From d2bff46d60ffe30328f386eb152462247a8745a3 Mon Sep 17 00:00:00 2001 From: Joris Snellenburg Date: Sun, 12 Dec 2021 02:12:53 +0100 Subject: [PATCH] =?UTF-8?q?=F0=9F=9A=80=F0=9F=A9=B9=20v0.4.2=20release=20p?= =?UTF-8?q?reparation=20and=20bugfix=20backport=20for=20result=20consisten?= =?UTF-8?q?cy=20checking=20purposes=20(#935)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 🩹🚧 Backport of bugfix Backport of bugfix #927 discovered in PR #860 It was [found](https://github.com/glotaran/pyglotaran/pull/860#issuecomment-985467588) in #860 that the a_matrix when calculated for result saving was calculated without normalized initial_concentrations while the calculation for the optimization was (correctly) using the normalized version. Fixing this bug in #927 then breaks result consistency checking for some case studies, thus requiring backporting of this bugfix to the 0.4 maintenance branch which we continue to use for result/consistency checking. * 🚀🚧 v0.4.2 Maintenance release - 🩹🚧 Backport of bugfix #927 discovered in PR #860 related to initial_concentration normalization when saving results (#935). * 🚇🚧 Updated 'gold standard' result comparison reference Updated pyglotaran-examples result-comparison branch for pyglotaran v0.4.2 Note: comments in PR #936 provide explanation for a small test deviation in the results comparison check for this PR. --- changelog.md | 10 ++++++++++ glotaran/__init__.py | 2 +- .../models/kinetic_image/kinetic_image_result.py | 2 +- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/changelog.md b/changelog.md index 98fffb212..6c5bdf73d 100644 --- a/changelog.md +++ b/changelog.md @@ -1,5 +1,15 @@ # Changelog +## 0.4.2 (2021-12-12) + +### 🩹 Bug fixes + +- 🩹🚧 Backport of bugfix #927 discovered in PR #860 related to initial_concentration normalization when saving results (#935). + +### 🚧 Maintenance + +- 🚇🚧 Updated 'gold standard' result comparison reference ([old](https://github.com/glotaran/pyglotaran-examples/commit/9b8591c668ad7383a908b853339966d5a5f7fe43) -> [new](https://github.com/glotaran/pyglotaran-examples/commit/fc5a5ca0c7fd8b224c85027b510a15717c696c7b)) + ## 0.4.1 (2021-09-07) ### ✨ Features diff --git a/glotaran/__init__.py b/glotaran/__init__.py index 196df8c62..861fe447c 100644 --- a/glotaran/__init__.py +++ b/glotaran/__init__.py @@ -8,7 +8,7 @@ load_plugins() -__version__ = "0.4.1" +__version__ = "0.4.2" def __getattr__(attribute_name: str): diff --git a/glotaran/builtin/models/kinetic_image/kinetic_image_result.py b/glotaran/builtin/models/kinetic_image/kinetic_image_result.py index ce0c45f69..9f6a464d7 100644 --- a/glotaran/builtin/models/kinetic_image/kinetic_image_result.py +++ b/glotaran/builtin/models/kinetic_image/kinetic_image_result.py @@ -78,7 +78,7 @@ def retrieve_decay_associated_data(model, dataset, dataset_descriptor, name): matrix = k_matrix.full(compartments) matrix_reduced = k_matrix.reduced(compartments) - a_matrix = k_matrix.a_matrix(dataset_descriptor.initial_concentration) + a_matrix = k_matrix.a_matrix(dataset_descriptor.initial_concentration.normalized()) rates = k_matrix.rates(dataset_descriptor.initial_concentration) lifetimes = 1 / rates