Fix MATLAB interface samples by ssun30 · Pull Request #1911 · Cantera/cantera

ssun30 · 2025-06-18T17:16:34Z

There are numerous changes to class structures to the MATLAB interface that necessitate modifications to our current collection of MATLAB samples.

Changes proposed in this pull request

Fix crashes/solver errors in MATLAB samples.
Compare the results to their equivalent Python samples to make sure the solutions are correct.

If applicable, fill in the issue number this pull request is fixing

~~Not a fix to #1722~~ Flame fixes have been deferred to a later PR.

Checklist

The pull request includes a clear description of this code change
Commit messages have short titles and reference relevant issues
Build passes (scons build & scons test) and unit tests address code coverage
Style & formatting of contributed code follows contributing guidelines
The pull request is ready for review

codecov · 2025-06-18T17:40:14Z

Codecov Report

❌ Patch coverage is 34.42623% with 40 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.43%. Comparing base (4cac7ac) to head (c70683f).
⚠️ Report is 25 commits behind head on main.

Files with missing lines	Patch %	Lines
interfaces/matlab_experimental/Utility/ctPaths.m	0.00%	31 Missing ⚠️
interfaces/matlab_experimental/Utility/ctLoad.m	69.23%	8 Missing ⚠️
interfaces/matlab_experimental/OneDim/Sim1D.m	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1911      +/-   ##
==========================================
+ Coverage   75.04%   75.43%   +0.39%     
==========================================
  Files         450      450              
  Lines       56236    56276      +40     
  Branches     9302     9302              
==========================================
+ Hits        42201    42453     +252     
+ Misses      10898    10687     -211     
+ Partials     3137     3136       -1

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ischoegl

@ssun30 ... thanks for addressing!

Out of curiosity: for the Python API, all examples are tested as part of a CI job, see run-examples in .github/workflows/main.yml.

The relevant code is:

   - name: Run the examples
        # See https://unix.stackexchange.com/a/392973 for an explanation of the -exec part.
        run: |
          ln -s libcantera_shared.so build/lib/libcantera_shared.so.3
          export LD_LIBRARY_PATH=build/lib
          find samples/python -type f -iname "*.py" \
          -exec sh -c 'for n; do echo "$n" | tee -a results.txt && python3 "$n" >> results.txt || exit 1; done' sh {} +

I believe it's possible to do something similar here as it's possible to run MATLAB scripts from the command line:

matlab -r "try, run('rankine.m'), catch, exit(1), end, exit(0)"

where I had set matlab to

alias matlab="/Applications/MATLAB_R2023b.app/bin/matlab -nojvm -nodesktop"

on macOS (fwiw, I just ran a quick test so the options may not be the greatest selection)

interfaces/matlab_experimental/OneDim/Sim1D.m

ischoegl

@ssun30 ... thanks for pushing the MATLAB toolbox closer to the finishing line. Changes to the samples are ok, but I do have comments regarding the updated approach for folder management:

The ctPaths interface is too complicated - it should be sufficient to provide the root location, and use logic based on known relative paths
Except for unit tests, compiled Cantera should use the installed location
Unit tests don't need to be installed or distributed with the MLTBX

At this juncture, it also makes sense to start testing all operating systems in CI jobs, i.e., Windows, macOS, and Linux. This can likely be done as a standard matrix job. Further, examples should be run as part of the CI jobs as pointed out in a comment above.

interfaces/matlab_experimental/Func/Func1.m

interfaces/matlab_experimental/OneDim/Sim1D.m

interfaces/matlab_experimental/Utility/ctPaths.m

interfaces/matlab_experimental/readme.md

.github/workflows/main.yml

interfaces/matlab_experimental/Utility/ctPaths.m

ischoegl

Thanks @ssun30. Thanks for addressing the ctPaths issue which to me was the biggest concern. There are some remaining issues that should be easy to address.

I'm 👍 with deferring some decisions regarding installation and CI runs, but hope that you'll address that feedback in other PRs. Both should be addressed before the 'experimental' suffix can be removed.

interfaces/matlab_experimental/Utility/ctPaths.m

interfaces/matlab_experimental/readme.md

interfaces/matlab_experimental/Utility/ctPaths.m

speth

I think there's a fair bit of improvement still needed with how paths are set up, but I would suggest that we hold off on that for now in the interest of getting the main feature of this PR in place, which is to have the Matlab CI job run successfully and include running the examples as part of the testing in that job.

speth · 2025-08-26T19:12:40Z

samples/matlab_experimental/conhp.m

    % It assumes that the ``gas`` object represents a reacting ideal gas mixture.

    % Set the state of the gas, based on the current solution vector.
+    gas.basis = 'mass';


The default basis should already be "mass", which would be consistent with the Python interface, though I see that the behavior defined in ThermoPhase.m is in fact to default to molar properties.

I agree that default behaviors across interfaces should be consistent. The mass/mole switching is unfortunately handled by the interfaces, see Cantera/enhancements#219. Obviously not something that should be addressed here.

@speth

I will defer to @speth for the final approval.

bryanwweber

I'm likewise interested in resolving the installation question, but I also feel fine with deferring that to after this work. I just had a few simple fixes for consistency and maybe some cleanup.

samples/matlab_experimental/isentropic.m

samples/matlab_experimental/rankine.m

samples/matlab_experimental/test_examples.m

test/matlab_experimental/ctTestSamples.m

bryanwweber

Thanks @ssun30 this looks good to me now

ischoegl

Thanks, @ssun30! While some issues remain to be resolved in follow-up PRs, this is progress.

Changed refine criteria for Diff_flame

Modified several samples to include this change

Replaced ctRoot with ctPaths, this will allow the user to set paths to the shared libraries, header files, and toolboxes more freely, instead of relying on relative paths to a fixed path for a certain conda environment.

to how paths are set

Currently Func1 may have a partially constructed object that gets destructed when checks for the types of input arguments fail, a warning will pop up when the destructor is called.

Now it only uses relative paths to the environment where cantera is installed.

The test_examples script can still be used to run all examples by the user, but it's not necessary for the unit test suite.

for installing the MATLAB toolbox

Fixed some formatting with cell markers

Now the unit test suite has its own set up methods to handle the paths

speth

This is definitely progress in the right direction. Looking forward to more in additional PRs.

ischoegl added the Matlab label Jun 19, 2025

ssun30 force-pushed the matlab_fix_samples branch from 9a6a562 to f8ebb67 Compare June 20, 2025 13:38

ischoegl reviewed Jun 21, 2025

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ssun30 force-pushed the matlab_fix_samples branch from 182f7b9 to bb891cb Compare June 26, 2025 01:00

This was referenced Jun 26, 2025

Add sundials mpi check #1918

Merged

Sporadic test failures on CI runners using macOS on Intel hardware #1916

Open

ischoegl reviewed Jun 26, 2025

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ssun30 force-pushed the matlab_fix_samples branch 2 times, most recently from f6520e5 to 4863f99 Compare June 30, 2025 20:10

ssun30 force-pushed the matlab_fix_samples branch 2 times, most recently from 36f788e to 123e0e8 Compare July 18, 2025 22:14

ssun30 force-pushed the matlab_fix_samples branch 3 times, most recently from 0aec705 to fc5bd71 Compare August 5, 2025 02:31

ssun30 marked this pull request as ready for review August 5, 2025 02:32

ssun30 requested a review from ischoegl August 5, 2025 02:32

ischoegl previously requested changes Aug 5, 2025

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ssun30 force-pushed the matlab_fix_samples branch from fc5bd71 to 1493921 Compare August 8, 2025 14:15

ischoegl mentioned this pull request Aug 9, 2025

[MATLAB] Create MLTBX toolbox file that can be published on File Exchange #1882

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ssun30 force-pushed the matlab_fix_samples branch from 1493921 to 79fb01a Compare August 13, 2025 20:59

ssun30 force-pushed the matlab_fix_samples branch from 79fb01a to 26ab152 Compare August 21, 2025 03:35

ssun30 requested a review from ischoegl August 21, 2025 03:47

ischoegl reviewed Aug 21, 2025

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ssun30 force-pushed the matlab_fix_samples branch from 26ab152 to 7c00e73 Compare August 26, 2025 16:31

ssun30 requested review from bryanwweber, ischoegl and speth August 26, 2025 18:04

speth requested changes Aug 26, 2025

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ischoegl mentioned this pull request Aug 31, 2025

Matlab-to-Clib Interface Overhaul #1868

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ssun30 force-pushed the matlab_fix_samples branch from b20f051 to 837625c Compare September 4, 2025 17:03

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ischoegl previously approved these changes Sep 7, 2025

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ssun30 and others added 18 commits September 7, 2025 18:35

[MATLAB] Fixed Sim1D.display

27b11e2

Changed refine criteria for Diff_flame

[MATLAB] add correct units for axis for periodic_cstr.m sample

56160ee

[MATLAB] Added massDensity property to ThermoPhase

d0816a1

Modified several samples to include this change

[MATLAB] Fixed some samples and added try catch to test_examples.m

9270483

[MATLAB] Changed how search paths are set

7e46396

Replaced ctRoot with ctPaths, this will allow the user to set paths to the shared libraries, header files, and toolboxes more freely, instead of relying on relative paths to a fixed path for a certain conda environment.

[MATLAB] Changed CI workflow to account for change

cd36853

to how paths are set

[MATLAB] Removed ctRoot

14f844b

[MATLAB] Added checks for Func1 class destructor

095d4fd

Currently Func1 may have a partially constructed object that gets destructed when checks for the types of input arguments fail, a warning will pop up when the destructor is called.

[MATLAB] Fixed multicomponent transport test

0efe4de

[MATLAB] Changed installation instructions

9b72670

[MATLAB] Changed how ctPaths work

96bd830

Now it only uses relative paths to the environment where cantera is installed.

[MATLAB] Incorporated sample tests into CI

98c13f9

The test_examples script can still be used to run all examples by the user, but it's not necessary for the unit test suite.

[MATLAB] Changed installation guide and docs

711c526

for installing the MATLAB toolbox

[MATLAB] Removed savepath behavior from ctPaths

d74f84a

[MATLAB] Renamed Sim1D.display to Sim1D.show

d74842f

[MATLAB] Fixed issues with ignition examples

ba14b29

Fixed some formatting with cell markers

[MATLAB] Removed the pre-test set up steps

92c6f1d

Now the unit test suite has its own set up methods to handle the paths

Update authors list

c70683f

speth dismissed stale reviews from ischoegl and bryanwweber via c70683f September 7, 2025 22:44

speth force-pushed the matlab_fix_samples branch from 1f2b74a to c70683f Compare September 7, 2025 22:44

speth approved these changes Sep 7, 2025

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speth merged commit 2e01594 into Cantera:main Sep 7, 2025
50 of 51 checks passed

ssun30 deleted the matlab_fix_samples branch September 9, 2025 19:19

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