Comments (12)
leejm516
commented on August 22, 2024
1
@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.
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laurentheirendt
commented on August 22, 2024
Can only be tackled once #38 is solved.
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laurentheirendt
commented on August 22, 2024
@leejm516, would you mind lending a hand here? 👍
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leejm516
commented on August 22, 2024
Nope. What can I do here?
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laurentheirendt
commented on August 22, 2024
Essentially we need to make sure that the tutorial is running on Julia 1.0.
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laurentheirendt
commented on August 22, 2024
@leejm516, may you update the tutorial before we'll tag the new version?
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leejm516
commented on August 22, 2024
Okay. I will have a look in the weekend
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laurentheirendt
commented on August 22, 2024
@leejm516, is there any news on this? 👍
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leejm516
commented on August 22, 2024
Oh, sorry. I haven't tested yet. I will start from tonight :)
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leejm516
commented on August 22, 2024
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.
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leejm516
commented on August 22, 2024
https://discourse.julialang.org/t/how-to-input-path-in-run-and-joinpath-on-windows/29183
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laurentheirendt
commented on August 22, 2024
homedir() should fix this. See #54
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Related Issues (20)
- Overload loadModel for new coupled model structure HOT 1
- Info about upcoming removal of packages in the General registry HOT 4
- Run tests for PALM.jl on Windows
- Test code coverage submission to codecov fails for PRs HOT 1
- Bump version v0.3.0 HOT 1
- Increase coverage
- Bump version v0.3.1 HOT 3
- Bump version v0.3.2 HOT 1
- Trying to run doubleGeneDeeletion script on PALM.jl HOT 1
- New .mat file in test script is causing script to fail HOT 5
- Empty tutorial
- how to update WinRPM in julia version 0.6.4 HOT 1
- JuliaError: Exception 'The solver `GLPK` or `GLPKMathProgInterface` cannot be set using `changeCobraSolver()'. HOT 1
- Bump version 0.4.0 HOT 3
- TagBot trigger issue HOT 6
- Bump version 0.4.1 HOT 3
- Bump version 0.4.2 HOT 1
- How to use the C matrix with Julia
- Bump version 0.4.3 HOT 1
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