{"action":"created","issue":{"url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/70","labels_url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/70/labels{/name}","comments_url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/70/comments","events_url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/70/events","html_url":"https://github.com/kroneckerbio/kroneckerbio/issues/70","id":113171182,"number":70,"title":"Allow dots in analytic expressions","user":{"login":"drhagen","id":2952478,"avatar_url":"https://avatars.githubusercontent.com/u/2952478?v=3","gravatar_id":"","url":"https://api.github.com/users/drhagen","html_url":"https://github.com/drhagen","followers_url":"https://api.github.com/users/drhagen/followers","following_url":"https://api.github.com/users/drhagen/following{/other_user}","gists_url":"https://api.github.com/users/drhagen/gists{/gist_id}","starred_url":"https://api.github.com/users/drhagen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drhagen/subscriptions","organizations_url":"https://api.github.com/users/drhagen/orgs","repos_url":"https://api.github.com/users/drhagen/repos","events_url":"https://api.github.com/users/drhagen/events{/privacy}","received_events_url":"https://api.github.com/users/drhagen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-10-24T16:44:46Z","updated_at":"2015-10-24T19:00:19Z","closed_at":null,"body":"Any species names that contain operators must be quoted in order for them to be parsed unambiguously. This currently includes dots `.`. We could allow dots and still not be ambiguous because dots are not valid mathematical operators. I don't want to get into the habit of allowing every possible unambiguous operator, but because the dot has a special meaning in Kronecker expressions it is likely to appear more often than others. This would allow users to write `cell.glucose*membrane.transporter*kon` rather than `\"cell.glucose\"*\"membrane.transporter\"*kon`. If people stay away from operators in names, they can avoid all use of quotes in expressions, which is kind of nice.\r\n\r\nI am currently on the fence with this proposal and wanted to see what other people thought. This is a backwards compatible change if we delay it to the future.\r\n\r\nBonus proposal: If we *disallowed* compartment indicator dots in quotes *and* allowed them outside quotes *and* allowed compartment indicator dots between quoted names, we could lift the restriction on dots in component names. You could name a species `glucose 2.0` and refer to it as `cell.\"glucose 2.0\"`. This cannot be added in a backwards compatible way in the future because dots currently have special meaning within quotes."},"comment":{"url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/comments/150841331","html_url":"https://github.com/kroneckerbio/kroneckerbio/issues/70#issuecomment-150841331","issue_url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/70","id":150841331,"user":{"login":"xpspectre","id":4530441,"avatar_url":"https://avatars.githubusercontent.com/u/4530441?v=3","gravatar_id":"","url":"https://api.github.com/users/xpspectre","html_url":"https://github.com/xpspectre","followers_url":"https://api.github.com/users/xpspectre/followers","following_url":"https://api.github.com/users/xpspectre/following{/other_user}","gists_url":"https://api.github.com/users/xpspectre/gists{/gist_id}","starred_url":"https://api.github.com/users/xpspectre/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xpspectre/subscriptions","organizations_url":"https://api.github.com/users/xpspectre/orgs","repos_url":"https://api.github.com/users/xpspectre/repos","events_url":"https://api.github.com/users/xpspectre/events{/privacy}","received_events_url":"https://api.github.com/users/xpspectre/received_events","type":"User","site_admin":false},"created_at":"2015-10-24T19:00:19Z","updated_at":"2015-10-24T19:00:19Z","body":"Ultimately, I'm in favor of allowing this. Allowing dots to appear in a qualified compartment.species w/o having to quote the expression, plus the rules for reaction compartments, take us back full circle to system I settled on when updating the model conversion code a few months ago. \r\n\r\nTo make the proposed changes here, pretty annoying changes would have to be made. I think it's worth waiting until after release 0.5 to do it, so we can reorganize the internals to put all the user interface code together and simplify the changes.\r\n\r\nThe bonus proposal basically looks like SimBiology's convention, except with quotes instead of square brackets."}}