From 491a8f0079a2ae9fdebf4b47c50faecc37441ee0 Mon Sep 17 00:00:00 2001 From: PaulJonasJost Date: Wed, 15 Nov 2023 17:37:45 +0100 Subject: [PATCH 1/3] Updated version and changelog --- CHANGELOG.rst | 26 ++++++++++++++++++++++++++ pypesto/version.py | 2 +- 2 files changed, 27 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index e65d84e6d..11e389e19 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,32 @@ Release notes .......... +0.3.4 (2023-11-16) +------------------- + +* General + * Documentation (#1140, #1146, #1152, #1149 ) + * Updated Jupyter Notebooks (#1141 ) + * Update code to avoid deprecations (#1158) + * Updated maintainers and codeownership (#1171, #1170) +* Profile: + * Fix problem overwrite of profiling (#1153) + * Add warning, trying to profile fixed parameter (#1155) + * ProfileOptions: add some basic integrity checking (#1163) + * Fix pypesto.profile.parameter_profile incorrectly assuming symmetric bounds (#1166) + * Improve pypesto/profile/profile_next_guess.py (#1167) +* Problem: + * Add/forward startpoint_kwargs in PetabImporter.create_problem (#1135) + * Support valid AMICI noise distributions that are invalid in PEtab (#1157) + * Fix startpoint sampling for PEtab-derived problems with fixed parameters (#1169) +* Optimize + * Log traceback in case of exceptions during optimizations (#1156) +* Hierarchical: + * Fix HierarchicalAmiciCalculator.__call__ not setting 'hess' in result (#1161) +* Visualization: + * Fix legend argument checking for waterfall/parameter/history plots (#1139) + + 0.3.3 (2023-10-19) ------------------- diff --git a/pypesto/version.py b/pypesto/version.py index e19434e2e..334b89956 100644 --- a/pypesto/version.py +++ b/pypesto/version.py @@ -1 +1 @@ -__version__ = "0.3.3" +__version__ = "0.3.4" From b3229bb045e31b0d33643f362d13a51732ca0797 Mon Sep 17 00:00:00 2001 From: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com> Date: Thu, 16 Nov 2023 09:06:59 +0100 Subject: [PATCH 2/3] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Fabian Fröhlich --- CHANGELOG.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 11e389e19..adbd9e8d2 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -10,8 +10,8 @@ Release notes ------------------- * General - * Documentation (#1140, #1146, #1152, #1149 ) - * Updated Jupyter Notebooks (#1141 ) + * Documentation (#1140, #1146, #1152, #1149) + * Updated Jupyter Notebooks (#1141) * Update code to avoid deprecations (#1158) * Updated maintainers and codeownership (#1171, #1170) * Profile: From 496c3859aea05ba318eb45b7674358047cdcda89 Mon Sep 17 00:00:00 2001 From: PaulJonasJost Date: Wed, 22 Nov 2023 11:30:50 +0100 Subject: [PATCH 3/3] Update Changelog and version --- CHANGELOG.rst | 21 +++++++++++++++++---- pypesto/version.py | 2 +- 2 files changed, 18 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index adbd9e8d2..f954fa7b8 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,34 +2,47 @@ Release notes ============= -0.3 series +0.4 series .......... -0.3.4 (2023-11-16) +0.4.0 (2023-11-22) ------------------- * General - * Documentation (#1140, #1146, #1152, #1149) + * Documentation (#1140, #1146, #1152, #1149, #1192) * Updated Jupyter Notebooks (#1141) - * Update code to avoid deprecations (#1158) + * Update code to avoid deprecations/warnings (#1158, #1184) * Updated maintainers and codeownership (#1171, #1170) + * Improve tests and GHA (#1178, #1185, #1188, #1190, #1193, #1199, #1198, #1197, #1208) * Profile: * Fix problem overwrite of profiling (#1153) * Add warning, trying to profile fixed parameter (#1155) * ProfileOptions: add some basic integrity checking (#1163) * Fix pypesto.profile.parameter_profile incorrectly assuming symmetric bounds (#1166) * Improve pypesto/profile/profile_next_guess.py (#1167) + * Parameter profile: retry optimization in case of failure (#1168) + * Fix incorrect types in pypesto.result.profile.ProfilerResult (#1210) * Problem: * Add/forward startpoint_kwargs in PetabImporter.create_problem (#1135) * Support valid AMICI noise distributions that are invalid in PEtab (#1157) * Fix startpoint sampling for PEtab-derived problems with fixed parameters (#1169) * Optimize * Log traceback in case of exceptions during optimizations (#1156) + * Saccess optimizer improvements (#1177, #1187, #1194, #1195, #1201, #1202, #1204) + * ESS optimizer improvements (#1176, #1181, #1182) + * Fix check for allow_failed_starts (#1180) + * Handle message and exitflag in histories (#1203) + * Fix indexing error for 0-dimensional HDF5 datasets (#1206) * Hierarchical: * Fix HierarchicalAmiciCalculator.__call__ not setting 'hess' in result (#1161) * Visualization: * Fix legend argument checking for waterfall/parameter/history plots (#1139) + * Fix waterfall start indices for multiple results (#1200) + + +0.3 series +.......... 0.3.3 (2023-10-19) diff --git a/pypesto/version.py b/pypesto/version.py index 334b89956..6a9beea82 100644 --- a/pypesto/version.py +++ b/pypesto/version.py @@ -1 +1 @@ -__version__ = "0.3.4" +__version__ = "0.4.0"