{"action":"created","issue":{"url":"https://api.github.com/repos/stan-dev/stan/issues/2601","repository_url":"https://api.github.com/repos/stan-dev/stan","labels_url":"https://api.github.com/repos/stan-dev/stan/issues/2601/labels{/name}","comments_url":"https://api.github.com/repos/stan-dev/stan/issues/2601/comments","events_url":"https://api.github.com/repos/stan-dev/stan/issues/2601/events","html_url":"https://github.com/stan-dev/stan/pull/2601","id":348539465,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA2ODY3MDY5","number":2601,"title":"Cleaning up makefiles. Fixes the makefile issues.","user":{"login":"syclik","id":425751,"node_id":"MDQ6VXNlcjQyNTc1MQ==","avatar_url":"https://avatars2.githubusercontent.com/u/425751?v=4","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":37,"created_at":"2018-08-08T01:12:07Z","updated_at":"2018-09-22T22:41:14Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/stan-dev/stan/pulls/2601","html_url":"https://github.com/stan-dev/stan/pull/2601","diff_url":"https://github.com/stan-dev/stan/pull/2601.diff","patch_url":"https://github.com/stan-dev/stan/pull/2601.patch"},"body":"#### Submission 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\nThis pull request simplifies the build and gets the makefiles in order. The makefiles got tangled up through a few recent changes. This uses changes from the PR in Math: stan-dev/math#956.\r\n\r\nHere are some of the highlights:\r\n- `CXX` is the only compiler setting used. In develop, both `CXX` and `CC` have to be set\r\n- Windows: removed the `uname: not found` message\r\n- `CXXFLAGS` are now broken into smaller components that can be set by the user:\r\n    - `CXXFLAGS_LANG` for language-specific flags\r\n    - `CXXFLAGS_WARNINGS` for ignoring warnings\r\n    - `CXXFLAGS_BOOST` for boost-specific flags\r\n    - `CXXFLAGS_SUNDIALS` for sundials-specific flags\r\n    - `CXXFLAGS_EIGEN` for eigen-specific flags\r\n    - `CXXFLAGS_GTEST` for google-test-specific flags\r\n    - `CXXFLAGS_OS` for a catch-all and any os-specific flags.\r\n- `CPPFLAGS` are broken into components (`CPPFLAGS` are the C preprocessor flags):\r\n    - `CPPFLAGS_BOOST` for boost-specific flags\r\n    - `CPPFLAGS_SUNDIALS` for sundials-specific flags\r\n    - `CPPFLAGS_EIGEN` for eigen-specific flags\r\n    - `CPPFLAGS_GTEST` for google-test-specific flags\r\n    - `CPPFLAGS_OPENCL` for opencl\r\n\r\n  breaking apart the flags this way makes it clearer how to extend the flags for MPI and GPU.\r\n- each of the flags can be set within `make/local` and it will take precedence over the default values\r\n- the dependency generation now generates with dummy targets for each file. This means more robustness in that -- this fixes problems where a header file is removed from the source tree. This caused a lot of trouble with stability of make.\r\n- this should fix the dependencies with updating `function_signatures.h`\r\n- we no longer have to update the `make/tests` folder with hand-coded dependencies to the generated `.hpp` file from `.stan` files! This will cut down error. Just need to `#include <test/test-models/good/*.hpp>` in the test file and it'll auto-generate!\r\n\r\n#### Intended Effect\r\n\r\nCleans up a lot of the build. Gets us up and building for Windows too.\r\n\r\n#### How to Verify\r\n\r\nRun all the tests and other things we've done before:\r\n```\r\n./runTests.py src/test/unit\r\n./runTests.py src/test/integration\r\nmake doc\r\nmake\r\n```\r\n\r\n#### Side Effects\r\n\r\nThese changes will affect CmdStan. We'll need to update that repo too.\r\n\r\n#### Documentation\r\n\r\n- [ ] This needs to be documented on the wiki and in the installation instructions. We'll see if we can get the build to pass first.\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\nGenerable\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"},"comment":{"url":"https://api.github.com/repos/stan-dev/stan/issues/comments/423778474","html_url":"https://github.com/stan-dev/stan/pull/2601#issuecomment-423778474","issue_url":"https://api.github.com/repos/stan-dev/stan/issues/2601","id":423778474,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMzc3ODQ3NA==","user":{"login":"mitzimorris","id":5466612,"node_id":"MDQ6VXNlcjU0NjY2MTI=","avatar_url":"https://avatars1.githubusercontent.com/u/5466612?v=4","gravatar_id":"","url":"https://api.github.com/users/mitzimorris","html_url":"https://github.com/mitzimorris","followers_url":"https://api.github.com/users/mitzimorris/followers","following_url":"https://api.github.com/users/mitzimorris/following{/other_user}","gists_url":"https://api.github.com/users/mitzimorris/gists{/gist_id}","starred_url":"https://api.github.com/users/mitzimorris/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mitzimorris/subscriptions","organizations_url":"https://api.github.com/users/mitzimorris/orgs","repos_url":"https://api.github.com/users/mitzimorris/repos","events_url":"https://api.github.com/users/mitzimorris/events{/privacy}","received_events_url":"https://api.github.com/users/mitzimorris/received_events","type":"User","site_admin":false},"created_at":"2018-09-22T22:41:14Z","updated_at":"2018-09-22T22:41:14Z","author_association":"MEMBER","body":"not fixing it for this PR is OK - filing an issue is good enough - I can provide more details to show how to test if you need them.\r\n"}}
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