release 0.5.2 #1406
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release 0.5.2 #1406
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Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
) The most recent arviz should now work with the most recent scipy (but requires python>=3.10): https://github.com/arviz-devs/arviz/blob/main/CHANGELOG.md#maintenance-and-fixes-1 Closes #1354
…ectly. (#1364) Co-authored-by: Maren Philipps <55318391+m-philipps@users.noreply.github.com>
* Fix log of zero in hierarchical calculate_nllh by masking * Fix in `compute_bounded_optimal_scaling_offset_coupled` * Update numerical solver with data mask --------- Co-authored-by: Jonas Arruda <69197639+arrjon@users.noreply.github.com>
* Added option to sample startpoints of a problem, from the problem directly. Also safety checks for startindices like "all" or "clustered" * Fixed error in correlation matrix, if there were nn values. Also safety checks in general for start indices. Added a test for correlation matrix * log filtering in process_start_indices * update docstring --------- Co-authored-by: Maren Philipps <maren.philipps@uni-bonn.de>
For ESSOptimizer and SacessOptimizer: * supporess divide-by-zero warnings * report number of function evaluations
* Update setup.cfg Remove python 3.9 * Update ci.yml Remove python 3.9 and update to 3.11 * Update deploy.yml Change python 3.9 by 3.11 * Update ci.yml Add python 3.10 * Update setup.cfg Add python 3.12 * Update ci.yml Update from python 3.11 to 3.12 * Update deploy.yml Update from python 3.11 to 3.12 * Skip aesara tests on case of python >= 3.12 and use 3.11 for building the documentation. * Update test/base/test_objective.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * Update .github/workflows/ci.yml --------- Co-authored-by: PaulJonasJost <jost.pauljonas@gmail.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
Prevents unclear timeouts that occur with `macos-14-arm64` (see #1383).
So far, most stats from different SacessOptimizer workers have only been available from the logs. Now they are also available via `SacessOptimizer.worker_results`. Additionally, the total number of objective evaluations across all workers ís logged.
For `nfft<=3`, this function computed `k` by converting infinity to int64. For the last [4 years](fdbacb4), this seemed to not cause any trouble, because `np.float64("inf").astype(int)` yielded -9223372036854775808 and the loop did not run. However, with the current `macos-14` GitHub runner, this yields 9223372036854775807, and accordingly, rather long computation times (this is what caused #1383). I am not really sure what caused this change. macos-12 vs macos-14, arm64 vs x86, ...? all should be IEEE 754-compliant. Maybe some different integer type? 🤷♂️ With this change `macos-14` runners yield the same results as the other runners. However, I am not familiar with computing power spectral density and I don't know if this is indeed what should happen. It would be great if somebody more familiar with that topic could double-check. (Also, can't we use [scipy.signal.welch](https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.welch.html#scipy.signal.welch) here?)
* switch to `macos-14` previous issues with macos-14 were a mix of #1388 and caching with seemingly random switching between macos-12 and macos-14 runners when using macos-latest * include arch in cache keys; use uniform cache keys * change some imports in `test/sample/test_sample.py` to be able to run subsets of tests despite missing optional dependencies * adjust resource limits to avoid [random](https://github.com/ICB-DCM/pyPESTO/actions/runs/8945258779/job/24573887731) [failures](https://github.com/ICB-DCM/pyPESTO/actions/runs/8945870387/job/24575587898?pr=1387) such as: ``` /Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/_pytest/main.py:339: PluggyTeardownRaisedWarning: A plugin raised an exception during an old-style hookwrapper teardown. Plugin: _cov, Hook: pytest_runtestloop DataError: Couldn't use data file '/Users/runner/work/pyPESTO/pyPESTO/.coverage.Mac-1714771409828.local.9672.XvRVVmRx': unable to open database file For more information see https://pluggy.readthedocs.io/en/stable/api_reference.html#pluggy.PluggyTeardownRaisedWarning config.hook.pytest_runtestloop(session=session) ..FFFF [100%] INTERNALERROR> Traceback (most recent call last): INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqlitedb.py", line 52, in _connect INTERNALERROR> sqlite3.OperationalError: unable to open database file INTERNALERROR> INTERNALERROR> The above exception was the direct cause of the following exception: INTERNALERROR> INTERNALERROR> Traceback (most recent call last): INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/_pytest/main.py", line 285, in wrap_session INTERNALERROR> session.exitstatus = doit(config, session) or 0 INTERNALERROR> ^^^^^^^^^^^^^^^^^^^^^ INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/_pytest/main.py", line 339, in _main INTERNALERROR> config.hook.pytest_runtestloop(session=session) INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/pluggy/_hooks.py", line 513, in __call__ INTERNALERROR> return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) INTERNALERROR> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/pluggy/_manager.py", line 120, in _hookexec INTERNALERROR> return self._inner_hookexec(hook_name, methods, kwargs, firstresult) INTERNALERROR> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/pluggy/_callers.py", line 156, in _multicall INTERNALERROR> teardown[0].send(outcome) INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/pytest_cov/plugin.py", line 339, in pytest_runtestloop INTERNALERROR> self.cov_controller.finish() INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/pytest_cov/engine.py", line 46, in ensure_topdir_wrapper INTERNALERROR> return meth(self, *args, **kwargs) INTERNALERROR> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/pytest_cov/engine.py", line 256, in finish INTERNALERROR> self.cov.save() INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/control.py", line 785, in save INTERNALERROR> data = self.get_data() INTERNALERROR> ^^^^^^^^^^^^^^^ INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/control.py", line 865, in get_data INTERNALERROR> if self._collector.flush_data(): INTERNALERROR> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/collector.py", line 535, in flush_data INTERNALERROR> self.covdata.add_lines(self.mapped_file_dict(line_data)) INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqldata.py", line 124, in _wrapped INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqldata.py", line 495, in add_lines INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqldata.py", line 564, in _choose_lines_or_arcs INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqldata.py", line 344, in _connect INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqldata.py", line 287, in _open_db INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqldata.py", line 291, in _read_db INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqlitedb.py", line 88, in __enter__ INTERNALERROR> File "/Users/runner/work/pyPESTO/pyPESTO/.tox/base/lib/python3.12/site-packages/coverage/sqlitedb.py", line 54, in _connect INTERNALERROR> coverage.exceptions.DataError: Couldn't use data file '/Users/runner/work/pyPESTO/pyPESTO/.coverage.Mac-1714771409828.local.9672.XvRVVmRx': unable to open database file ```
* add load method to Hdf5AmiciHistory
Removed a spacebar preventing header to be seen as such (#1394)
* remove random.see in favor of np.random.seed * added import numpy as np import
* update readme links * Add relative to READ_ME.md --------- Co-authored-by: Doresic <domagoj.doresic@gmail.com>
* Made get_full_vector more intuitive * Corrected he usage of get_full vector. Removed it for lb and ub in favor of lb_full and ub_full. * Apply suggestions from code review Co-authored-by: Maren Philipps <55318391+m-philipps@users.noreply.github.com> --------- Co-authored-by: Maren Philipps <55318391+m-philipps@users.noreply.github.com>
Papers using pypesto
* Fixed doc example from generic call (that did not exists) to apropriate call * Marked code as codeblocks
* fixing call of prior in sampling * check if priors not None * remove deepcopy
* Lowered samples, removed comparison of two different amount of chains * Removed even argument, due to scipy wanting to go for "simpson" and depracating "even" * Removed warning for `test_thermodynamic_integration` --------- Co-authored-by: Jonas Arruda <69197639+arrjon@users.noreply.github.com> Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
* variational inference fit * remove variational from sample * make pymc object accessible * save as McmcPtResult * tests added * add warning in write_result()
* Saves pypesto and python version to the problem. * Update pypesto/problem/base.py Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> --------- Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
Codecov ReportAttention: Patch coverage is
❗ Your organization needs to install the Codecov GitHub app to enable full functionality. Additional details and impacted files@@ Coverage Diff @@
## main #1406 +/- ##
==========================================
- Coverage 84.50% 83.92% -0.58%
==========================================
Files 157 160 +3
Lines 12917 13061 +144
==========================================
+ Hits 10915 10962 +47
- Misses 2002 2099 +97 ☔ View full report in Codecov by Sentry. |
* Add pre_post_processor.setter and base_objective wrapper functions * fix docstring & simplify implementation * extend tests * fix tests * add returns to docstring * fix max sensi orders, add test --------- Co-authored-by: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com> Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Fabian Fröhlich <fabian.frohlich@crick.ac.uk>
* Update Changelog and Version --------- Co-authored-by: Fabian Fröhlich <fabian.frohlich@crick.ac.uk> Co-authored-by: Maren Philipps <55318391+m-philipps@users.noreply.github.com>
PaulJonasJost
requested review from
stephanmg,
m-philipps,
dilpath,
vwiela,
dweindl,
FFroehlich and
Doresic
as code owners
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problem.get_full_vector#1393)pypesto.sample.geweke_test.spectrumfor nfft<=3 #1388)test_thermodynamic_integration#1385)