Update the tutorials to Julia 1.0

[laurentheirendt]

No description provided.

[laurentheirendt]

Can only be tackled once #38 is solved.

[laurentheirendt]

@leejm516, would you mind lending a hand here? 👍

[leejm516]

Nope. What can I do here?

[laurentheirendt]

Essentially we need to make sure that the tutorial is running on Julia 1.0.

[laurentheirendt]

@leejm516, may you update the tutorial before we'll tag the new version?

[leejm516]

Okay. I will have a look in the weekend

[laurentheirendt]

@leejm516, is there any news on this? 👍

[leejm516]

Oh, sorry. I haven't tested yet. I will start from tonight :)

[leejm516]

@laurentheirendt Almost done. Everything seems OK after changing some old julia macros and functions. It take some doing PR since I have to refork from the latest develop branch.

[leejm516]

I run Julia on Windows, and during the test of the PALM tutorial I encountered a funny error.

run(`git clone --depth=1 --recurse-submodules https://github.com/opencobra/cobratoolbox.git $installDir`);
@info "The COBRA Toolbox has been cloned successfully to the $installDir directory."

Cloning into '~/tmp/cobratoolbox'...
Checking out files: 100% (1752/1752), done.
Submodule 'binary' (https://github.com/opencobra/COBRA.binary.git) registered for path 'binary'
Submodule 'external/analysis/CnaCobraInterface' (https://github.com/SteffKlamt/CnaCobraInterface.git) registered for path 'external/analysis/CnaCobraInterface'
Submodule 'external/analysis/Volume-and-Sampling' (https://github.com/Bounciness/Volume-and-Sampling.git) registered for path 'external/analysis/Volume-and-Sampling'
Submodule 'external/analysis/gaimc' (https://github.com/dgleich/gaimc.git) registered for path 'external/analysis/gaimc'
Submodule 'external/analysis/mptoolbox' (https://github.com/LCSB-BioCore/mptoolbox.git) registered for path 'external/analysis/mptoolbox'
Submodule 'external/analysis/octave-networks-toolbox' (https://github.com/aeolianine/octave-networks-toolbox.git) registered for path 'external/analysis/octave-networks-toolbox'
Submodule 'external/base/solvers/lusol' (https://github.com/nwh/lusol.git) registered for path 'external/base/solvers/lusol'
Submodule 'external/base/solvers/pdco' (https://github.com/mxsaunders/pdco.git) registered for path 'external/base/solvers/pdco'
Submodule 'external/base/utilities/Smith-Decomposition' (https://github.com/nbfigueroa/Smith-Decomposition.git) registered for path 'external/base/utilities/Smith-Decomposition'
Submodule 'external/base/utilities/rdir' (https://github.com/LCSB-BioCore/rdir.git) registered for path 'external/base/utilities/rdir'
Submodule 'COBRA.papers' (https://github.com/opencobra/COBRA.papers.git) registered for path 'papers'
Submodule 'test/models' (https://github.com/LCSB-BioCore/COBRA.models) registered for path 'test/models'
Submodule 'COBRA.tutorials' (https://github.com/opencobra/COBRA.tutorials.git) registered for path 'tutorials'
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/binary'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/analysis/CnaCobraInterface'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/analysis/Volume-and-Sampling'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/analysis/gaimc'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/analysis/mptoolbox'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/analysis/octave-networks-toolbox'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/base/solvers/lusol'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/base/solvers/pdco'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/base/utilities/Smith-Decomposition'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/external/base/utilities/rdir'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/papers'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/test/models'...
Cloning into 'D:/Documents/julia/~/tmp/cobratoolbox/tutorials'...

Git did create a "~" folder, instead of seeking the home directory, which might be realted to #50
Mayhbe revising tutorials will have been finished tonight except for the above issue.

[leejm516]

https://discourse.julialang.org/t/how-to-input-path-in-run-and-joinpath-on-windows/29183

[laurentheirendt]

homedir() should fix this. See #54