squash of 153 commits

5318cf8f · Sylvain Arreckx · Laurent Heirendt · b1752b49 · b1752b49 · 5318cf8f
Commit 5318cf8f authored Apr 09, 2020 by Sylvain Arreckx Committed by Laurent Heirendt Oct 19, 2020
--- a/.gitattributes
+++ b/.gitattributes
-*.mat filter=lfs diff=lfs merge=lfs -text
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,8 +6,6 @@ stages:

 test:
  stage: test
-  before_script:
-    - git lfs pull

  script:
    - julia --project=@. -e "import Pkg; Pkg.test(; coverage = true)"

--- a/Project.toml
+++ b/Project.toml
-name = "***REMOVED***"
+name = "COBREXA"
 uuid = "babc4406-5200-4a30-9033-bf5ae714c842"
 authors = ["Some people"]
 version = "0.1.0"

 [deps]
+Clp = "e2554f3b-3117-50c0-817c-e040a3ddf72d"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
--- a/README.md
+++ b/README.md
-# exaCOBRA.jl
+<div align="center">
+    <img src="docs/src/assets/header.svg?maxAge=0" width="80%">
+</div>
+<br>
+
+# Constraint-Based Reconstruction and EXascale Analysis
\ No newline at end of file
--- a/docs/make.jl
+++ b/docs/make.jl
-using Documenter, ***REMOVED***
+using Documenter, COBREXA

-makedocs(sitename="My Documentation")
+makedocs(modules = [COBREXA],
+        clean = false,
+        sitename = "COBREXA.jl",
+        format = Documenter.HTML(
+            # Use clean URLs, unless built as a "local" build
+            prettyurls = !("local" in ARGS),
+            assets = ["assets/favicon.ico"],
+            highlights = ["yaml"],
+        ),
+        authors = "The developers of COBREXA.jl",
+        linkcheck = !("skiplinks" in ARGS),
+        pages = [
+                "Home" => "index.md",
+                "Functions" => "functions.md",
+                "How to contribute" => "howToContribute.md",
+                ],
+        )
\ No newline at end of file
--- a/docs/src/assets/header.svg
+++ b/docs/src/assets/header.svg
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 469.0243 73.5502">
+  <title>cobrexa</title>
+  <g>
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+  </g>
+</svg>
--- a/docs/src/assets/logo.svg
+++ b/docs/src/assets/logo.svg
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 176.4426 148.4338">
+  <title>cobrexa</title>
+  <line x1="69.5239" y1="140.1331" x2="69.5239" y2="140.1331" style="fill: none"/>
+  <g>
+    <path d="M87.7693,122.2541l9.0657-12.08,4.63-6.17,8.1718-10.889a4.0163,4.0163,0,0,0,.0131-4.8041l-3.8846-5.2353a4.0164,4.0164,0,0,0-6.4262-.0329l-5.2929,6.9826L87.9007,98.133l-9.0928,11.9957L63.0907,130.8638a4.0165,4.0165,0,0,1-3.2008,1.59H26.011L55.3056,94.01a4.0162,4.0162,0,0,0,.0354-4.8214L51.588,84.11a4.0164,4.0164,0,0,0-6.4369-.0309L2.6247,140.4784a4.0163,4.0163,0,0,0,3.2069,6.4344H67.2564a4.0164,4.0164,0,0,0,3.2124-1.6056l3.4128-4.5477Z" style="fill: #b890c2;stroke: #a673b1;stroke-linejoin: round"/>
+    <path d="M98.0825,37.8725h0l15.4768-20.3106a4.0161,4.0161,0,0,1,3.1946-1.5821h33.4192L121.4561,53.865a4.0163,4.0163,0,0,0-.0307,4.8113l3.7652,5.1011a4.0164,4.0164,0,0,0,6.4438.0256l13.8432-18.4463L173.5513,7.9481a4.0164,4.0164,0,0,0-3.2124-6.4272h-60.935a4.0163,4.0163,0,0,0-3.2069,1.5983l-17.0633,22.63-21.5572,28.59-.2928.3883a4.0163,4.0163,0,0,0-.0186,4.8113l3.8762,5.2239a4.0164,4.0164,0,0,0,6.42.0411L89.0356,49.7449l9.0468-11.8724" style="fill: #df796f;stroke: #d75544;stroke-miterlimit: 10"/>
+    <path d="M106.6178,73.44h0l8.8417,11.916,34.9466,47.0975H115.388a4.0165,4.0165,0,0,1-3.2254-1.6231L104.0367,119.88a4.0163,4.0163,0,0,0-6.4378-.0175l-4.0477,5.3936a4.0164,4.0164,0,0,0-.0176,4.7979l11.2558,15.23a4.0164,4.0164,0,0,0,3.23,1.6292h62.5917a4.0163,4.0163,0,0,0,3.2314-6.4015L124.3686,73.4848h0l-8.774-11.8869L105.238,47.5669a4.0163,4.0163,0,0,0-6.426-.0491l-3.96,5.1968a4.0165,4.0165,0,0,0-.0308,4.8276Z" style="fill: #7e96cd;stroke: #5b78bb;stroke-miterlimit: 10"/>
+    <path d="M70.27,74.3718,61.4418,62.4742,26.9429,15.98H61.9606a4.0164,4.0164,0,0,1,3.2255,1.6231l7.7326,10.4213a4.0164,4.0164,0,0,0,6.4323.0248l3.9974-5.3014a4.0164,4.0164,0,0,0,.0246-4.8033L72.4545,3.1521a4.0165,4.0165,0,0,0-3.2314-1.6312H6.5031a4.0163,4.0163,0,0,0-3.23,6.4035L52.4257,74.4315,61.189,86.2889l6.4517,8.73,2.4863,3.3642,1.4521,1.9648.0587.0794a4.0163,4.0163,0,0,0,6.4307.0391l4.0238-5.3084a4.0163,4.0163,0,0,0,.0247-4.8194L70.27,74.3718Z" style="fill: #71b964;stroke: #49a648;stroke-miterlimit: 10"/>
+  </g>
+</svg>
--- a/docs/src/functions.md
+++ b/docs/src/functions.md
+# Functions
+
+## Base and header modules
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["header/types.jl", "base/types,jl", "base/solver.jl", "base/utilities.jl"]
+```
+
+## I/O module
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["io/reader.jl"]
+```
+
+## Reconstruction module
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["reconstruction/coupling.jl", "reconstruction/microbiome.jl","reconstruction/modeling.jl"]
+```
+
+## Analysis module
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["analysis/fba.jl", "analysis/fva.jl"]
+```
--- a/docs/src/howToContribute.md
+++ b/docs/src/howToContribute.md
+# How to contribute to/develop COBREXA
+
+If you want to contribute to the `COBREXA` package, please fork the present
+repository by following [these instructions](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo).
+
+## Step 1: Retrieve a local version of COBREXA
+
+There are two ways that you can retrieve a local copy of the package: one is to
+manually clone the forked repository, and the second one is to use the
+intergrated Julia package manager.
+
+### Option 1: Manually clone your fork
+
+:warning: Please make sure you have _forked_ the repository, as described above.
+
+You can do this as follows from the command line:
+
+```bash
+$ git clone git@github.com:yourUsername/COBREXA.jl.git COBREXA.jl
+$ cd COBREXA.jl
+$ git checkout -b yourNewBranch origin/develop
+```
+
+where `yourUsername` is your Github username and `yourNewBranch` is the name of a new branch.
+
+Then, in order to develop the package, you can install your cloned version as
+follows (make sure you are in the `COBREXA.jl` directory):
+
+```julia
+(v1.1) pkg> add .
+```
+
+(press `]` to get into the packaging environment)
+
+This adds the `COBREXA.jl` package and all its dependencies. You can verify
+that the installation worked by typing:
+
+```julia
+(v1.1) pkg> status
+```
+
+If everything went smoothly, this should print something similar to:
+
+```julia
+(v1.1) pkg> status
+    Status `~/.julia/environments/v1.1/Project.toml`
+    [babc4406] COBREXA v0.1.0 #yourNewBranch (.)
+```
+
+Now, you can readily start using the `COBREXA` module:
+
+```julia
+julia> using COBREXA
+```
+
+### Option 2: Use the Julia package manager
+
+When you are used to using the Julia package manager for developing or
+contributing to packages, you can type:
+
+```julia
+(v1.1) pkg> dev COBREXA
+```
+
+This will install the `COBREXA` package locally and check it out for
+development. You can check the location of the package with:
+
+```julia
+(v1.1) pkg> status
+    Status `~/.julia/environments/v1.4/Project.toml`
+  [a03a9c34] COBREXA v0.0.5 [`~/.julia/dev/COBREXA`]
+```
+
+The default location of the package is `~/.julia/dev/COBREXA`.
+
+You can then set your remote by executing these commands in a regular shell:
+
+```bash
+$ cd ~/.julia/dev/COBREXA
+$ git remote rename origin upstream # renames the origin as upstream
+$ git remote add origin git@github.com:yourUsername/COBREXA.jl.git
+$ git fetch origin
+```
+
+where `yourUsername` is your Github username.
+
+:warning: Make sure that your fork exists under `github.com/yourUsername/COBREXA.jl`.
+
+Then, checkout a branch `yourNewBranch`:
+
+```bash
+$ cd ~/.julia/dev/COBREXA
+$ git checkout -b yourNewBranch origin/develop
+```
+
+Then, you can readily use the `COBREXA` package:
+
+```julia
+julia> using COBREXA
+```
+
+After making changes, precompile the package:
+
+```julia
+(v1.1) pkg> precompile
+```
+
+## Step 2: Activate COBREXA
+
+:warning: Please note that you cannot use the dependencies of COBREXA directly,
+unless they are installed separately or the environment has been activated:
+
+```julia
+(v1.1) pkg> activate .
+(COBREXA) pkg> instantiate
+```
+
+Now, the environment is activated (you can see it with the prompt change
+`(COBREXA) pkg>`). Now, you can use the dependency. For instance:
+
+```julia
+julia> using DataFrames
+```
+
+:warning: If you do not  `activate` the environment before using any of the dependencies, you will see a red error messages prompting you to install the dependency explicity.
--- a/docs/src/index.md
+++ b/docs/src/index.md
-# Documentation
+```@raw html
+<br>
+<div align="center">
+    <img src="assets/header.svg?maxAge=0" width="80%">
+</div>
+<br>
+```
+
+# Constraint-Based Reconstruction and EXascale Analysis
+
+# Functions
+
+A full reference to all functions is given here:
+
+```@contents
+Pages = ["functions.md"]
+```
+
+# How to contribute?
+
+If you want to contribute, please read these guidelines first:
+
+```@contents
+Pages = ["howToContribute.md"]
+```
\ No newline at end of file
--- a/src/COBREXA.jl
+++ b/src/COBREXA.jl
+module COBREXA
+
+using Logging
+using SparseArrays
+using DelimitedFiles
+using LinearAlgebra
+using JuMP
+using MAT
+import Pkg
+
+# import src files
+include(joinpath("header", "header.jl"))
+include(joinpath("header", "types.jl"))
+
+const PKG_ROOT_DIR = normpath(joinpath(@__DIR__, ".."))
+include_dependency(joinpath(PKG_ROOT_DIR, "Project.toml"))
+const COBREXA_VERSION = VersionNumber(Pkg.TOML.parsefile(joinpath(PKG_ROOT_DIR, "Project.toml"))["version"])
+
+c = Base.text_colors
+tx = c[:normal] # text
+b = c[:bold] * c[:blue]
+r = c[:bold] * c[:red]
+g = c[:bold] * c[:green]
+m = c[:bold] * c[:magenta]
+banner = "
+      ____ ___  ____  ____  _____$(g)__$(tx)  $(r)__$(tx)    _     |
+     / ___/ _ \\| __ )|  _ \\| ____$(g)\\ \\$(tx)$(r)/ /$(tx)   / \\    | Constraint-Based Reconstruction
+    | |  | | | |  _ \\| |_) |  _|  $(g)\\$(tx)  $(r)/$(tx)   / _ \\   | and EXascale Analysis in Julia
+    | |__| |_| | |_) |  _ <| |___ $(m)/$(tx)  $(b)\\$(tx)  / ___ \\  |
+     \\____\\___/|____/|_| \\_\\_____$(m)/_/$(tx)$(b)\\_\\$(tx)/_/   \\_\\ | Version: v$(COBREXA_VERSION)
+                                                 |
+"
+
+print(banner)
+
+
+loadSource(["base", "io", "reconstruction", "analysis"], @__DIR__)
+
+# export functions
+export speye, LinearModel, nReactions, nMetabolites, nCouplingConstraints,
+       addReaction, addReactions, removeReactions, changeBounds!,
+       addCouplingConstraints!, addCouplingConstraints,
+       removeCouplingConstraints!, removeCouplingConstraints,
+       changeCouplingBounds!, changeCouplingBounds,
+       verifyConsistency, findExchangeReactions, findExchangeMetabolites,
+       solveLP, loadModel, fluxBalanceAnalysis, fluxVariabilityAnalysis,
+       writeModel, convertToExportable
+
+end
--- a/src/ExaCOBRA.jl
+++ b/src/ExaCOBRA.jl
-module ***REMOVED***
-
-export LinearModel, addReaction, addReactions, solveLP, loadModel,
-    nReactions, nMetabolites
-
-include("modeling.jl")
-include("solveLP.jl")
-include("io/matReader.jl")
-end
--- a/src/analysis/fba.jl
+++ b/src/analysis/fba.jl
+"""
+Flux Balance Analysis
+```
+max cᵀx
+s.t. S x = b
+     xₗ ≤ x ≤ xᵤ
+```
+"""
+function fluxBalanceAnalysis(model::LinearModel, optimizer)
+   m, n = size(model.S)
+
+   optimization_model = JuMP.Model(optimizer)
+   @variable(optimization_model, x[i=1:n], lower_bound=model.xl[i], upper_bound=model.xu[i])
+   @objective(optimization_model, Max, model.c' * x)
+   @constraint(optimization_model, model.S * x .== model.b)
+
+   JuMP.optimize!(optimization_model)
+
+   return (optimization_model, x)
+end
--- a/src/analysis/fva.jl
+++ b/src/analysis/fva.jl
+"""
+Flux variability analysis (FVA)
+
+FVA solves the pair of optimization problems for each flux xᵢ
+```
+min/max xᵢ
+s.t. S x = b
+     xₗ ≤ x ≤ xᵤ
+     cᵀx ≥ γ Z₀
+```
+where Z₀:= cᵀx₀ is the objective value of an optimal solution to the associated
+FBA problem
+"""
+function fluxVariabilityAnalysis(model::LinearModel, optimizer)
+   (m, n) = size(model.S)
+   return fluxVariabilityAnalysis(model, collect(1:n), optimizer)
+end
+
+function fluxVariabilityAnalysis(model::LinearModel, reactions::Array{Int64, 1}, optimizer)
+   (maximum(reactions) > length(model.rxns)) && error("Index exceeds number of reactions.")
+   γ = 1.
+   fluxes = zeros(length(reactions), 2)
+
+   (optimization_model, x₀) = fluxBalanceAnalysis(model::LinearModel, optimizer)
+   Z₀ = JuMP.objective_value(optimization_model)
+   x = all_variables(optimization_model)
+   @constraint(optimization_model, model.c' * x ≥ γ * Z₀)
+
+   for i in eachindex(reactions)
+      sense = MOI.MIN_SENSE
+      @objective(optimization_model, sense, x[reactions[i]])
+      JuMP.optimize!(optimization_model)
+      fluxes[i, 1] = JuMP.objective_value(optimization_model)
+
+      sense = MOI.MAX_SENSE
+      JuMP.set_objective_sense(optimization_model, sense)
+      JuMP.optimize!(optimization_model)
+      fluxes[i, 2] = JuMP.objective_value(optimization_model)
+   end
+   return fluxes
+end
--- a/src/solveLP.jl
+++ b/src/solveLP.jl
-import ..LinearModel
-using JuMP
-using GLPK
-
 """
 Use JuMP to solve an instance of LinearModel
 """
-function solveLP(model::LinearModel)
+function solveLP(model::LinearModel, optimizer)
   m, n = size(model.S)

-   optimization_model = JuMP.Model(GLPK.Optimizer)
-   @variable(optimization_model, x[i=1:n], lower_bound=model.lb[i], upper_bound=model.ub[i])
+   optimization_model = JuMP.Model(optimizer)
+   @variable(optimization_model, x[i=1:n], lower_bound=model.xl[i], upper_bound=model.xu[i])
   @objective(optimization_model, Min, model.c' * x)
   @constraint(optimization_model, model.S * x .== model.b)


--- a/src/base/utilities.jl
+++ b/src/base/utilities.jl
+"""
+`n` by `n` sparse identity matrix.
+"""
+speye(n) = sparse(1.0I, n, n)
+
+function Base.isequal(model1::LinearModel, model2::LinearModel)
+    return model1.S == model2.S && model1.b == model2.b && model1.C == model2.C &&
+           model1.cl == model2.cl && model1.cu == model2.cu &&
+           model1.c == model2.c &&
+           model1.xl == model2.xl && model1.xu == model2.xu &&
+           model1.rxns == model2.rxns && model1.mets == model2.mets
+end
+
+function Base.copy(model::LinearModel)
+    return LinearModel(model.S, model.b, model.C, model.cl, model.cu,
+                       model.c, model.xl, model.xu, model.rxns, model.mets)
+end
--- a/src/header/header.jl
+++ b/src/header/header.jl
+
+"""
+loadSource(srcDirs, root=@__DIR__)
+
+Load source files
+"""
+function loadSource(srcDirs, rootDir=@__DIR__, testMode=false)
+    returnFlag = []
+    for d in srcDirs
+        srcDir = joinpath(rootDir, d)
+        if testMode
+            println(" > srcDir = $srcDir")
+        end
+        for file in filter(f -> endswith(f, ".jl"), readdir(srcDir))
+            if file != "header.jl"
+                srcFile = joinpath(rootDir, d, file)
+                if !testMode
+                    include(srcFile)
+                else
+                    println(" > srcFile = $srcFile")
+                end
+                push!(returnFlag, true)
+            end
+        end
+    end
+    return returnFlag
+end
\ No newline at end of file
--- a/src/header/types.jl
+++ b/src/header/types.jl
+const VT = Union{Array{Float64,1}, SparseVector{Float64,Int64}}
+const MT = Union{AbstractMatrix, SparseMatrixCSC{Float64,Int64}}
+const ST = Union{Array{String,1}, SparseVector{String,Int64}}
+
+"""
+A linear optimization problem of the form:
+```
+min c^T x
+s.t. S x = b
+    cₗ ≤ C x ≤ cᵤ
+    xₗ ≤ x ≤ xᵤ
+```
+"""
+mutable struct LinearModel{M<:MT, V<:VT, K<:ST}
+    S       ::M
+    b       ::V
+    C       ::M
+    cl      ::V
+    cu      ::V
+    c       ::V
+    xl      ::V
+    xu      ::V
+    rxns    ::K
+    mets    ::K
+
+    function LinearModel(
+        S       ::M,
+        b       ::V,
+        c       ::V,
+        xl      ::V,
+        xu      ::V,
+        rxns    ::K,
+        mets    ::K) where {V<:VT,M<:MT,K<:ST}
+
+
+        sS = sparse(S)
+        sb = sparse(b)
+        sC = spzeros(0, length(c))
+        scl = spzeros(0)
+        scu = spzeros(0)
+        sc = sparse(c)
+        sxl = sparse(xl)
+        sxu = sparse(xu)
+
+        LinearModel(sS, sb, sC, scl, scu, sc, sxl, sxu, rxns, mets)
+    end
+
+    function LinearModel(
+        S       ::M1,
+        b       ::V,
+        C       ::M2,
+        cl      ::V,
+        cu      ::V,
+        c       ::V,
+        xl      ::V,
+        xu      ::V,
+        rxns    ::K,
+        mets    ::K) where {V<:VT,M1<:MT,M2<:MT,K<:ST}
+
+        checkInputDimensions(S, b, C, cl, cu, c, xl, xu, rxns, mets)
+
+        sS = sparse(S)
+        sb = sparse(b)
+        sC = sparse(C)
+        scl = sparse(cl)
+        scu = sparse(cu)
+        sc = sparse(c)
+        sxl = sparse(xl)
+        sxu = sparse(xu)
+
+        new{SparseMatrixCSC{Float64,Int64}, SparseVector{Float64,Int64}, Array{String,1}}(sS, sb, sC, scl, scu, sc, sxl, sxu, rxns, mets)
+    end
+end
+
+mutable struct ReactionStatus
+    alreadyPresent::Bool
+    index::Int
+    info::String
+end
--- a/src/io/matReader.jl
+++ b/src/io/matReader.jl
-import ..LinearModel
-
-using MAT
-
 """
 Load a model in MAT (Matlab) format and returns a `LinearModel`

@@ -13,27 +9,10 @@ function loadModel(filePath::String, varName::String)
    file = matopen(filePath)
    vars = matread(filePath)

-    if exists(file, varName)
-
-        model = vars[varName]
-        modelKeys = ["S", "b", "c", "ub", "lb"]

-        for key = modelKeys
-            if !(key in keys(model))
-                error("No variable $key found in the MAT file.")
-            end
-        end
-
-        S = model["S"]
-        b = vec(model["b"])
-        c = vec(model["c"])
-        ub = vec(model["ub"])
-        lb = vec(model["lb"])
-        # rxns and mets get loaded as Array{Any,2} need to convert
-        rxns = conversionMetRxns(model["rxns"])
-        mets = conversionMetRxns(model["mets"])
+    if exists(file, varName)

-        return LinearModel(S, b, c, lb, ub, rxns, mets)
+        return convertToLinearModel(vars[varName])

    else
        error("Variable `varName` does not exist in the specified MAT file.")
@@ -41,10 +20,25 @@ function loadModel(filePath::String, varName::String)
    close(file)
 end

-function conversionMetRxns(x)
-    if x isa Array{Any, 2}
-        return convert(Array{String, 1}, vec(x))
-    else
-        return vec(x)
+"""
+Convert a dictionary read from a MAT file to LinearModel
+"""
+function convertToLinearModel(model::Dict)
+    modelKeys = ["S", "b", "c", "ub", "lb"]
+
+    for key = modelKeys
+        if !(key in keys(model))
+            error("No variable $key found in the MAT file.")
+        end
    end
+
+    S = model["S"]
+    b = vec(model["b"])
+    c = vec(model["c"])
+    ub = vec(model["ub"])
+    lb = vec(model["lb"])
+    rxns = vec(string.(model["rxns"]))
+    mets = vec(string.(model["mets"]))
+
+    return LinearModel(S, b, c, lb, ub, rxns, mets)
 end