Commit ab01e267 authored by St. Elmo's avatar St. Elmo
Browse files

update

parent 09587228
name: Documentation
on:
push:
branches:
- master
tags: '*'
pull_request:
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: julia-actions/setup-julia@latest
with:
version: '1.5'
- name: Install dependencies
run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
- name: Build and deploy
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
run: julia --project=docs/ docs/make.jl
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......@@ -5,6 +5,10 @@
# Ignore data files
*.brenda.txt
/models
!/models/iML1515.xml
!/models/iML1515.json
!/models/iML1515.mat
# Ignore working files
/notebooks_and_scripts/imgs
......
language: julia
os:
- linux
- osx
- windows
julia:
- nightly
- release
- 1.5
notifications:
email: false
The CobraTools.jl package is licensed under the MIT "Expat" License:
> Copyright (c) 2021: St. Elmo Wilken.
>
> Permission is hereby granted, free of charge, to any person obtaining
> a copy of this software and associated documentation files (the
> "Software"), to deal in the Software without restriction, including
> without limitation the rights to use, copy, modify, merge, publish,
> distribute, sublicense, and/or sell copies of the Software, and to
> permit persons to whom the Software is furnished to do so, subject to
> the following conditions:
>
> The above copyright notice and this permission notice shall be
> included in all copies or substantial portions of the Software.
>
> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
> EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
> MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
> IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
> CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
> TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
> SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
\ No newline at end of file
# CobraTools.jl
*CobraTools is a Julia package for constraint based reconstruction and analysis of metabolic models.*
This is package aims to provide constraint based reconstruction and analysis (COBRA) tools in the Julia environment.
This is package aims to provide constraint based reconstruction and analysis (COBRA) tools in the Julia environment, similar to Cobrapy in Python and the Cobra Toolbox in Matlab.
This package provides basic convenience functions, e.g. FBA, pFBA, sampling, model construction, etc.
More importantly, it also exposes the user to the core machinery used in this type of analysis, e.g. the stoichiometric matrix, so that custom optimization routines can be written as painlessly as possible (due in large part to JuMP).
......@@ -39,4 +39,5 @@ TODO.
### Citations
1) Ebrahim, A., Lerman, J.A., Palsson, B.O. & Hyduke, D. R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Systems Biology, 7(74). https://doi.org/10.1186/1752-0509-7-74
2) Noor, E., Bar-Even, A., Flamholz, A., Lubling, Y., Davidi, D., & Milo, R. (2012). An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics, 28(15), 2037–2044. https://doi.org/10.1093/bioinformatics/bts317
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2) Heirendt, L., Arreckx, S., Pfau, T. et al. (2019). Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc 14, 639–702. https://doi.org/10.1038/s41596-018-0098-2
3) Noor, E., Bar-Even, A., Flamholz, A., Lubling, Y., Davidi, D., & Milo, R. (2012). An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics, 28(15), 2037–2044. https://doi.org/10.1093/bioinformatics/bts317
\ No newline at end of file
......@@ -5,35 +5,24 @@ include("testfuncs.jl")
# E. coli models
iJO1366_xml = joinpath("..", "models", "iJO1366.xml")
iJO1366_mat = joinpath("..", "models", "iJO1366.mat")
iJO1366_json = joinpath("..", "models", "iJO1366.json")
jsonmodel_ecoli = CobraTools.readmodel(iJO1366_json)
matlabmodel_ecoli = CobraTools.readmodel(iJO1366_mat)
sbmlmodel_ecoli = CobraTools.readmodel(iJO1366_xml)
# Yeast GEM models
yeast_xml = joinpath("..", "models", "yeastGEM.xml")
yeast_mat = joinpath("..", "models", "yeastGEM.mat")
matlabmodel_yeast = CobraTools.readmodel(yeast_mat) # matlab issue
sbmlmodel_yeast = CobraTools.readmodel(yeast_xml)
# iJO1366_mat = joinpath("..", "models", "iJO1366.mat") # not sure how to get travis to do this
# matlabmodel_ecoli = CobraTools.readmodel(iJO1366_mat)
iJO1366_json = joinpath("..", "models", "iJO1366.json")
jsonmodel_ecoli = CobraTools.readmodel(iJO1366_json)
@testset "CobraTools Tests" begin
@testset "Reading & Writing" begin
# Are the models be read correctly individually?
@test length(jsonmodel_ecoli.rxns) == 2583
@test_broken length(matlabmodel_yeast) == 0
@test_broken length(sbmlmodel_yeast) == 0
@test length(sbmlmodel_ecoli.rxns) == 2583
@test model_comparison_test(jsonmodel_ecoli, matlabmodel_ecoli)
@test_broken model_comparison_test(sbmlmodel_ecoli, matlabmodel_ecoli) # SBML not implemented yet
@test_broken model_comparison_test(matlabmodel_yeast, sbmlmodel_yeast) # yeast GEM matlab format issue?
@test model_comparison_test(jsonmodel_ecoli, sbmlmodel_ecoli)
@test read_write_read_test(jsonmodel_ecoli, "json")
@test read_write_read_test(matlabmodel_ecoli, "mat")
@test_broken read_write_read_test(sbmlmodel_ecoli, "xml") # SBML not implemented yet
end
......
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