Fix examples in `samples` folder

[ischoegl]

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System information

• Cantera version: 2.5.0a3 (master branch)
• OS: Linux
• Python/MATLAB version: N/A

Expected behavior

All samples work without errors/warnings.

Actual behavior

One sample fails (missing input file)

$ ./LiC6_electrode 

***********************************************************************
CanteraError thrown by Application::findInputFile:

Input file LiC6_electrodebulk.xml not found in directories 
'.', 
'/usr/local/share/cantera/data'

To fix this problem, either:
    a) move the missing files into the local directory;
    b) define environment variable CANTERA_DATA to
         point to the directory containing the file.
***********************************************************************

and another raises a warning (issue caused by PR #632)

$ ./combustor 
DeprecationWarning: FlowDevice::setMassFlowRate(): To be removed after Cantera 2.5. Use device-specific functions (e.g. Valve::setValveCoeff) instead.
DeprecationWarning: Valve::setParameters(): To be removed after Cantera 2.5. Use Valve::setValveCoeff instead.

A clear and concise description of what the bug is.

To Reproduce

Steps to reproduce the behavior:

1. Compile cantera from master (e.g. c4c30e3)
2. Run scons samples
3. Run examples in build/samples

[bryanwweber]

The input file for the first one is in samples/cxx/LiC6_electrode. If you add CANTERA_DATA=path/to/samples/cxx/LiC6_electrode ./LiC6_electrode it should work. I'm not sure what the appropriate resolution is here - maybe copy the input file into the build/samples directory associated with the example? That won't solve the problem if you run the sample from another directory, e.g., CANTERA_DATA=path/to/samples/cxx/LiC6_electrode build/samples/cxx/LiC6_electrode/LiC6_electrode will fail with the same message I think.

[ischoegl]

The input file for the first one is in samples/cxx/LiC6_electrode.

I believe the expected behavior would be that build scripts copy the input file to the build directory. (it probably needs to be converted to yaml as well)

[bryanwweber]

Yeah, I think copying the input file is probably the right thing to do. I converted the input file in #768

[ischoegl]

Great. Can you add this to #768? I can fix the other one as it's clearly caused by yours truly.

Before tackling that, I'd like to see whether the updated example should pass a locally defined function (there just was a question on the UG that's waiting for a related answer). Edit: decided to fix the second issue with a very limited PR (#776).

[ischoegl]

Issue should eventually be taken care of by steps discussed in Cantera/enhancements#22

[speth]

I think I disagree that this is a problem. The build directory is just a staging location for build artifacts. While it is often useful to run things from that location for testing purposes, that does frequently require some path / environment variable manipulations. This sample runs fine from from its installed location (after being compiled with one of the generated build scripts), since the input file is already copied to that directory.

Also, I don't think the change proposed in #789 fixes the problem, since <cantera source directory>/build/data is never automatically part of the Cantera data path. The only case where this would work is if you had already run scons install before navigating into build/samples/cxx/LiC6_electrode and running that sample.

[ischoegl]

Hm. My assumption was that the build directory was complete. I guess #776 already resolved the other issue.