Unverified Commit 613d70c7 authored by Laurent Heirendt's avatar Laurent Heirendt Committed by GitHub
Browse files

Merge pull request #4 from LCSB-BioCore/mk-docs

add the documentation
parents 5653d9e4 3c9bee08
# ref: https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#GitHub-Actions-1
name: Documentation
on:
push:
branches:
- master
tags: '*'
release:
types: [published, created]
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:
DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
run: julia --project=docs/ docs/make.jl
# SBML.jl
This is a simple wrap of some of the libSBML functionality.
| Build status | Documentation |
|:---:|:---:|
| ![CI](https://github.com/LCSB-BioCore/SBML.jl/workflows/CI/badge.svg?branch=develop) | [![doc](https://img.shields.io/badge/docs-stable-blue)](https://lcsb-biocore.github.io/SBML.jl/stable/) [![doc](https://img.shields.io/badge/docs-dev-blue)](https://lcsb-biocore.github.io/SBML.jl/dev/) |
Current status is "under development", something works, more wrapped stuff will
be added by need.
This is a simple wrap of some of the libSBML functionality, mainly the model loading for purposes of COBRA analysis methods.
Other functionality will be added as needed. Feel free to submit a PR that increases the loading "coverage".
## Usage
......@@ -11,7 +15,7 @@ be added by need.
using SBML
m = readSBML("myModel.xml")
# m is now a Model with
# m is now a Model structure with:
m.reactions
m.species
m.compartments
......
......@@ -2,7 +2,9 @@ using Documenter, SBML
makedocs(modules = [SBML],
clean = false,
format = Documenter.HTML(prettyurls = !("local" in ARGS)),
format = Documenter.HTML(
prettyurls = !("local" in ARGS),
canonical = "https://lcsb-biocore.github.io/DistributedData.jl/stable/"),
sitename = "SBML.jl",
authors = "The developers of SBML.jl",
linkcheck = !("skiplinks" in ARGS),
......@@ -16,5 +18,5 @@ deploydocs(
target = "build",
branch = "gh-pages",
devbranch = "develop",
versions = "stable" => "v^",
push_preview = true
)
"""
Part of a measurement unit definition that corresponds to the SBML definition of `Unit`. For example, "per square megahour", Mh^(-2), is written as:
Part of a measurement unit definition that corresponds to the SBML definition
of `Unit`. For example, the unit "per square megahour", Mh^(-2), is written as:
UnitPart("second", # base unit of time
-2, # exponent, says "per square"
6, # scale in powers of 10, says "mega"
1/3600) # second-to-hour multiplier
UnitPart("second", # base SI unit, this says we are measuring time
-2, # exponent, says "per square"
6, # log-10 scale of the unit, says "mega"
1/3600) # second-to-hour multiplier
Compound units (such as "volt-amperes" and "dozens of yards per ounce") are
built from multiple `UnitPart`s; see the definition of field `units` in
[`Model`](@ref).
"""
struct UnitPart
kind::String
......@@ -17,8 +22,9 @@ end
"""
Reaction with stoichiometry that assigns reactants and products their relative
consumption/production rates, lower/upper bounds (in tuples with unit names),
and objective coefficient.
consumption/production rates (accessible in field `stoichiometry`), lower/upper
bounds (in tuples `lb` and `ub`, with unit names), and objective coefficient
(`oc`).
"""
struct Reaction
stoichiometry::Dict{String,Float64}
......@@ -29,7 +35,8 @@ struct Reaction
end
"""
Species metadata -- human-readable name and compartment identifier
Species metadata -- contains a human-readable `name`, and a `compartment`
identifier
"""
struct Species
name::String
......@@ -38,8 +45,9 @@ struct Species
end
"""
Structure that collects the model-related data. Dictionaries are indexed by
identifiers of the corresponding objects.
Structure that collects the model-related data. Contains `units`,
`compartments`, `species` and `reactions`. The contained dictionaries are
indexed by identifiers of the corresponding objects.
"""
struct Model
units::Dict{String,Vector{UnitPart}}
......
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