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sys-bio / roadrunner

libRoadRunner: A high-performance SBML simulator
http://libroadrunner.org/
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The feature to get and set parametric stoichiometries is added #1145

Closed adelhpour closed 10 months ago

adelhpour commented 12 months ago

Users can now set and get parameters used to define stoichiometries if the species associated with that parametric stoichiometry appears only once in a reaction. Note that, it is not possible to set and get stoichiometries while conserved moiety is turned on.

luciansmith commented 12 months ago

Oh, stoich(rxn, species) is brilliant.

Also, none of the tests are going to pass because it's trying to download a specific libroadrunner-deps file instead of 'the latest'. My plan was to investigate this at some point, but if you manage to figure it out before me, go for it! ;-) An Antimony run went fine, and it also downloads librr-deps, so maybe start with that? Maybe compare https://github.com/sys-bio/antimony/blob/develop/azure-pipelines.yml with roadrunner's.

adelhpour commented 12 months ago

Oh, stoich(rxn, species) is brilliant.

Also, none of the tests are going to pass because it's trying to download a specific libroadrunner-deps file instead of 'the latest'. My plan was to investigate this at some point, but if you manage to figure it out before me, go for it! ;-) An Antimony run went fine, and it also downloads librr-deps, so maybe start with that? Maybe compare https://github.com/sys-bio/antimony/blob/develop/azure-pipelines.yml with roadrunner's.

Just did it. Let's see what happens!

luciansmith commented 12 months ago

That worked! And now you hit a bug in conda itself, which I was REALLY HOPING would be fixed by now, because it literally breaks everything.

https://github.com/conda/conda/issues/12531

adelhpour commented 12 months ago

That worked! And now you hit a bug in conda itself, which I was REALLY HOPING would be fixed by now, because it literally breaks everything.

conda/conda#12531

Shall we wait for them to fix it, or we have to do something now?

luciansmith commented 11 months ago

github seems to be having connectivity problems right now; the checks had problems just checking out the repository. I killed the pipeline run; I think if I close and re-open the PR, it'll start it again from scratch.