Speed up travis #329

yannikschaelte · 2020-05-13T09:40:13Z

don't run push checks on pr level too

dweindl · 2020-05-13T10:41:41Z

test/test_storage.py

@@ -12,7 +12,7 @@

 def test_storage_opt_result():
    minimize_result = create_optimization_result()
-    with tempfile.TemporaryDirectory(dir=f".") as tmpdirname:


Haha, also did that on #326

* speed up travis * travis likes ; * fix flake8

* set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add failing test * refactor problem * fix * fix * remove unneeded arg * add test * add tests for different orders * reduction should be from full vector * fixup * fix flake8 * fix problem storage * fixup * fix unnecessary list calls * make doc, x_free_indices properties * fix style * fix docs * check profiles to plot whether profiles were actually computed * fix plotting for fixed pars; add test Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de>

* Objective.initialize(); minor edits (#281) * implement objective.initialize() * implement initialize for amici * cache sbml test model * catch module not found error * fix strange os behavior# * Fix least squares options (closes #282) (#283) * Pass options to least squares optimizer * Different default options for least squares optimizer * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * move res grad check to fun * implement res check for hier solver * cont * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add test model * Feature qualitative (#325) * Basic implementation of reduced optimal scaling approach * Split inner solver for qualitative data and scalings / offests * Some clean up and comments * Implementation for standard approach * Raise error for standard and reparameterized as its not implemented * Fixed flake8 * Changed parameterType for qualitative data * Added some comments and typehints * more typehints * added docstrings and simplified some functions * Print warning, if inner optimization fails * Update pypesto/hierarchical/optimal_scaling_solver.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Feature qualitative (#338) * Basic implementation of reduced optimal scaling approach * Split inner solver for qualitative data and scalings / offests * Some clean up and comments * Implementation for standard approach * Raise error for standard and reparameterized as its not implemented * Fixed flake8 * Changed parameterType for qualitative data * Added some comments and typehints * more typehints * added docstrings and simplified some functions * Print warning, if inner optimization fails * Update pypesto/hierarchical/optimal_scaling_solver.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Example notebook for qualitative data optimization Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Tidy up profiles (#363) * update, document profiles * tidy up * review comments * fix minus sign in get_error_output (#361) * fix minus sign in get_error_output * fix 2 signs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * progress bar for MCMC sampling (#366) * progress bar added in MCMC * remove empty line * remove empty line * PR change * minor edits; rerun sampling nbs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Refactor profiles; add locally approximated profiles (#369) * update, document profiles * tidy up * review comments * refactor profiles * refactro profile visualizations * refactor * fix previous test error * refactor options * fix profile list index not set * fix wrong docstring * minor edits * extend profile tests * add problem conversion test (tb extended) * add test for profiles_ci * add problem conversion function * add approximate profiles * extend profiles visualization functions * add recompute hessian test * extend rosenbrock nb * fix docs build warning * compute cis by interpolation * fix wrong # args * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Tidy up profiles (#363) * update, document profiles * tidy up * review comments * fix minus sign in get_error_output (#361) * fix minus sign in get_error_output * fix 2 signs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * progress bar for MCMC sampling (#366) * progress bar added in MCMC * remove empty line * remove empty line * PR change * minor edits; rerun sampling nbs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Refactor profiles; add locally approximated profiles (#369) * update, document profiles * tidy up * review comments * refactor profiles * refactro profile visualizations * refactor * fix previous test error * refactor options * fix profile list index not set * fix wrong docstring * minor edits * extend profile tests * add problem conversion test (tb extended) * add test for profiles_ci * add problem conversion function * add approximate profiles * extend profiles visualization functions * add recompute hessian test * extend rosenbrock nb * fix docs build warning * compute cis by interpolation * Interface ipopt optimizer (#373) * interface ipopt * fix args * update pip reqs * move to setup.py optional deps * remove upgrade * test * test * tmp fix * check ipopt on travis * test * test * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> * Fix visu 372 (#375) * fix palette vector length depending on hue parameter * Fix geweke - fixes #354 (#376) * add failing geweke test * fix geweke * add test for short chains * rerun notebooks * update argument name * flake8 * fix * fix Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Feature parameter priors with gradients #357 Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> add paramter priors initial commit for PEtab import chage parameter scaling small fixes in tests update recent local changes, prepare to merge new restructured objective fix merge conflictsin aggregated.py finish up testing fix x_names typo in params in test fix flake8 adapt dependencies increase readability fix test fix sphinx resolve last comments on docs add __deepcopy__ again fix flake 8 ... adress second code review round bugfix fix petab import parameter scales pseudo commit to restart travis... * use amici.import_model_module (#384) * use amici.import_model_module * update amici version * fix amici test (#385) * fix amici test * fix * fix * diverge * Additional code quality checks, minor simplifications (#395) * additional code quality checks * fix geweke * fix flake8 runner * fix v2 * Refactor problem; Fix profiles (#393) * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add failing test * refactor problem * fix * fix * remove unneeded arg * add test * add tests for different orders * reduction should be from full vector * fixup * fix flake8 * fix problem storage * fixup * fix unnecessary list calls * make doc, x_free_indices properties * fix style * fix docs * check profiles to plot whether profiles were actually computed * fix plotting for fixed pars; add test Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> * Refactor logging, specify logger name. (#398) * Specify logger name. * Refactor, new function. * Multiple profile plotting (#399) * introduces handling of multiple results and multiple profile_lists * fix #371 * fix #374 * Require packaging version 20.0 for pymc3. (#401) * Feature temper likelihood - close #324 (#396) * rename trace_fval to trace_neglogpost * rename llh to lpost * add log prior * add log prior -> pt * add log prior -> sampler * add log prior -> result * flake8 * if priors are None -> set log prior to zero instead of None * REVERT if priors are None -> set log prior to zero instead of None * if prior is empty set to zero * fixes * empty prior result in pymc3 sampler * rerun notebook * rerun sampling notebook * add test * fix * fixes PR * add kwargs * fix flake8 * Update pypesto/sampling/metropolis.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix PR * review PR * simplify * Update pypesto/sampling/sampler.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * docs * test for prior in sampling * typo * short is better Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * Prepare release 0.1.0 (#402) * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * prepare release 0.0.14 * fix doc warnings; address reviewer comments * 0.0.14 -> 0.1.0 * increase sample size in tests Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * small fix visu mcmc (#405) * fix visu mcmc * PR * fix #390: Hessian computation (#407) * Fix exception type for `import_module` in PEtab import (#403) Correctly use `MuduleNotFoundError` instead of `RuntimeError`, as in AMICI. Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Improve hdf5 error output (#409) * improve hdf5 error message; fixes #391 * fixup * outlaw large files; fixes #388 (#408) * outlaw large files; fixes #388 * error output * fixup * fix travis bash code * add log * fix test * Fix metropolis initial parameters (#412) * fix initial parameters from optimization results * flake8 * test * fix pymc3 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * Modularize (#413) * init modularize * modularize work packages; use active descriptions * fixup * fix autocorrect * Update pypesto/objective/base.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update test/test_sample.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update test/test_sample.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * address reviewer comments * Update pypesto/result.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * add typehints * fix noqa Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> Co-authored-by: ErikaDudkin <49193148+erikadudki@users.noreply.github.com> Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: dilpath <59329744+dilpath@users.noreply.github.com> Co-authored-by: lcontento <lcontento@users.noreply.github.com>

* Basic implementation of reduced optimal scaling approach * Split inner solver for qualitative data and scalings / offests * Some clean up and comments * Implementation for standard approach * Raise error for standard and reparameterized as its not implemented * Fixed flake8 * Changed parameterType for qualitative data * Added some comments and typehints * more typehints * added docstrings and simplified some functions * Print warning, if inner optimization fails * Update pypesto/hierarchical/optimal_scaling_solver.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Example notebook for qualitative data optimization * Feature hierarchical (#422) * Objective.initialize(); minor edits (#281) * implement objective.initialize() * implement initialize for amici * cache sbml test model * catch module not found error * fix strange os behavior# * Fix least squares options (closes #282) (#283) * Pass options to least squares optimizer * Different default options for least squares optimizer * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * move res grad check to fun * implement res check for hier solver * cont * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add test model * Feature qualitative (#325) * Basic implementation of reduced optimal scaling approach * Split inner solver for qualitative data and scalings / offests * Some clean up and comments * Implementation for standard approach * Raise error for standard and reparameterized as its not implemented * Fixed flake8 * Changed parameterType for qualitative data * Added some comments and typehints * more typehints * added docstrings and simplified some functions * Print warning, if inner optimization fails * Update pypesto/hierarchical/optimal_scaling_solver.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Feature qualitative (#338) * Basic implementation of reduced optimal scaling approach * Split inner solver for qualitative data and scalings / offests * Some clean up and comments * Implementation for standard approach * Raise error for standard and reparameterized as its not implemented * Fixed flake8 * Changed parameterType for qualitative data * Added some comments and typehints * more typehints * added docstrings and simplified some functions * Print warning, if inner optimization fails * Update pypesto/hierarchical/optimal_scaling_solver.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Example notebook for qualitative data optimization Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Tidy up profiles (#363) * update, document profiles * tidy up * review comments * fix minus sign in get_error_output (#361) * fix minus sign in get_error_output * fix 2 signs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * progress bar for MCMC sampling (#366) * progress bar added in MCMC * remove empty line * remove empty line * PR change * minor edits; rerun sampling nbs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Refactor profiles; add locally approximated profiles (#369) * update, document profiles * tidy up * review comments * refactor profiles * refactro profile visualizations * refactor * fix previous test error * refactor options * fix profile list index not set * fix wrong docstring * minor edits * extend profile tests * add problem conversion test (tb extended) * add test for profiles_ci * add problem conversion function * add approximate profiles * extend profiles visualization functions * add recompute hessian test * extend rosenbrock nb * fix docs build warning * compute cis by interpolation * fix wrong # args * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Tidy up profiles (#363) * update, document profiles * tidy up * review comments * fix minus sign in get_error_output (#361) * fix minus sign in get_error_output * fix 2 signs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * progress bar for MCMC sampling (#366) * progress bar added in MCMC * remove empty line * remove empty line * PR change * minor edits; rerun sampling nbs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Refactor profiles; add locally approximated profiles (#369) * update, document profiles * tidy up * review comments * refactor profiles * refactro profile visualizations * refactor * fix previous test error * refactor options * fix profile list index not set * fix wrong docstring * minor edits * extend profile tests * add problem conversion test (tb extended) * add test for profiles_ci * add problem conversion function * add approximate profiles * extend profiles visualization functions * add recompute hessian test * extend rosenbrock nb * fix docs build warning * compute cis by interpolation * Interface ipopt optimizer (#373) * interface ipopt * fix args * update pip reqs * move to setup.py optional deps * remove upgrade * test * test * tmp fix * check ipopt on travis * test * test * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> * Fix visu 372 (#375) * fix palette vector length depending on hue parameter * Fix geweke - fixes #354 (#376) * add failing geweke test * fix geweke * add test for short chains * rerun notebooks * update argument name * flake8 * fix * fix Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Feature parameter priors with gradients #357 Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> add paramter priors initial commit for PEtab import chage parameter scaling small fixes in tests update recent local changes, prepare to merge new restructured objective fix merge conflictsin aggregated.py finish up testing fix x_names typo in params in test fix flake8 adapt dependencies increase readability fix test fix sphinx resolve last comments on docs add __deepcopy__ again fix flake 8 ... adress second code review round bugfix fix petab import parameter scales pseudo commit to restart travis... * use amici.import_model_module (#384) * use amici.import_model_module * update amici version * fix amici test (#385) * fix amici test * fix * fix * diverge * Additional code quality checks, minor simplifications (#395) * additional code quality checks * fix geweke * fix flake8 runner * fix v2 * Refactor problem; Fix profiles (#393) * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add failing test * refactor problem * fix * fix * remove unneeded arg * add test * add tests for different orders * reduction should be from full vector * fixup * fix flake8 * fix problem storage * fixup * fix unnecessary list calls * make doc, x_free_indices properties * fix style * fix docs * check profiles to plot whether profiles were actually computed * fix plotting for fixed pars; add test Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> * Refactor logging, specify logger name. (#398) * Specify logger name. * Refactor, new function. * Multiple profile plotting (#399) * introduces handling of multiple results and multiple profile_lists * fix #371 * fix #374 * Require packaging version 20.0 for pymc3. (#401) * Feature temper likelihood - close #324 (#396) * rename trace_fval to trace_neglogpost * rename llh to lpost * add log prior * add log prior -> pt * add log prior -> sampler * add log prior -> result * flake8 * if priors are None -> set log prior to zero instead of None * REVERT if priors are None -> set log prior to zero instead of None * if prior is empty set to zero * fixes * empty prior result in pymc3 sampler * rerun notebook * rerun sampling notebook * add test * fix * fixes PR * add kwargs * fix flake8 * Update pypesto/sampling/metropolis.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix PR * review PR * simplify * Update pypesto/sampling/sampler.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * docs * test for prior in sampling * typo * short is better Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * Prepare release 0.1.0 (#402) * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * prepare release 0.0.14 * fix doc warnings; address reviewer comments * 0.0.14 -> 0.1.0 * increase sample size in tests Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * small fix visu mcmc (#405) * fix visu mcmc * PR * fix #390: Hessian computation (#407) * Fix exception type for `import_module` in PEtab import (#403) Correctly use `MuduleNotFoundError` instead of `RuntimeError`, as in AMICI. Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Improve hdf5 error output (#409) * improve hdf5 error message; fixes #391 * fixup * outlaw large files; fixes #388 (#408) * outlaw large files; fixes #388 * error output * fixup * fix travis bash code * add log * fix test * Fix metropolis initial parameters (#412) * fix initial parameters from optimization results * flake8 * test * fix pymc3 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * Modularize (#413) * init modularize * modularize work packages; use active descriptions * fixup * fix autocorrect * Update pypesto/objective/base.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update test/test_sample.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update test/test_sample.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * address reviewer comments * Update pypesto/result.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * add typehints * fix noqa Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> Co-authored-by: ErikaDudkin <49193148+erikadudki@users.noreply.github.com> Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: dilpath <59329744+dilpath@users.noreply.github.com> Co-authored-by: lcontento <lcontento@users.noreply.github.com> * Fixed example notebook * Fixed example notebook * Fixed inputs of hierarchical calculator * Addes some tests * Fixed setup Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> Co-authored-by: ErikaDudkin <49193148+erikadudki@users.noreply.github.com> Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: dilpath <59329744+dilpath@users.noreply.github.com> Co-authored-by: lcontento <lcontento@users.noreply.github.com>

* Basic implementation of reduced optimal scaling approach * Split inner solver for qualitative data and scalings / offests * Some clean up and comments * Implementation for standard approach * Raise error for standard and reparameterized as its not implemented * Fixed flake8 * Changed parameterType for qualitative data * Added some comments and typehints * more typehints * added docstrings and simplified some functions * Print warning, if inner optimization fails * Update pypesto/hierarchical/optimal_scaling_solver.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Example notebook for qualitative data optimization * Feature hierarchical (#422) * Objective.initialize(); minor edits (#281) * implement objective.initialize() * implement initialize for amici * cache sbml test model * catch module not found error * fix strange os behavior# * Fix least squares options (closes #282) (#283) * Pass options to least squares optimizer * Different default options for least squares optimizer * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * move res grad check to fun * implement res check for hier solver * cont * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add test model * Feature qualitative (#325) * Basic implementation of reduced optimal scaling approach * Split inner solver for qualitative data and scalings / offests * Some clean up and comments * Implementation for standard approach * Raise error for standard and reparameterized as its not implemented * Fixed flake8 * Changed parameterType for qualitative data * Added some comments and typehints * more typehints * added docstrings and simplified some functions * Print warning, if inner optimization fails * Update pypesto/hierarchical/optimal_scaling_solver.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Feature qualitative (#338) * Basic implementation of reduced optimal scaling approach * Split inner solver for qualitative data and scalings / offests * Some clean up and comments * Implementation for standard approach * Raise error for standard and reparameterized as its not implemented * Fixed flake8 * Changed parameterType for qualitative data * Added some comments and typehints * more typehints * added docstrings and simplified some functions * Print warning, if inner optimization fails * Update pypesto/hierarchical/optimal_scaling_solver.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Example notebook for qualitative data optimization Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Tidy up profiles (#363) * update, document profiles * tidy up * review comments * fix minus sign in get_error_output (#361) * fix minus sign in get_error_output * fix 2 signs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * progress bar for MCMC sampling (#366) * progress bar added in MCMC * remove empty line * remove empty line * PR change * minor edits; rerun sampling nbs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Refactor profiles; add locally approximated profiles (#369) * update, document profiles * tidy up * review comments * refactor profiles * refactro profile visualizations * refactor * fix previous test error * refactor options * fix profile list index not set * fix wrong docstring * minor edits * extend profile tests * add problem conversion test (tb extended) * add test for profiles_ci * add problem conversion function * add approximate profiles * extend profiles visualization functions * add recompute hessian test * extend rosenbrock nb * fix docs build warning * compute cis by interpolation * fix wrong # args * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Tidy up profiles (#363) * update, document profiles * tidy up * review comments * fix minus sign in get_error_output (#361) * fix minus sign in get_error_output * fix 2 signs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * progress bar for MCMC sampling (#366) * progress bar added in MCMC * remove empty line * remove empty line * PR change * minor edits; rerun sampling nbs Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Refactor profiles; add locally approximated profiles (#369) * update, document profiles * tidy up * review comments * refactor profiles * refactro profile visualizations * refactor * fix previous test error * refactor options * fix profile list index not set * fix wrong docstring * minor edits * extend profile tests * add problem conversion test (tb extended) * add test for profiles_ci * add problem conversion function * add approximate profiles * extend profiles visualization functions * add recompute hessian test * extend rosenbrock nb * fix docs build warning * compute cis by interpolation * Interface ipopt optimizer (#373) * interface ipopt * fix args * update pip reqs * move to setup.py optional deps * remove upgrade * test * test * tmp fix * check ipopt on travis * test * test * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps * TravisCI: Install pyipopt deps Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> * Fix visu 372 (#375) * fix palette vector length depending on hue parameter * Fix geweke - fixes #354 (#376) * add failing geweke test * fix geweke * add test for short chains * rerun notebooks * update argument name * flake8 * fix * fix Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Feature parameter priors with gradients #357 Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> add paramter priors initial commit for PEtab import chage parameter scaling small fixes in tests update recent local changes, prepare to merge new restructured objective fix merge conflictsin aggregated.py finish up testing fix x_names typo in params in test fix flake8 adapt dependencies increase readability fix test fix sphinx resolve last comments on docs add __deepcopy__ again fix flake 8 ... adress second code review round bugfix fix petab import parameter scales pseudo commit to restart travis... * use amici.import_model_module (#384) * use amici.import_model_module * update amici version * fix amici test (#385) * fix amici test * fix * fix * diverge * Additional code quality checks, minor simplifications (#395) * additional code quality checks * fix geweke * fix flake8 runner * fix v2 * Refactor problem; Fix profiles (#393) * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * write amici solver settings to stream (#308) * write amici solver settings to stream * fix sampling test failure * save result to hdf5, update of an existing file (#290) * save result to hdf5, update of an existing file Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fixes history (#315) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * implement test without fixed pars, fix string writing, fix grad/sres retrieval * address review comments * Fix failed starts (#317) * change testcase to include fixed parameters and update tests accordingly * refactor ObjectiveHistory, fix AmiciCalculator, implement and test reload_from_csv * improve asserts and typechecks * fix aggregated * fixups history * fixup * fixups * fix repeated import * fix flake * fix failing test * fix out of bounds * doh * fix bad access * fix #316 * implement test without fixed pars, fix string writing, fix grad/sres retrieval * implement test without fixed pars, fix string writing, fix grad/sres retrieval * Revert "implement test without fixed pars, fix string writing, fix grad/sres retrieval" This reverts commit 5de118f. * address review comments * more maintainable error handling * tidy up * fix unused * fix profiles * fix bad merge * FVAL != CHI2 * report chi2 and fix reporting of chi2 * fixups history * add test for runtime error when running ls solver with ssigma * better filling of results from history * fixups * herp derp, fix tests not doing what they are supposed to * add test for memory history * fixup flake * address review comments * doh * Speed up travis (#329) * speed up travis * travis likes ; * fix flake8 * Create required directories before creating hdf5 file (Fixes #323) (#326) * Create required directories before creating hdf5 file (Fixes #323) * Create directories as required * Set h5py as requirement * Update tests * improve storage+docs documentation (#328) * improve storage+docs documentation * make latest flake8 happy * speed up travis * travis likes ; * fix flake8 * install recommonmark * Update CI system (#330) * cosmetics * update travic run system * Feature storage result (#334) * saving also x_free_indices for x_labels in parameters plot * doc * Customizable xLabels and tight layout for profile plots (fix #321) (#331) * customizable xLabels of profile plot (fix #321) * default x_labels to problem.x_names if available * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/visualize/profiles.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix problem h5 return format (#336) * fix problem h5 return format * fix docs * implement partial trace (#337) * implement partial trace * fix return type * implement as lists * add check for type in test * fix flake * fix typehints; add test Co-authored-by: FFroehlich <fabian@schaluck.com> * Convergence: Geweke test (#339) * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * plot positive log posterior value * geweke test * print burn in * notebook example * auto correlation added * notebook showing ac * fix fft in geweke * ess added * notebook update * fix * doc * fix flake8 * burn in and time save in result object * fix * extract burn in from results in visu * updated notebook * fix visu * minor fix * burn in in plotting * notebook updated * fix test * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/diagnostics.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix names * fix function names * fix flake8 * fix flake8 * fix format * rename field to time * fix fft * PR fix * PR fix * fix * fix * fix doc * initial burn in set to None * warning when burn in is None in visu * doc fix * notebook update * use numba for auto corr calculation * update notebook * fix doc * fix is to == in profile_next_guess * add numba in install requires * fix flake8 * fix geweke * test for geweke * remove print * notebook added in rst * fix * Update pypesto/sampling/auto_correlation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * rename function * fix * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * replace int -> numpy floor * fix error print * PR fix * fix pep * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * revert numpy floor to int due to indexing problems * use numpy floor * prepare PR * Update pypesto/sampling/sample.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update test/test_sampling.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fixes * fixes * Update pypesto/sampling/geweke_test.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix * fix * add warning * fix Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Fix 255 (#348) * check bounds for waterfall plot in log scale, fixes #255 * Refactor Objective (#347) * make extract values respect options, fixes #340 * add test that disabled traces are not recorded * fix aggregation, add test, fixes #341 * update docstring & typehints * refactor objective logic * fixups * fix flake * fix tests * fix occasional test hiccup * Objective->Objectivebase, FunctionObjective->Objective * fixups * fixup * fix flake * adress review comments * fix tests * fix tests * fix tests * Pymc3 sampler (#351) * implement basic pymc3 sampler in new format * update pymc3 sampler for variable grad+fval * pymc3: return llh * add arviz to setup optional reqs * add travis req * fix kwargs * add docstring * fix arviz 0.7.0 * fix docs * address review comments * address review comments * update sampling nb * fix amici * fix nb * unfix sympy * Make theano (for pymc3) optional dependency (#356) * fix docs * fix2 * make theano rtd req * catch optional deps * remove inherited members, restrict specials, from docs * Delete hierarchical.ipynb * simpliy autodoc * inc sphinx v * test * test * test * test * test * restructure * fixup * fixup2 * saving all attributes of a pypesto.problem to hdf5 (#342) * saving all attributes of a pypesto.problem to hdf5 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add failing test * refactor problem * fix * fix * remove unneeded arg * add test * add tests for different orders * reduction should be from full vector * fixup * fix flake8 * fix problem storage * fixup * fix unnecessary list calls * make doc, x_free_indices properties * fix style * fix docs * check profiles to plot whether profiles were actually computed * fix plotting for fixed pars; add test Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> * Refactor logging, specify logger name. (#398) * Specify logger name. * Refactor, new function. * Multiple profile plotting (#399) * introduces handling of multiple results and multiple profile_lists * fix #371 * fix #374 * Require packaging version 20.0 for pymc3. (#401) * Feature temper likelihood - close #324 (#396) * rename trace_fval to trace_neglogpost * rename llh to lpost * add log prior * add log prior -> pt * add log prior -> sampler * add log prior -> result * flake8 * if priors are None -> set log prior to zero instead of None * REVERT if priors are None -> set log prior to zero instead of None * if prior is empty set to zero * fixes * empty prior result in pymc3 sampler * rerun notebook * rerun sampling notebook * add test * fix * fixes PR * add kwargs * fix flake8 * Update pypesto/sampling/metropolis.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * fix PR * review PR * simplify * Update pypesto/sampling/sampler.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * docs * test for prior in sampling * typo * short is better Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * Prepare release 0.1.0 (#402) * set allow_failed_starts to TRUE, closes #280 * add notebook plotting before writing * copy parameter vector to avoid side effects (#291) * fix hdf5 file ignore * remove hdf5 part from this commit * restore notebook * fix header names in csv history (#299) * Docker (#288) * Dockerfile * installation of libhdf5 is added to the dockerfile, plus error message about hdf5 support Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Relax amici_objective test tolerances (#304) * relax amici_objective test * fixup * update releasenotes * address review comments * prepare release 0.0.14 * fix doc warnings; address reviewer comments * 0.0.14 -> 0.1.0 * increase sample size in tests Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * small fix visu mcmc (#405) * fix visu mcmc * PR * fix #390: Hessian computation (#407) * Fix exception type for `import_module` in PEtab import (#403) Correctly use `MuduleNotFoundError` instead of `RuntimeError`, as in AMICI. Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Improve hdf5 error output (#409) * improve hdf5 error message; fixes #391 * fixup * outlaw large files; fixes #388 (#408) * outlaw large files; fixes #388 * error output * fixup * fix travis bash code * add log * fix test * Fix metropolis initial parameters (#412) * fix initial parameters from optimization results * flake8 * test * fix pymc3 Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> * Modularize (#413) * init modularize * modularize work packages; use active descriptions * fixup * fix autocorrect * Update pypesto/objective/base.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update pypesto/objective/history.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update test/test_sample.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update test/test_sample.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * address reviewer comments * Update pypesto/result.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * add typehints * fix noqa Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> Co-authored-by: ErikaDudkin <49193148+erikadudki@users.noreply.github.com> Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: dilpath <59329744+dilpath@users.noreply.github.com> Co-authored-by: lcontento <lcontento@users.noreply.github.com> * Fixed example notebook * Fixed example notebook * Fixed inputs of hierarchical calculator * Addes some tests * Fixed setup * Fixed example for qualitative optimization Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <38346459+jvanhoefer@users.noreply.github.com> Co-authored-by: Jakob Vanhoefer <ja131va@yahoo.de> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Elba Raimúndez Alvarez <elba.raimundez@helmholtz-muenchen.de> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> Co-authored-by: ErikaDudkin <49193148+erikadudki@users.noreply.github.com> Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: dilpath <59329744+dilpath@users.noreply.github.com> Co-authored-by: lcontento <lcontento@users.noreply.github.com>

* visualization: allow for optional columns * add test for minimal visu spec file * non-mandatory columns in measurement file are handled in visu routine * new test cases for minimal measurement file, only mandatory columns * add error: xvalues in visu file is mandatory Closes #165, closes #333, closes #329, closes #326, closes #320

speed up travis

92fdc20

yannikschaelte self-assigned this May 13, 2020

yannikschaelte added 2 commits May 13, 2020 11:59

travis likes ;

6f5f798

fix flake8

85c0525

yannikschaelte requested review from dweindl and jvanhoefer May 13, 2020 10:15

yannikschaelte changed the title ~~[WIP] speed up travis~~ Speed up travis May 13, 2020

yannikschaelte mentioned this pull request May 13, 2020

improve storage+docs documentation #328

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dweindl approved these changes May 13, 2020

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yannikschaelte merged commit 9805ed0 into develop May 13, 2020

yannikschaelte deleted the separate_travis branch May 13, 2020 11:05

yannikschaelte mentioned this pull request Jun 8, 2020

Release 0.1.0 #387

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dweindl pushed a commit that referenced this pull request Jun 8, 2020

Speed up travis (#329)

05a69a2

* speed up travis * travis likes ; * fix flake8

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Speed up travis #329

Speed up travis #329

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dweindl May 13, 2020

Speed up travis #329

Speed up travis #329

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