Add scaffolding for SBML and python wrappers by kwabenantim · Pull Request #4 · Chaste/template_project

kwabenantim · 2026-06-16T14:17:46Z

Supports #3

When setup_project.py is run with Python bindings opted in, it: - Substitutes the project name into dynamic/config.yaml and dynamic/CMakeLists.txt, which set up CPPWG-based wrapper generation - Renames src/py/template_project/ to src/py/<project_name>/ and substitutes the project name into the Python package files - Leaves dynamic/ and src/py/ in place for the build system to use When opted out, dynamic/ and src/py/ are removed. The build scripts are extended accordingly: - common.sh auto-detects Chaste_ENABLE_PYCHASTE from dynamic/config.yaml and guards against CHASTE_BUILD_DIR pointing at the project root - configure.sh passes Chaste_ENABLE_PYCHASTE to cmake - compile.sh builds pychaste then _<project>_all when pychaste is enabled, or the C++ project library only when it is not - install.sh (new) creates .virtualenv/ and pip-installs the pychaste and project Python packages from the build directory - .github/workflows/test-python-project.yml (new) tests the full pipeline using the chaste/develop container Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

kwabenantim · 2026-07-03T11:42:17Z

This currently needs hardening for cases where errors in config.yaml cause configuration to fail. Re-running the config to regenerate wrappers can fail persistently.

Some potential steps to address this:

Remove the "if wrappers already exist, don't regenerate them" gating in CMakeLists.txt. This setting was fine in main Chaste where wrappers don't change too often, but may not be a good idea in a user project where wrappers may change constantly during development.
Throw a warning if no wrappers were generated. This will make it easier to diagnose errors further down when trying to make a compile target for the wrappers with no source files.
Add more documentation on what to do when user runs into problems with generating / compiling wrappers in a python bindings template.

kwabenantim · 2026-07-03T11:47:53Z

This also needs to work outside a chaste docker environment where the extra pychaste dependencies are preinstalled.

Potential steps to address this:

Add user docs explaining which extra dependencies need to be installed for creating python bindings.
Allow user to install petsc4py etc. into a virtualenv.

Add SBML template project

Copilot

Pull request overview

Copilot reviewed 44 out of 46 changed files in this pull request and generated 8 comments.

- Stop vendoring the SBML base classes in src/; sbml_install.sh now copies them from the installed chaste-sbml package via 'chaste-sbml copy-base-classes'. - Drop the vendored-file handling from setup_project.py. - Use the chaste-sbml command and its generate subcommand in the workflow, README, and Goldbeter example. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Copilot

Pull request overview

Copilot reviewed 31 out of 33 changed files in this pull request and generated 2 comments.

kwabenantim and others added 29 commits June 16, 2026 14:16

#3 Fix minor setup bugs

e26d52e

#3 Add convenience scripts

f7ed54d

#3 Update gitignore

444e6e8

#3 Add setup query about project name

ee9479c

#3 Summarise chosen options

871bf1e

#3 Add docstrings in setup.py

16dc0e4

#3 Add linting, update gitignore

c8cf2ed

#3 Add safe delete in scripts

4e27e93

#3 Update safe delete in scripts

539336f

#3 Update reset, add setup settings

9eebf7c

#3 Remove complicated reset

abf6caa

#3 Add end of setup message

76e0f1b

#3 Check if project is already setup

238ffc7

#3 Update setup answer defaults

23f60a0

#3 Simplify cmake project substitutions

c3e5bf5

#3 Verify Chaste source directory exists

fa11860

#3 Fix test workflow

dc6703e

#3 Default to checkout v6

d257012

#3 Use privileged test container

f1b6294

#3 Fix workflow template path

6151fd0

#3 Auto-set chaste source dir

a79d642

#3 Add standard project github workflow

3ab6d49

#3 Add BUILD_PROJECT_PYTHON_BINDINGS script var

6075a2a

#3 Simplify python bindings build

5470b1f

#3 Update safe_rm

f4cb2d7

#3 Simplify python src copy

a1675f0

#3 Add chaste src dir guard

efc28ca

#3 Add pybind11 OPT_SIZE flag

48dc02a

kwabenantim requested a review from Copilot June 23, 2026 09:33

kwabenantim added 6 commits June 30, 2026 13:16

Merge branch 'pychaste_template' into sbml-template

246455e

#3 Update workflow prompts and dependencies

4b35e12

#3 Include Goldbeter example

061cf3a

#3 Switch CI to chaste/base

24c616f

Merge branch 'pychaste_template' into sbml-template

ce2d655

#3 Fix Goldbeter1991 example

a2dc66a

kwabenantim added 8 commits July 3, 2026 13:52

#3 Remove wrapper generation guard

753d18e

#3 Update wrapping troubleshooting docs

52b0f96

#3 Update force example

8f8294a

#3 Update force example

091e0a7

#3 Create virtualenv during python setup

82b9612

Merge branch 'pychaste_template' into sbml-template

de3e7ad

#3 Add create_venv.sh

7f2ebac

Merge pull request #5 from Chaste/sbml-template

1d578a1

Add SBML template project

kwabenantim changed the title ~~Add pychaste scaffolding~~ Add scaffolding for SBML and python wrappers Jul 3, 2026

kwabenantim requested a review from Copilot July 3, 2026 20:22

Copilot started reviewing on behalf of kwabenantim July 3, 2026 20:23 View session

Copilot AI reviewed Jul 3, 2026

View reviewed changes

Copilot started work on behalf of kwabenantim July 3, 2026 20:34 View session

Fix missing CHASTE_SOURCE_DIR env var in workflow files

a13463b

Copilot finished work on behalf of kwabenantim July 3, 2026 20:37

kwabenantim requested a review from Copilot July 4, 2026 13:15

Copilot started reviewing on behalf of kwabenantim July 4, 2026 13:15 View session

Copilot AI reviewed Jul 4, 2026

View reviewed changes

Comment thread .github/workflows/test-force-example.yml Outdated

Comment thread src/py/MANIFEST.in Outdated

Copilot started work on behalf of kwabenantim July 4, 2026 13:36 View session

Fix review comments in workflow and manifest

202d8cd

Copilot finished work on behalf of kwabenantim July 4, 2026 13:40

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Add scaffolding for SBML and python wrappers#4

Add scaffolding for SBML and python wrappers#4
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kwabenantim commented Jun 16, 2026

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kwabenantim commented Jul 3, 2026 •

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