Truncation changes

[AlfredMayhew]

Hi, This request relates to the recent issue I raised, and takes two parts (two commits).

I was running into issues with the maximum size of species names allowed. I have increased the maximum species name length, and the maximum length in the output files (concentration and rate outputs), to 50 characters. Clearly this limit is arbitrary, and with the fixed width of columns in the output file this value does alter the readability of the speciesConcentrations.output file. I also increased the grouping of species at the top of the speciesConcentrations.output file from 100 species before a newline character to 1000. Again, this is subjective as a limit but I think that over 100 compounds isn't a ridiculous amount, and it makes processing the output file more difficult to have groupings into 100 species.

Secondly, I added the -ffree-line-length-none flag to the Makefile.skel file to prevent lines being truncated if they are too long in the mechanism file. I ran into this issue because my rate expressions were too long. I added this flag to my Makefile directly previously so have not tested using the .skel file when building a new Makefile, but I'm assuming this should pose no issue.

Thanks, Alfie

[codecov[bot]]

Codecov Report

Merging #428 into master will decrease coverage by 3.18%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #428      +/-   ##
==========================================
- Coverage   88.72%   85.53%   -3.19%     
==========================================
  Files          17       12       -5     
  Lines        2262     1867     -395     
==========================================
- Hits         2007     1597     -410     
- Misses        255      270      +15     

Flag	Coverage Δ
#build	62.45% <100.00%> (ø)
#tests	85.32% <100.00%> (-2.57%)	:arrow_down:
#unittests	?

Impacted Files	Coverage Δ
src/dataStructures.f90	92.90% <ø> (-2.13%)	:arrow_down:
src/outputFunctions.f90	89.30% <100.00%> (ø)
src/argparse.f90	56.11% <0.00%> (-8.64%)	:arrow_down:
travis/unit_tests/argparse_test.f90
travis/unit_tests/atmosphere_test.f90
travis/unit_tests/solar_test.f90
travis/unit_tests/date_test.f90
travis/unit_tests/config_test.f90

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[spco]

I've just opened #429 to attempt to fix the broken MacOS build, but I won't wait for that to hold this one up. Are you satisfied this is complete, @AlfredMayhew ? Looks it to me, in which case I will merge.

[rs028]

Thanks for this guys.

@AlfredMayhew you can also add your name to the doc/latex/Credits.tex (line 60) :)

[AlfredMayhew]

Thanks very much, I have added the credit (in the wrong place initially!). Hopefully that is all correct. I'm happy for you to merge the changes, thank you again.

[rs028]

@spco, does it need to be rebased to #429 before merging?

[spco]

No, this should be fine without rebase.

[spco]

Thanks @AlfredMayhew!