Merge pull request #260 from ModellingWebLab/update_ontology

Update ontology and docs for doing it

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

RELEASE.md

@@ -1,6 +1,11 @@
 # 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`).
+- 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.
 - 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.

chaste_codegen/version.txt

@@ -1 +1 @@
-0.10.2
+0.10.3

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 <name_of_new_branch>`
-- `git add`, `git commit` and `git push` the changes
+- create a new branch ``git checkout -b <name_of_new_branch>``
+- ``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 <name_of_new_branch>`
-- `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 <name_of_new_branch>``
+- ``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.