From 8e8b367d2b9f65f2c4ea8dcd01a7b435d424d1b4 Mon Sep 17 00:00:00 2001 From: Gary Mirams Date: Fri, 7 Jul 2023 17:15:16 +0100 Subject: [PATCH 1/5] Update ontology and docs for doing it --- chaste_codegen/ontologies | 2 +- docs/index.rst | 22 +++++++++++----------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/chaste_codegen/ontologies b/chaste_codegen/ontologies index ffd8e42c..affd3996 160000 --- a/chaste_codegen/ontologies +++ b/chaste_codegen/ontologies @@ -1 +1 @@ -Subproject commit ffd8e42c0b3112b71e572e0071c6a1c1f04b010c +Subproject commit affd399689e4637c11db2d5361576d6cf00fc27b diff --git a/docs/index.rst b/docs/index.rst index 0fbd7f6f..800d678f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -14,30 +14,30 @@ Sympy or any other python package may need to be updated, especially as python v - change the version listed in setup.py, e.g. for sympy it currently lists 'sympy>=1.9, <1.11', which means that the version is at least 1.9 and is less than 1.11. - update dev-requirements/dev.txt if you want to also update your development pinned (fixed) versions -- create a new branch `git checkout -b ` -- `git add`, `git commit` and `git push` the changes +- create a new branch ``git checkout -b `` +- ``git add``, ``git commit`` and ``git push`` the changes - make a pull request. The tests may throw up some errors that may need fixing. The tests are in the tests folder and the reference data in data/tests. In data/tests/chaste_reference_models you'll see a few reference files ending in .cpp_python36, This is as due to sympy versions supported python 3.6 leads to an equivalent but subtly different generated model. -- Mention the changes made in the release notes `release.txt` +- Mention the changes made in the release notes ``release.txt`` - To use the changes with chaste, do a new release of chaste_codegen. Updating the ontology and including it in chaste_codegen ================= - update the ontology according to the instructions in https://github.com/ModellingWebLab/ontologies -- the ontology is included in chaste_codegen via a submodule, update this with `git submodule update --remote chaste_codegen/ontologies`. -- *Please note* this same way can be used to update the `cellml` in `chaste_codegen/data/tests/cellml` submodule if required. -- create a new branch `git checkout -b ` -- `git add`, `git commit` and `git push` the changes +- the ontology is included in chaste_codegen via a submodule, update this with ``git submodule update --remote chaste_codegen/ontologies``. +- *Please note* this same way can be used to update the ``cellml`` in ``chaste_codegen/data/tests/cellml`` submodule if required. +- create a new branch ``git checkout -b `` +- ``git add``, ``git commit`` and ``git push`` the changes - make a pull run the tests and fix any issues that arise -- update the release notes `release.txt` with information about the updated ontology. +- update the release notes ``release.txt`` with information about the updated ontology. - To use the changes with chaste, do a new release of chaste_codegen. Doing a new chaste_codegen release ================= -- Update the release version number in `chaste_codegen/version.txt`. -- Update the release notes `release.txt` with the latest release number. -- For this version number: minor numbers will be picked up by chaste automatically, for major version numbers, `chaste_codegen.txt` will need updating in the chaste repository. +- Update the release version number in ``chaste_codegen/version.txt``. +- Update the release notes ``release.txt`` with the latest release number. +- For this version number: minor numbers will be picked up by chaste automatically, for major version numbers, ``chaste_codegen.txt`` will need updating in the chaste repository. - Follow the following tutorial to publish the package: https://packaging.python.org/en/latest/tutorials/packaging-projects/ - You will need a login to pypi.org and the account you are using will need access to chaste_codegen. From c0bda05937c3868bbce3456f3ed2f2f202d60653 Mon Sep 17 00:00:00 2001 From: Gary Mirams Date: Fri, 7 Jul 2023 17:17:34 +0100 Subject: [PATCH 2/5] Update release notes --- RELEASE.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/RELEASE.md b/RELEASE.md index e00a2637..176854d4 100644 --- a/RELEASE.md +++ b/RELEASE.md @@ -1,6 +1,9 @@ # Unreleased - Improved the developer documentation with regards to updating python packages, the ontology and releasing new versions of chaste_codegen. +# Release 0.10.3 +- Updated ontology submodule (includes new `membrane_rapid_delayed_rectifier_potassium_current_open_probability`). + # Release 0.10.2 - Added checks to the resulting C++ code that will throw an error if concentrations go below 0, or if probabilities ere below 0 or above 1. Concetrations and probabilities are identified via existing metadata in the CellML. - Added an exception using the ontology annotation not_a_probability_even_though_it_should_be to indicate probabilities that should not be checked as they may go outside the 0 ... 1 range. From caf1eb48a5a6ef40f59e32cd768401dedcb8441b Mon Sep 17 00:00:00 2001 From: Gary Mirams Date: Fri, 7 Jul 2023 17:20:58 +0100 Subject: [PATCH 3/5] Update licence year --- LICENSE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index 9a123c3d..26de0230 100644 --- a/LICENSE +++ b/LICENSE @@ -1,7 +1,7 @@ BSD 3-Clause License Unless otherwise noted, all files within this distribution are -Copyright (c) 2005-2021, University of Oxford, University College London, University of Nottingham +Copyright (c) 2005-2023, University of Oxford, University College London, University of Nottingham All rights reserved. University of Oxford means the Chancellor, Masters and Scholars of the From 0c6e542e9d747325c73611542f7f8065057be7e8 Mon Sep 17 00:00:00 2001 From: Gary Mirams Date: Fri, 7 Jul 2023 17:21:09 +0100 Subject: [PATCH 4/5] Increment version --- chaste_codegen/version.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chaste_codegen/version.txt b/chaste_codegen/version.txt index 5eef0f10..a3f5a8ed 100644 --- a/chaste_codegen/version.txt +++ b/chaste_codegen/version.txt @@ -1 +1 @@ -0.10.2 +0.10.3 From 10c101cb3573f20f012170a1f21ca11954206897 Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Wed, 12 Jul 2023 12:31:39 +0100 Subject: [PATCH 5/5] Adding updated dependencies to release notes --- RELEASE.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/RELEASE.md b/RELEASE.md index 176854d4..2ac3ccc6 100644 --- a/RELEASE.md +++ b/RELEASE.md @@ -3,6 +3,8 @@ # Release 0.10.3 - Updated ontology submodule (includes new `membrane_rapid_delayed_rectifier_potassium_current_open_probability`). +- Updated `requests` from 2.25.1 to 2.31.0 in /dev-requirements +- Updated `mpmath` from 1.2.1 to 1.3.0 in /dev-requirements # Release 0.10.2 - Added checks to the resulting C++ code that will throw an error if concentrations go below 0, or if probabilities ere below 0 or above 1. Concetrations and probabilities are identified via existing metadata in the CellML.