Expand Project Template for Python and SBML #3

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1. kwabenantim

   added 15 commits that reference this issue on Jun 16, 2026

   #3 Fix minor setup bugs

   e26d52e

   #3 Add convenience scripts

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   #3 Update gitignore

   444e6e8

   #3 Add setup query about project name

   ee9479c

   #3 Summarise chosen options

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   #3 Add docstrings in setup.py

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   #3 Add linting, update gitignore

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   #3 Add safe delete in scripts

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   #3 Update safe delete in scripts

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   #3 Update reset, add setup settings

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   #3 Remove complicated reset

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   #3 Add end of setup message

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   #3 Check if project is already setup

   238ffc7

   #3 Update setup answer defaults

   23f60a0

   #3 Simplify cmake project substitutions

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3. kwabenantim

   added 3 commits that reference this issue on Sep 17, 2026

   #3 Fix sbml_example CI

   7d5cbcd

   #3 Fix python force example

   72ef349

   #3 Update sbml example timescale

   257de85
4. mirams

   linked a pull request that will close this issueAdd scaffolding for python wrappers and SBML #4on Sep 21, 2026
5. mirams commented on Sep 21, 2026

   

   mirams

   on Sep 21, 2026

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   There's a bit of a risk this makes it look as if a 'normal' C++ project (just about 3 extra source and test hpp and cpp files) is a lot more complicated and difficult than it really is.

   Maybe we could have separate readmes for Python bindings and SBML, I don't know whether the rest of the folder structure could be simplified so that all the python_binding stuff is in one folder and all the sbml in another, possibly not...
6. kwabenantim commented on Sep 24, 2026

   

   kwabenantim

   on Sep 24, 2026

   Last edited by kwabenantim

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   folder structure could be simplified so that all the python_binding stuff is in one folder and all the sbml in another

   That should be possible, I think. I'll experiment with moving things around into a folder structure like this:

   template_project/
   ├── CMakeLists.txt              # add_subdirectory(bindings)
   ├── README.md                   # trimmed; sbml and bindings sections moved out
   ├── setup_project.py
   ├── apps/                       # UNCHANGED
   ├── src/{Hello.cpp,Hello.hpp}   # UNCHANGED
   ├── test/                       # UNCHANGED
   ├── scripts/                    # configure, compile, test
   │
   ├── bindings/
   │   ├── CMakeLists.txt
   │   ├── config.yaml
   │   ├── README.md               # extracted from main README
   │   ├── install.sh              # was scripts/bindings_install.sh
   │   ├── package/                # was src/py/
   │   └── example/                # was examples/python_example/
   │
   └── sbml/
       ├── README.md               # extracted from main README
       ├── install.sh              # was scripts/sbml_install.sh
       └── example/                # was examples/sbml_example/
   
7. kwabenantim

   added 9 commits that reference this issue on Sep 24, 2026

   #3 Move bindings and SBML files into top-level folders

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   #3 Update path references for the bindings and sbml folders

   54c1821

   #3 Split the README across the bindings and sbml folders

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   #3 Update bindings and SBML examples

   c356c43

   #3 Simplify helper scripts

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   #3 Improve sbml and bindings READMEs

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   #3 Split sbml and bindings in setup

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   #3 Tweak docs

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   #3 Remove deprecated chaste provenance

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