Commit 1520578a authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
Browse files

add docs directory

parent 0b807550
[deps]
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
using Documenter, SBML
makedocs(modules = [SBML],
clean = false,
format = Documenter.HTML(prettyurls = !("local" in ARGS)),
sitename = "SBML.jl",
authors = "The developers of SBML.jl",
linkcheck = !("skiplinks" in ARGS),
pages = [
"Documentation" => "index.md",
],
)
deploydocs(
repo = "github.com/LCSB-BioCore/SBML.jl.git",
target = "build",
branch = "gh-pages",
devbranch = "develop",
versions = "stable" => "v^",
)
# SBML.jl — load systems biology models from SBML files
This package provides a straightforward way to load model- and
simulation-relevant information from SBML files.
The library provides a single function [`readSBML`](@ref) to load a
[`Model`](@ref):
```julia
julia> using SBML
julia> mdl = readSBML("Ec_core_flux1.xml")
Model()
julia> mdl.compartments
2-element Array{String,1}:
"Extra_organism"
"Cytosol"
```
There are several functions to help you with using the data in the usual
COBRA-style workflows, such as [`getS`](@ref):
```julia
julia> metabolites, reactions, S = getS(mdl)
julia> metabolites
77-element Array{String,1}:
"M_succoa_c"
"M_ac_c"
"M_etoh_c"
julia> S
77×77 Array{Float64,2}:
0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 -1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 -1.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 0.0
```
## Functions
### Data structures
```@autodocs
Modules = [SBML]
Pages = ["structs.jl"]
```
### Base functions
```@autodocs
Modules = [SBML]
Pages = ["version.jl", "readsbml.jl"]
```
## Data helpers
```@autodocs
Modules = [SBML]
Pages = ["utils.jl"]
```
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