{"action":"closed","number":1892,"pull_request":{"url":"https://api.github.com/repos/stan-dev/stan/pulls/1892","id":70244609,"html_url":"https://github.com/stan-dev/stan/pull/1892","diff_url":"https://github.com/stan-dev/stan/pull/1892.diff","patch_url":"https://github.com/stan-dev/stan/pull/1892.patch","issue_url":"https://api.github.com/repos/stan-dev/stan/issues/1892","number":1892,"state":"closed","locked":false,"title":"Feature/issue 1886 integrate ode","user":{"login":"bob-carpenter","id":3383807,"avatar_url":"https://avatars.githubusercontent.com/u/3383807?v=3","gravatar_id":"","url":"https://api.github.com/users/bob-carpenter","html_url":"https://github.com/bob-carpenter","followers_url":"https://api.github.com/users/bob-carpenter/followers","following_url":"https://api.github.com/users/bob-carpenter/following{/other_user}","gists_url":"https://api.github.com/users/bob-carpenter/gists{/gist_id}","starred_url":"https://api.github.com/users/bob-carpenter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bob-carpenter/subscriptions","organizations_url":"https://api.github.com/users/bob-carpenter/orgs","repos_url":"https://api.github.com/users/bob-carpenter/repos","events_url":"https://api.github.com/users/bob-carpenter/events{/privacy}","received_events_url":"https://api.github.com/users/bob-carpenter/received_events","type":"User","site_admin":false},"body":"#### Submisison Checklist\r\n\r\n- [x] Run unit tests: `./runTests.py src/test/unit`\r\n- [x] Run cpplint: `make cpplint`\r\n- [x] Declare copyright holder and open-source license: see below\r\n\r\n#### Summary\r\n\r\nAdd `integrate_ode_rk45` and `integrate_ode_bdf` functions with and without control arguments.  Deprecate unmarked `integrate_ode`.\r\n\r\n#### Intended Effect\r\n\r\nEnable stiff ODE solving, call out names of solvers in functions, and allow for user-specified control parameters.\r\n\r\n#### How to Verify\r\n\r\nUnit tests for integrators and for the language components.\r\n\r\n#### Side Effects\r\n\r\n* deprecation messages for old version, `integrate_ode()`\r\n\r\n* interfaces must add `-DFUSION_MAX_VECTOR_SIZE=12` to makefile `CFLAGS` \r\n\r\n\r\n#### Documentation\r\n\r\nODE chapter rewritten in manual with clarifications on signatures and discussion of stiffnes.  New ODE chapter in function signatures reference manual.\r\n\r\n#### Reviewer Suggestions\r\n\r\nAnyone.\r\n\r\n#### Copyright and Licensing\r\n\r\nPlease list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):\r\n\r\nColumbia University\r\n\r\nBy submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:\r\n- Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)\r\n- Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)\r\n","created_at":"2016-05-16T19:08:41Z","updated_at":"2016-05-27T13:21:18Z","closed_at":"2016-05-27T13:21:18Z","merged_at":"2016-05-27T13:21:18Z","merge_commit_sha":"94f717b9758cb5fd88cc4cecbda61c19c542a9b3","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/stan-dev/stan/pulls/1892/commits","review_comments_url":"https://api.github.com/repos/stan-dev/stan/pulls/1892/comments","review_comment_url":"https://api.github.com/repos/stan-dev/stan/pulls/comments{/number}","comments_url":"https://api.github.com/repos/stan-dev/stan/issues/1892/comments","statuses_url":"https://api.github.com/repos/stan-dev/stan/statuses/bc047efca562ef4121f6528d23f5e76d3a629cbb","head":{"label":"stan-dev:feature/issue-1886-integrate_ode","ref":"feature/issue-1886-integrate_ode","sha":"bc047efca562ef4121f6528d23f5e76d3a629cbb","user":{"login":"stan-dev","id":3374820,"avatar_url":"https://avatars.githubusercontent.com/u/3374820?v=3","gravatar_id":"","url":"https://api.github.com/users/stan-dev","html_url":"https://github.com/stan-dev","followers_url":"https://api.github.com/users/stan-dev/followers","following_url":"https://api.github.com/users/stan-dev/following{/other_user}","gists_url":"https://api.github.com/users/stan-dev/gists{/gist_id}","starred_url":"https://api.github.com/users/stan-dev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stan-dev/subscriptions","organizations_url":"https://api.github.com/users/stan-dev/orgs","repos_url":"https://api.github.com/users/stan-dev/repos","events_url":"https://api.github.com/users/stan-dev/events{/privacy}","received_events_url":"https://api.github.com/users/stan-dev/received_events","type":"Organization","site_admin":false},"repo":{"id":8043756,"name":"stan","full_name":"stan-dev/stan","owner":{"login":"stan-dev","id":3374820,"avatar_url":"https://avatars.githubusercontent.com/u/3374820?v=3","gravatar_id":"","url":"https://api.github.com/users/stan-dev","html_url":"https://github.com/stan-dev","followers_url":"https://api.github.com/users/stan-dev/followers","following_url":"https://api.github.com/users/stan-dev/following{/other_user}","gists_url":"https://api.github.com/users/stan-dev/gists{/gist_id}","starred_url":"https://api.github.com/users/stan-dev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stan-dev/subscriptions","organizations_url":"https://api.github.com/users/stan-dev/orgs","repos_url":"https://api.github.com/users/stan-dev/repos","events_url":"https://api.github.com/users/stan-dev/events{/privacy}","received_events_url":"https://api.github.com/users/stan-dev/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/stan-dev/stan","description":"Stan development repository (home page is linked below). The master branch contains the current release. The develop branch contains the latest stable development.  See the Developer Process Wiki for details.  ","fork":false,"url":"https://api.github.com/repos/stan-dev/stan","forks_url":"https://api.github.com/repos/stan-dev/stan/forks","keys_url":"https://api.github.com/repos/stan-dev/stan/keys{/key_id}","collaborators_url":"https://api.github.com/repos/stan-dev/stan/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/stan-dev/stan/teams","hooks_url":"https://api.github.com/repos/stan-dev/stan/hooks","issue_events_url":"https://api.github.com/repos/stan-dev/stan/issues/events{/number}","events_url":"https://api.github.com/repos/stan-dev/stan/events","assignees_url":"https://api.github.com/repos/stan-dev/stan/assignees{/user}","branches_url":"https://api.github.com/repos/stan-dev/stan/branches{/branch}","tags_url":"https://api.github.com/repos/stan-dev/stan/tags","blobs_url":"https://api.github.com/repos/stan-dev/stan/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/stan-dev/stan/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/stan-dev/stan/git/refs{/sha}","trees_url":"https://api.github.com/repos/stan-dev/stan/git/trees{/sha}","statuses_url":"https://api.github.com/repos/stan-dev/stan/statuses/{sha}","languages_url":"https://api.github.com/repos/stan-dev/stan/languages","stargazers_url":"https://api.github.com/repos/stan-dev/stan/stargazers","contributors_url":"https://api.github.com/repos/stan-dev/stan/contributors","subscribers_url":"https://api.github.com/repos/stan-dev/stan/subscribers","subscription_url":"https://api.github.com/repos/stan-dev/stan/subscription","commits_url":"https://api.github.com/repos/stan-dev/stan/commits{/sha}","git_commits_url":"https://api.github.com/repos/stan-dev/stan/git/commits{/sha}","comments_url":"https://api.github.com/repos/stan-dev/stan/comments{/number}","issue_comment_url":"https://api.github.com/repos/stan-dev/stan/issues/comments{/number}","contents_url":"https://api.github.com/repos/stan-dev/stan/contents/{+path}","compare_url":"https://api.github.com/repos/stan-dev/stan/compare/{base}...{head}","merges_url":"https://api.github.com/repos/stan-dev/stan/merges","archive_url":"https://api.github.com/repos/stan-dev/stan/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/stan-dev/stan/downloads","issues_url":"https://api.github.com/repos/stan-dev/stan/issues{/number}","pulls_url":"https://api.github.com/repos/stan-dev/stan/pulls{/number}","milestones_url":"https://api.github.com/repos/stan-dev/stan/milestones{/number}","notifications_url":"https://api.github.com/repos/stan-dev/stan/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/stan-dev/stan/labels{/name}","releases_url":"https://api.github.com/repos/stan-dev/stan/releases{/id}","deployments_url":"https://api.github.com/repos/stan-dev/stan/deployments","created_at":"2013-02-06T03:25:04Z","updated_at":"2016-05-25T21:06:31Z","pushed_at":"2016-05-27T13:21:18Z","git_url":"git://github.com/stan-dev/stan.git","ssh_url":"git@github.com:stan-dev/stan.git","clone_url":"https://github.com/stan-dev/stan.git","svn_url":"https://github.com/stan-dev/stan","homepage":"http://mc-stan.org","size":260551,"stargazers_count":615,"watchers_count":615,"language":"Stan","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":134,"mirror_url":null,"open_issues_count":201,"forks":134,"open_issues":201,"watchers":615,"default_branch":"develop"}},"base":{"label":"stan-dev:develop","ref":"develop","sha":"fb1b76962cd8495812c87f0a0e0d8ab328444f34","user":{"login":"stan-dev","id":3374820,"avatar_url":"https://avatars.githubusercontent.com/u/3374820?v=3","gravatar_id":"","url":"https://api.github.com/users/stan-dev","html_url":"https://github.com/stan-dev","followers_url":"https://api.github.com/users/stan-dev/followers","following_url":"https://api.github.com/users/stan-dev/following{/other_user}","gists_url":"https://api.github.com/users/stan-dev/gists{/gist_id}","starred_url":"https://api.github.com/users/stan-dev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stan-dev/subscriptions","organizations_url":"https://api.github.com/users/stan-dev/orgs","repos_url":"https://api.github.com/users/stan-dev/repos","events_url":"https://api.github.com/users/stan-dev/events{/privacy}","received_events_url":"https://api.github.com/users/stan-dev/received_events","type":"Organization","site_admin":false},"repo":{"id":8043756,"name":"stan","full_name":"stan-dev/stan","owner":{"login":"stan-dev","id":3374820,"avatar_url":"https://avatars.githubusercontent.com/u/3374820?v=3","gravatar_id":"","url":"https://api.github.com/users/stan-dev","html_url":"https://github.com/stan-dev","followers_url":"https://api.github.com/users/stan-dev/followers","following_url":"https://api.github.com/users/stan-dev/following{/other_user}","gists_url":"https://api.github.com/users/stan-dev/gists{/gist_id}","starred_url":"https://api.github.com/users/stan-dev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stan-dev/subscriptions","organizations_url":"https://api.github.com/users/stan-dev/orgs","repos_url":"https://api.github.com/users/stan-dev/repos","events_url":"https://api.github.com/users/stan-dev/events{/privacy}","received_events_url":"https://api.github.com/users/stan-dev/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/stan-dev/stan","description":"Stan development repository (home page is linked below). The master branch contains the current release. The develop branch contains the latest stable development.  See the Developer Process Wiki for details.  ","fork":false,"url":"https://api.github.com/repos/stan-dev/stan","forks_url":"https://api.github.com/repos/stan-dev/stan/forks","keys_url":"https://api.github.com/repos/stan-dev/stan/keys{/key_id}","collaborators_url":"https://api.github.com/repos/stan-dev/stan/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/stan-dev/stan/teams","hooks_url":"https://api.github.com/repos/stan-dev/stan/hooks","issue_events_url":"https://api.github.com/repos/stan-dev/stan/issues/events{/number}","events_url":"https://api.github.com/repos/stan-dev/stan/events","assignees_url":"https://api.github.com/repos/stan-dev/stan/assignees{/user}","branches_url":"https://api.github.com/repos/stan-dev/stan/branches{/branch}","tags_url":"https://api.github.com/repos/stan-dev/stan/tags","blobs_url":"https://api.github.com/repos/stan-dev/stan/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/stan-dev/stan/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/stan-dev/stan/git/refs{/sha}","trees_url":"https://api.github.com/repos/stan-dev/stan/git/trees{/sha}","statuses_url":"https://api.github.com/repos/stan-dev/stan/statuses/{sha}","languages_url":"https://api.github.com/repos/stan-dev/stan/languages","stargazers_url":"https://api.github.com/repos/stan-dev/stan/stargazers","contributors_url":"https://api.github.com/repos/stan-dev/stan/contributors","subscribers_url":"https://api.github.com/repos/stan-dev/stan/subscribers","subscription_url":"https://api.github.com/repos/stan-dev/stan/subscription","commits_url":"https://api.github.com/repos/stan-dev/stan/commits{/sha}","git_commits_url":"https://api.github.com/repos/stan-dev/stan/git/commits{/sha}","comments_url":"https://api.github.com/repos/stan-dev/stan/comments{/number}","issue_comment_url":"https://api.github.com/repos/stan-dev/stan/issues/comments{/number}","contents_url":"https://api.github.com/repos/stan-dev/stan/contents/{+path}","compare_url":"https://api.github.com/repos/stan-dev/stan/compare/{base}...{head}","merges_url":"https://api.github.com/repos/stan-dev/stan/merges","archive_url":"https://api.github.com/repos/stan-dev/stan/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/stan-dev/stan/downloads","issues_url":"https://api.github.com/repos/stan-dev/stan/issues{/number}","pulls_url":"https://api.github.com/repos/stan-dev/stan/pulls{/number}","milestones_url":"https://api.github.com/repos/stan-dev/stan/milestones{/number}","notifications_url":"https://api.github.com/repos/stan-dev/stan/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/stan-dev/stan/labels{/name}","releases_url":"https://api.github.com/repos/stan-dev/stan/releases{/id}","deployments_url":"https://api.github.com/repos/stan-dev/stan/deployments","created_at":"2013-02-06T03:25:04Z","updated_at":"2016-05-25T21:06:31Z","pushed_at":"2016-05-27T13:21:18Z","git_url":"git://github.com/stan-dev/stan.git","ssh_url":"git@github.com:stan-dev/stan.git","clone_url":"https://github.com/stan-dev/stan.git","svn_url":"https://github.com/stan-dev/stan","homepage":"http://mc-stan.org","size":260551,"stargazers_count":615,"watchers_count":615,"language":"Stan","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":134,"mirror_url":null,"open_issues_count":201,"forks":134,"open_issues":201,"watchers":615,"default_branch":"develop"}},"_links":{"self":{"href":"https://api.github.com/repos/stan-dev/stan/pulls/1892"},"html":{"href":"https://github.com/stan-dev/stan/pull/1892"},"issue":{"href":"https://api.github.com/repos/stan-dev/stan/issues/1892"},"comments":{"href":"https://api.github.com/repos/stan-dev/stan/issues/1892/comments"},"review_comments":{"href":"https://api.github.com/repos/stan-dev/stan/pulls/1892/comments"},"review_comment":{"href":"https://api.github.com/repos/stan-dev/stan/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/stan-dev/stan/pulls/1892/commits"},"statuses":{"href":"https://api.github.com/repos/stan-dev/stan/statuses/bc047efca562ef4121f6528d23f5e76d3a629cbb"}},"merged":true,"mergeable":null,"mergeable_state":"unknown","merged_by":{"login":"syclik","id":425751,"avatar_url":"https://avatars.githubusercontent.com/u/425751?v=3","gravatar_id":"","url":"https://api.github.com/users/syclik","html_url":"https://github.com/syclik","followers_url":"https://api.github.com/users/syclik/followers","following_url":"https://api.github.com/users/syclik/following{/other_user}","gists_url":"https://api.github.com/users/syclik/gists{/gist_id}","starred_url":"https://api.github.com/users/syclik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/syclik/subscriptions","organizations_url":"https://api.github.com/users/syclik/orgs","repos_url":"https://api.github.com/users/syclik/repos","events_url":"https://api.github.com/users/syclik/events{/privacy}","received_events_url":"https://api.github.com/users/syclik/received_events","type":"User","site_admin":false},"comments":5,"review_comments":0,"commits":14,"additions":2479,"deletions":493,"changed_files":76}}
{"actor":{"display_login":"syclik"}}