid exclude argument in pyproject.toml Set ignore-semiprivate to true (for now) for interrogate (else coverage dips below 59) Added a docstring to improve coverage (as measured by interrogate)
Minor improvements to documentation following code review on glotaran#1029. Fixed interrogate issues with invalid exclude argument in pyproject.toml Set ignore-semiprivate to true (for now) for interrogate (else coverage dips below 59) Added a docstring to improve coverage (as measured by interrogate)
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click>=8 breaks usage of glob patterns with interrogate Current docstring coverage is 65%
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This PR adds the
clp-guidemegacomplex.A model with a clp guide looks like this:
{ "dataset_groups": {"default": {"link_clp": True}}, "megacomplex": { "mc1": { "type": "decay-sequential", "compartments": ["s1", "s2"], "rates": ["1", "2"], }, "mc2": {"type": "clp-guide", "dimension": "time", "target": "s1"}, }, "dataset": { "dataset1": {"megacomplex": ["mc1"]}, "dataset2": {"megacomplex": ["mc2"]}, },Change summary
exclusiveattribute to megacomplex decorator which ensures that a megacomplex is the only one in a datasetClpGuideMegacomplexResult.create_clp_guide_datasetto create clp guides from resultsChecklist
Closes issues
closes #1027