Add octave and matlab to run module

[SarahAlidoost]

Related to EcoExtreML/STEMMUS_SCOPE#125

• update module
• update docs
• update tests
• update notebooks

Tests:

• crib with octave
• snellius with exe and matlab
• my linux with exe

closes #44
closes #39
closes #25
relates #46

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[SarahAlidoost]

I tried running the model using Octave, but it does not seem to work on my Windows machine. Subprocess just returns exit status 1:

CalledProcessError: Command '['octave --eval "STEMMUS_SCOPE_octave(\'C:\\STEMMUS_SCOPE_data\\workdir\\input\\ZA-Kru_2022-11-03-0927\\ZA-Kru_2022-11-03-0927_config.txt\');exit;"', '--no-gui', '--silent']' returned non-zero exit status 1.

code 1 Indicates that "Action has attempted to execute non-recognized command". This might be related to how we call octave executable here i.e. octave vs octave.bat on windows.

A solution would be to use shutil.which() as explained here.

[BSchilperoort]

Hi Sarah, you missed part of my suggestion which was to split up the octave --eval CODE into separate octave, --eval, and CODE list elements. This is required for it to work on Windows.

I also reviewed the rest of the PR and left some suggestions and comments! 👍

[SarahAlidoost]

Hi Sarah, you missed part of my suggestion which was to split up the octave --eval CODE into separate octave, --eval, and CODE list elements. This is required for it to work on Windows.

I also reviewed the rest of the PR and left some suggestions and comments! +1

Thanks for reviewing. I addressed your comments, Please have another look, thanks.

[BSchilperoort]

Hi Sarah, great work! Octave + Windows 10 works as intended now 😄.

Seeing as you'll be gone for a week, and to avoid merge conflicts, I will merge this PR once I fixed the Windows CI. The tests are failing due to a lack of Windows wheels for the netcdf 1.6.0 package. I will fix it to <1.6.0.

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
1 Code Smell

92.7% Coverage
0.0% Duplication

[BSchilperoort]

I noticed that the tests were failing on Windows, as trying to use a non-existent EXE results in a FileNotFoundError on Windows, instead of the ValueError you expected. I have updated the tests to account for this.

See the changes here:
6a0d024#diff-d57ca3aa8acb1482e37888eb52a0746872c9c36e6bc8c263dd3a1efed5f3196f

[SarahAlidoost]

I noticed that the tests were failing on Windows, as trying to use a non-existent EXE results in a FileNotFoundError on Windows, instead of the ValueError you expected. I have updated the tests to account for this.

See the changes here: 6a0d024#diff-d57ca3aa8acb1482e37888eb52a0746872c9c36e6bc8c263dd3a1efed5f3196f

Thanks for the review and fixes. I will merge the PR.