opencobra / cobra.jl Goto Github PK
View Code? Open in Web Editor NEWHigh-level, high-performance, constraint-based reconstruction and analysis in Julia
Home Page: https://git.io/COBRA.jl
License: Other
High-level, high-performance, constraint-based reconstruction and analysis in Julia
Home Page: https://git.io/COBRA.jl
License: Other
Hey, following up from JuliaCon. I am interested in using SBML files to generate differential equation models, and it seems like you might have the tools for at least parsing these files. Could we collaborate on getting a separate package for these? It sounds like it exists in Python, so could there be an easy package via PyCall that wraps the parser functionality? I think this would be generally useful to the Julia community.
Hello!
I receive the attached error
that the solver cannot be set through the changeCobraSolver
function, despite that is what is demonstrated in the docs. The corresponding files are all stored in this directory. This error seems to occur in Windows OS and not in Linux.
How can the error be resolved?
Thank you :)
Andrew
It seems as if code coverage is generated but not uploaded to codecov. See #46.
@JuliaRegistrator register
I have only both the model.mat and KO script 'Macrophage_KO.m' in the test directory.
PALM(modelDir, "$(joinpath(dirname(pathof(COBRA)), "../test/Macrophage_KO.m"))",
nMatlab=nWorkers, outputFile="modelCharacteristics.mat",
varsCharact=varsCharact, cobraToolboxDir=installDir)
but I am getting this error:
Every worker will run 17 model(s).
Load sharing is ideal.
-- Load distribution --
Number of models: 17
Number of workers: 1
True load (models/worker): 17.0
Realistic load (quotient): 17
Remaining load (remainder): 0
┌ Info: Directory with 17 models read successfully.
└ @ COBRA
~/COBRA.jl/src/PALM.jl:247
The poolsize is equal to 1. PALM.jl is meant to be used in parallel, not serial or sequential.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] PALM(::String, ::String; nMatlab::Int64, outputFile::String, varsCharact::Array{String,1}, cobraToolboxDir::String, printLevel::Int64, useCOBRA::Bool) at ~/COBRA.jl/src/PALM.jl:257
[3] top-level scope at In[122]:1
@JuliaRegistrator register
MathProgBase.jl will be replaced by MathOptInterface.jl in the near future.
solve.jl
will need to be adapted accordingly.
@JuliaRegistrator register()
@JuliaRegistrator register()
@JuliaRegistrator register
cc: @ithiele, @rmtfleming, @tpfau, @Fede-edef
I'm using COBRA.jl in julia v0.7.0 on macos 10.13.6.
These are error messages:
julia> using COBRA
[ Info: Precompiling COBRA [58298e0b-d05c-52ec-a210-0694647ebfc7]
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/COBRA.jl:19.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/COBRA.jl:19
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/checkSetup.jl:32.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/checkSetup.jl:32
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/checkSetup.jl:68.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/checkSetup.jl:68
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/load.jl:25.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/load.jl:25
┌ Warning: Deprecated syntax type
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/load.jl:25.
│ Use mutable struct
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/load.jl:25
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/load.jl:77.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/load.jl:77
WARNING: importing deprecated binding Base.SparseMatrixCSC into COBRA.
WARNING: Base.SparseMatrixCSC is deprecated, run using SparseArrays
to load sparse array functionality
likely near /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/load.jl:9
WARNING: Base.SparseMatrixCSC is deprecated, run using SparseArrays
to load sparse array functionality
likely near /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/load.jl:9
WARNING: Base.SparseMatrixCSC is deprecated, run using SparseArrays
to load sparse array functionality
likely near /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/load.jl:9
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/solve.jl:19.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/solve.jl:19
┌ Warning: Deprecated syntax type
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/solve.jl:19.
│ Use mutable struct
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/solve.jl:19
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/solve.jl:49.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/solve.jl:49
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/solve.jl:94.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/solve.jl:94
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/solve.jl:188.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/solve.jl:188
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/solve.jl:236.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/solve.jl:236
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:48.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:48
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:160.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:160
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:332.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:332
┌ Warning: Deprecated syntax multiple line breaks between doc string and object
at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:507.
│ Use at most one line break
instead.
└ @ ~/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:507
ERROR: LoadError: LoadError: syntax: invalid escape sequence
Stacktrace:
[1] include at ./boot.jl:317 [inlined]
[2] include_relative(::Module, ::String) at ./loading.jl:1038
[3] include at ./sysimg.jl:29 [inlined]
[4] include(::String) at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/COBRA.jl:19
[5] top-level scope at none:0
[6] include at ./boot.jl:317 [inlined]
[7] include_relative(::Module, ::String) at ./loading.jl:1038
[8] include(::Module, ::String) at ./sysimg.jl:29
[9] top-level scope at none:2
[10] eval at ./boot.jl:319 [inlined]
[11] eval(::Expr) at ./client.jl:399
[12] top-level scope at ./none:3
in expression starting at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/distributedFBA.jl:608
in expression starting at /Users/kousaka_tomoyuki/.julia/packages/COBRA/nAHE8/src/COBRA.jl:30
ERROR: Failed to precompile COBRA [58298e0b-d05c-52ec-a210-0694647ebfc7] to /Users/kousaka_tomoyuki/.julia/compiled/v0.7/COBRA/ChOhi.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] macro expansion at ./logging.jl:313 [inlined]
[3] compilecache(::Base.PkgId, ::String) at ./loading.jl:1185
[4] macro expansion at ./logging.jl:311 [inlined]
[5] _require(::Base.PkgId) at ./loading.jl:941
[6] require(::Base.PkgId) at ./loading.jl:852
[7] macro expansion at ./logging.jl:311 [inlined]
[8] require(::Module, ::Symbol) at ./loading.jl:834
As described in https://discourse.julialang.org/t/ann-plans-for-removing-packages-that-do-not-yet-support-1-0-from-the-general-registry/ we are planning on removing packages that do not support 1.0 from the General registry. This package has been detected to not support 1.0 and is thus slated to be removed. The removal of packages from the registry will happen approximately a month after this issue is open.
To transition to the new Pkg system using Project.toml
, see https://github.com/JuliaRegistries/Registrator.jl#transitioning-from-require-to-projecttoml.
To then tag a new version of the package, see https://github.com/JuliaRegistries/Registrator.jl#via-the-github-app.
If you believe this package has erroneously been detected as not supporting 1.0 or have any other questions, don't hesitate to discuss it here or in the thread linked at the top of this post.
@JuliaRegistrator register()
Is this package still actively maintained? In the tutorials for COBRA, all I see are installation instructions and not any explanations to run a model.
With #56, the coverage on master
dropped.
Ref pull request #80 merged to master branch in around 2020-09-07
The new ecoli model at
http://bigg.ucsd.edu/static/models/e_coli_core.mat (size 114736) is causing test script to fail.
The older URL
https://github.com/opencobra/COBRA.models/raw/master/mat/ecoli_core_model.mat does work but is a considerably smaller file of 8818 bytes)
URL is specified in file test/getTestModel.jl
To replicate error from command line on king.nuigalway.ie, create an empty directory and 'cd' into it. Then:
git clone https://github.com/opencobra/COBRA.jl
cd COBRA.jl
/home/vmhadmin/julia-1.2.0/bin/julia --color=yes -e 'import Pkg; Pkg.clone(pwd()); Pkg.test("COBRA", coverage=true); Pkg.rm("COBRA");'
Error text:
Running s_all.jl ...
[ Info: The ecoli_core model already exists.
ERROR: LoadError: LoadError: The variable named `model` does not exist. Please set `model` to a known variable in the `.mat` file.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] loadModel(::String, ::String, ::Int64) at /home/vmhadmin/tmp/t/COBRA.jl/src/load.jl:220
[3] loadModel at /home/vmhadmin/tmp/t/COBRA.jl/src/load.jl:226 [inlined] (repeats 3 times)
[4] top-level scope at /home/vmhadmin/tmp/t/COBRA.jl/test/s_all.jl:48
[5] include at ./boot.jl:328 [inlined]
[6] include_relative(::Module, ::String) at ./loading.jl:1094
[7] include(::Module, ::String) at ./Base.jl:31
[8] include(::String) at ./client.jl:431
[9] top-level scope at /home/vmhadmin/tmp/t/COBRA.jl/test/runtests.jl:133
[10] include at ./boot.jl:328 [inlined]
[11] include_relative(::Module, ::String) at ./loading.jl:1094
[12] include(::Module, ::String) at ./Base.jl:31
[13] include(::String) at ./client.jl:431
[14] top-level scope at none:5
in expression starting at /home/vmhadmin/tmp/t/COBRA.jl/test/s_all.jl:48
in expression starting at /home/vmhadmin/tmp/t/COBRA.jl/test/runtests.jl:118
ERROR: Package COBRA errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Types.jl:112
[2] #test#119(::Bool, ::Nothing, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Operations.jl:1288
[3] #test at ./none:0 [inlined]
[4] #test#62(::Bool, ::Nothing, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:245
[5] #test at ./none:0 [inlined]
[6] #test#61 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:230 [inlined]
[7] #test at ./none:0 [inlined]
[8] #test#60 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:229 [inlined]
[9] #test at ./none:0 [inlined]
[10] #test#59(::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:coverage,),Tuple{Bool}}}, ::typeof(Pkg.API.test), ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:228
[11] (::getfield(Pkg.API, Symbol("#kw##test")))(::NamedTuple{(:coverage,),Tuple{Bool}}, ::typeof(Pkg.API.test), ::String) at ./none:0
[12] top-level scope at none:1
@JuliaRegistrator register()
This issue is used to trigger TagBot; feel free to unsubscribe.
If you haven't already, you should update your TagBot.yml
to include issue comment triggers.
Please see this post on Discourse for instructions and more details.
If you'd like for me to do this for you, comment TagBot fix
on this issue.
I'll open a PR within a few hours, please be patient!
Hello, when I used the new version of COBRA Toolbox to generate the personalized community model, the C matrix replaced the original A matrix. When I tried to calculate the metabolic flux of C matrix with Julia, the code reported an error, which showed that there was no C matrix in the model. I wonder if the error was caused by the change of the internal structure of the model. Can Julia calculate C matrix now?
ERROR: LoadError: Matrix 'C' dose not exist in 'microbiota_model'.
I'm new to Julia and I want to use COBRA Package. For adding COBRA I use the command :
Pkg.add("COBRA")
But when running, I get these errors:
INFO: Building WinRPM
WARNING: skipping repodata/repomd.xml, not in cache -- call WinRPM.update() to download
WARNING: skipping repodata/repomd.xml, not in cache -- call WinRPM.update() to download
INFO: Downloading https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
WARNING: Unknown download failure, error code: 2148270086
WARNING: Retry 1/5 downloading: https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
until:
WARNING: Unknown download failure, error code: 2148270086
WARNING: Retry 5/5 downloading: https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
WARNING: received error 0 while downloading https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
After these errors, I have checked the link and I've found out the source is not there, anymore. So then I ran this command as said above:
WinRPM.update()
But it has thrown this error:
ERROR: UndefVarError: WinRPM not defined
I'm using version 0.6.4 (Windows 10).
Any help would be appreciated.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.