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Update Stan source to v2.19.1 #652
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This reverts commit 047dac7.
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riddell-stan
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* feat: Use Stan 2.19.1 source * Revert "fix: Disable STAN_THREADS test" This reverts commit 047dac7.
ahartikainen
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Oct 30, 2020
* CI: remove unused packages from test-requirements.txt Leaving the empty file. (Empty except for comments.) Packages required for tests may be added in the future. * remove unneeded extension under sphinx 1.3 * chore: update version number for development * Replace logger with print * Reduce Windows testing * use logger.warning * new extract function, old results unpack shape fix warmup and permuted, also fix dtype * revise to_dataframe change chain_idx to draw * declare Cython language version Closes #524 * faster implementation, lower memory usage * loop threading test maximum 10 times before failure * summary to invidual ess and split-rhat functions * ISSUE-534 model.py optimizing function raises ValueError for index of 'lp__' * Link to external Windows file * Fix windows docs * Update hmc diagnostics output (#540) :* fix bugs, redefine verbose levels * add possibility to select subset of checks * max flatname limit (1000) for diagnostics in model.sampling * fix: update source to Stan 2.18.1.0, fixes threading bug in Stan C++ * Fix formatting & broken/outdated links (#543) * Fix formatting of links on installation and Python for Windows pages * Fix markdown formatting on Pystan on Windows page * Fix typo * Fix whitespace * disable check_hmc_diagnostics when test_grad=True (#545) * chore: update version number for development (#547) * Add extra compile args to setup for _mics.pyx (#557) * Add extra compile args to setup for _mics.pyx * Update appveyor * ci: update wheel download script * Fix too long paths on Windows (#569) * Fix too long paths on Windows * fix extra -c * fix(ci): use newer gcc on travis Newer gcc needed for Stan 2.19. * feat(stan): Update Stan source to tag v2.19.0 * fix: update flags, library paths, tests for Stan 2.19 Includes a minor update to stan_fit.hpp to deal with the fact that ADVI now produces values for `lp__`, `log_p__`, and `log_g__`. Previously it only produced values for `lp__` (in addition to parameter values). * fix: minor setuptools adjustments Updates files which should be excluded from sdist and removes a stale reference in setup.py * remove long paths * fix c++14 for msvc (not tested) * read with codecs utf-8 * remove stan-math/lib test folder and files * chore: update release notes, version number * fix(doc): remove sphinx.ext.pngmath, unused * chore: bump version * fix(ci): manylinux1 32bit wheels no longer built * Adding support for 'allow_undefined' and 'includes' * switching to include_dirs * add warning for external C++ * remove duplicate 'save_iterations' in kwargs * add 'tol_rel_obj' to optimizing function doc * fix(ci): update appveyor wheelhouse secret, new appveyor acct * enable allow_undefined in stanc * add cpp external test * external cpp stan autograd * fix path * fix remove paths * add example to doc and update c++ compiler set-up * fix typos and add information about ostream * Update readme for projects and ArviZ (#600) * Update readme for projects and ArviZ * Add more information * Add instructions for pip * Fix links * Update appveyor link * ci: Correct wheel uploader key appveyor * fix: Fix appveyor link in README (#607) Closes #604. * Add CXX keyword to instructions (#610) * Load pickled fit without the model instance (#609) * add experimental function to load old fit objects without model * Test recovering old fits * py27 fixes and clean the code * change the function name * add docs * Doc explaining how to run PyStan in Atom editor on Windows (#588) * Create How to use PyStan in Atom editor (Windows).rst It took me quite a while to figure all this out and wanted to share what worked for me in case other people run into the same issue. * Rename How to use PyStan in Atom editor (Windows).rst to Run_PyStan_in_Atom.rst * Update Run_PyStan_in_Atom.rst Changed the text as suggested * Update Run_PyStan_in_Atom.rst corrected spelling mistakes * implement mass_matrix * add function to extract stepsize and mass-matrix * tests * general cleanup * add docs * update mass_matrix to inv_metric * add option to return inv_metric as dict * Update inv_metric behaviour (#616) * Update docstring for get_inv_metric * enable numbers with e syntax * fix adapt_engaged functionality * fix bugs and last_position * update tests * Add adapt_engaged = False * update width calculation (#618) * Update installation_beginner.rst (#623) Added clarification for OSX Conda compilers based off of https://github.com/stan-dev/pystan/issues/622 * Don't run tests twice (#624) * Don't run tests twice in travis * run tests once in appveyor * feat: Update Stan to v2.20.0 * fix: Disable STAN_THREADS test PyStan 2.20 will not support using STAN_THREADS as there appears no way to support it using gcc. Trying to use a model compiled with STAN_THREADS with gcc yields an immediate segfault. * Use prefix 'pystan_' with tempfolder (#628) * Increase verbosity for plotting (arviz) * change flatnames to sim fnames_oi (#642) * Update Stan source to v2.19.1 (#652) * feat: Use Stan 2.19.1 source * Revert "fix: Disable STAN_THREADS test" This reverts commit 047dac7. * Update README.rst * reshape with Fortran order (#649) * chore: Bump version, update release notes Closes #651 * ci: Enable stale bot * docs: Fix reStructuredText error in README * chore: Bump version, update release notes * chore: Post-release tasks Update version number for develop. Add placeholder in release notes. * ci: Update wheels downloading script (#657) * fix: Update .gitignore [ci skip] (#658) * ci: Do not test on or build wheels for Python 3.5 (#660) * docs: Minor updates to release howto (#665) * Remove Python 2 from Windows tests (#676) It is breaking and doesn't even work as other versions (python 3.x) * Update related packages (#672) * Update related packages * Update related for doc * add emcee to similar * fix: Separate projects using PyStan * docs: rearrange related projects * fix double list (#682) * fix double list * add data * Rename include_dirs * Update/stan 2.22.1 math 3.1.1 (#692) * moving forward * fix compilation * build tbb at setup * build tbb if not build * Update boost * update paths * import subprocess * Change tag * Fix tag * Import glob * Add star to glob * Add -D_REENTRANT to compiler flags * debug * Use abspath * fix workflow and test path in linux * move release to main * check folder only * fix * add L * fix move * remove extra_link_args * Use rpath * run only on windows * fix isystem typo * Move rpath to linker * change rpath * fix rpath * try LD_LIBRARY_PATH hack * use link args * cpu_count * tmp fix for njobs * update inspect.getfullargspec * fix experimental * fix missing virtual and py27 function * add n_threads * restructure for setup * fix typo * correct version number * fix wrong import * remove some imports * debug * print debug * Use abspath * import shutil * remove debug prints * update misc tbb func * clean check * reset STAN_NUM_THREADS * Update model.py * Delete env var if used * clean njobs settings and add default nthreads * update docs, abspath for tbb and overwrite tbb files * remove env vars use default locations * remove platform import * change elif to if * Remove tbb source * Change tbb include loc * Change tbb include location * Change tbb include loc * move tbb path in stanfit4model * ignore cached models * move libtbb to load_module function * update docs * reset argspec * remove n_threads * update version number * update tests and test threading on windows * Add comment for _REENTRANT Co-authored-by: ahartikainen <ahartikainen@github.com> * [doc] Update docs (#695) * Update API docs * Fix broken link * remove json comment * fix format * Update format * Fix links * Fix format * Fix stanfit4models link * Fix link * Create FUNDING.yml (add github sponsors info on behalf of SGB) [ci skip] * Add some troubleshooting the end of the installation instructions (#699) * Add minimal comment inv_metric dict keys (#718) * docs: Invite PyStan 3 testers * Update CI and model Co-authored-by: Allen Riddell <riddella+stan@indiana.edu> Co-authored-by: Alejandro Fernandez <alejandro@apache.org> Co-authored-by: Jenny Sahng <6475953+jennynz@users.noreply.github.com> Co-authored-by: Dan F-M <danfm@nyu.edu> Co-authored-by: Albert Chen <blahoink@gmail.com> Co-authored-by: riddell-stan <39928022+riddell-stan@users.noreply.github.com> Co-authored-by: S-Black <49724883+S-Black@users.noreply.github.com> Co-authored-by: William <gallamine@gmail.com> Co-authored-by: Semyeong Oh <semyeong.oh@gmail.com> Co-authored-by: ahartikainen <ahartikainen@github.com> Co-authored-by: Jonah Gabry <jgabry@gmail.com> Co-authored-by: Manish Goregaokar <manishsmail@gmail.com> Co-authored-by: Allen Riddell <riddella@indiana.edu>
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Reverts a disabled test (which was disabled for 2.20).