Unverified Commit 09bbe567 authored by Laurent Heirendt's avatar Laurent Heirendt Committed by GitHub
Browse files

Merge pull request #241 from LCSB-BioCore/mo-small-fixes

Small fixes to the docs
parents b8406efb 36aa996a
...@@ -30,8 +30,9 @@ temp.* ...@@ -30,8 +30,9 @@ temp.*
.ipynb_checkpoints .ipynb_checkpoints
# add generated tutorial specifics # add generated tutorial specifics
!docs/src/notebooks/.git-keep !docs/src/notebooks/*.jl
docs/src/notebooks/ docs/src/notebooks/
# add generated docs and tutorial specifics # add generated docs and tutorial specifics
docs/src/index.md docs/src/index.md
docs/src/assets/output.gif docs/src/assets/output.gif
...@@ -13,7 +13,7 @@ else ...@@ -13,7 +13,7 @@ else
end end
# generate notebooks # generate notebooks
notebooks_path = joinpath(@__DIR__, "src", "notebooks-src") notebooks_path = joinpath(@__DIR__, "src", "notebooks")
notebooks = notebooks =
joinpath.(notebooks_path, filter(x -> endswith(x, ".jl"), readdir(notebooks_path))) joinpath.(notebooks_path, filter(x -> endswith(x, ".jl"), readdir(notebooks_path)))
notebooks_outdir = joinpath(@__DIR__, "src", "notebooks") notebooks_outdir = joinpath(@__DIR__, "src", "notebooks")
......
...@@ -10,17 +10,20 @@ ...@@ -10,17 +10,20 @@
# Constraint-Based Reconstruction and EXascale Analysis # Constraint-Based Reconstruction and EXascale Analysis
COBREXA is a toolkit for working with large constraint-based metabolic models, COBREXA is a toolkit for working with large constraint-based metabolic models,
and running very large number of analysis tasks on these models in parallel. and a running very large number of analysis tasks on these models in parallel.
Its main purpose is to make the methods of Constraint-based Reconstruction and Its main purpose is to make the methods of Constraint-based Reconstruction and
Analysis (COBRA) scale to problem sizes that require the use of huge computer Analysis (COBRA) scale to problem sizes that require the use of huge computer
clusters and HPC environment, which allows to realistically approach the clusters and HPC environments, which allows them to be realistically applied to
pre-exascale-sized models. pre-exascale-sized models.
In the package, you will find the usual COBRA-like functions that inteface to In this package, you will find the usual COBRA-like functions that interface to
the underlying linear programming solvers. We use underlying linear programming solvers. We use
[`JuMP.jl`](https://github.com/jump-dev/JuMP.jl) as the unified interface for [`JuMP.jl`](https://github.com/jump-dev/JuMP.jl) as the unified interface for
many solvers; you can plug in whatever compatible solver you want, including many solvers; you can plug in whichever compatible solver you want, including
the popular `Tulip.jl`, `GLPK.jl`, `OSQP.jl`, and `Gurobi`. the popular [`Tulip.jl`](https://github.com/ds4dm/Tulip.jl),
[`GLPK.jl`](https://github.com/jump-dev/GLPK.jl),
[`OSQP.jl`](https://github.com/oxfordcontrol/OSQP.jl), and
[`Gurobi.jl`](https://github.com/jump-dev/Gurobi.jl).
```@raw html ```@raw html
<div align="center"> <div align="center">
...@@ -35,7 +38,7 @@ Development history of COBREXA.jl. ...@@ -35,7 +38,7 @@ Development history of COBREXA.jl.
## Tutorials ## Tutorials
Detailed tutorial contents is [available here](tutorials.md). Detailed tutorial content is [available here](tutorials.md).
```@contents ```@contents
Pages = joinpath.("tutorials", filter(x -> endswith(x, ".md"), readdir("tutorials"))) Pages = joinpath.("tutorials", filter(x -> endswith(x, ".md"), readdir("tutorials")))
...@@ -59,6 +62,5 @@ Pages = ["functions.md"] ...@@ -59,6 +62,5 @@ Pages = ["functions.md"]
## Contribution guide ## Contribution guide
If you aim to contribute code, patches or improvements to `COBREXA.jl` read the If you wish to contribute code, patches or improvements to `COBREXA.jl`, please
basic guidelines at a separate page with [contribution guidelines and read the basic [contribution guidelines and hints.](howToContribute.md).
hints](howToContribute.md).
...@@ -80,7 +80,7 @@ m.reactions["R_GLNS"].metabolites["M_co2_e"] = 1.0 ...@@ -80,7 +80,7 @@ m.reactions["R_GLNS"].metabolites["M_co2_e"] = 1.0
There are other functions that may be used to change the StandardModel in a There are other functions that may be used to change the StandardModel in a
more systematic way. See the documentation of [`add!`](@ref), [`rm!`](@ref), more systematic way. See the documentation of [`add!`](@ref), [`rm!`](@ref),
[`add_reactions!`](@ref), and [`set_bound`](@ref) for examples. [`@add_reactions!`](@ref), and [`set_bound`](@ref) for examples.
## Analysis modifiers ## Analysis modifiers
......
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