Commit 2e17aae2 authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
Browse files

clean and build the docs

Refs #2
parent 3d36eaf3
# ref: https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#GitHub-Actions-1
name: Documentation
on:
push:
branches:
- master
- develop
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
......@@ -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, "per square megahour", Mh^(-2), is written as:
UnitPart("second", # base unit of time
-2, # exponent, says "per square"
......@@ -17,8 +18,9 @@ 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}
......@@ -38,8 +40,9 @@ 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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