Merge pull request #21 from isaacsas/updates

updates

.github/workflows/CompatHelper.yml

@@ -0,0 +1,26 @@
+name: CompatHelper
+
+on:
+  schedule:
+    - cron: '00 * * * *'
+  issues:
+    types: [opened, reopened]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.3.0]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

README.md

@@ -3,20 +3,29 @@
 [![Build Status](https://travis-ci.org/isaacsas/ReactionNetworkImporters.jl.svg?branch=master)](https://travis-ci.org/isaacsas/ReactionNetworkImporters.jl)
 [![Build status](https://ci.appveyor.com/api/projects/status/wqq5flk2w8asad78/branch/master?svg=true)](https://ci.appveyor.com/project/isaacsas/reactionnetworkimporters-jl/branch/master)
 
+*Note, v0.2.0 is a breaking release in that ReactionNetworkImporters now
+generates a Catalyst.jl `ReactionSystem`. Do not upgrade if you rely on the
+previous DiffEqBiological.jl reaction network representation.*
+
 This package provides importers to load reaction networks into
 [Catalyst.jl](https://github.com/SciML/Catalyst.jl)
 [`ReactionSystem`s](https://catalyst.sciml.ai/dev/api/catalyst_api/#ModelingToolkit.ReactionSystem)
 from several file formats. Currently it supports loading networks in the
 following formats:
 1. A *subset* of the BioNetGen .net file format.
-2. Networks represented by dense or sparse substrate and product stoichiometric matrices.
+2. Networks represented by dense or sparse substrate and product stoichiometric
+   matrices.
 <!-- 3. The basic format used by the [RSSA](https://www.cosbi.eu/research/prototypes/rssa) group at COSBI in their [model collection](https://www.cosbi.eu/prototypes/jLiexDeBIgFV4zxwnKiW97oc4BjTtIoRGajqdUz4.zip). -->
 
 ----
 ## Examples
 
 ### Loading a BioNetGen .net file
-A simple network from the builtin BioNetGen bngl examples is the [repressilator](data/repressilator/Repressilator.bngl). The `generate_network` command in the bngl file outputs a reduced network description, i.e. a [.net](data/repressilator/Repressilator.net) file, which can be loaded into a Catalyst `ReactionSystem` as:
+A simple network from the builtin BioNetGen bngl examples is the
+[repressilator](data/repressilator/Repressilator.bngl). The `generate_network`
+command in the bngl file outputs a reduced network description, i.e. a
+[.net](data/repressilator/Repressilator.net) file, which can be loaded into a
+Catalyst `ReactionSystem` as:
 ```julia
 using ReactionNetworkImporters
 fname = "PATH/TO/Repressilator.net"
@@ -27,11 +36,19 @@ Here `BNGNetwork` is a type specifying the file format that is being loaded.
 - `rn`, a Catalyst `reaction_network`
 - `u₀`, the initial condition (as a `Vector{Float64}`)
 - `p`, the parameter vector (as a `Vector{Float64}`)
-- `paramexprs`, the parameter vector as a mix of `Numbers`, `Symbols` and `Exprs`. `p` is generated by evaluation of these expressions and symbols.
-- `varstonames`, a `Dict` mapping from the internal `Symbol` of a species used in the generated `ReactionSystem` to a `Symbol` generated from the name in the .net file. This is necessary as BioNetGen can generate exceptionally long species names, involving characters that lead to malformed species names when used with `Catalyst`.
-- `groupstoids`, a `Dict` mapping the `Symbol`s (i.e. names) for any species groups defined in the .net file to a vector of indices into `u₀` where the corresponding species are stored.
+- `paramexprs`, the parameter vector as a mix of `Numbers`, `Symbols` and
+  `Exprs`. `p` is generated by evaluation of these expressions and symbols.
+- `varstonames`, a `Dict` mapping from the internal `Symbol` of a species used
+  in the generated `ReactionSystem` to a `Symbol` generated from the name in the
+  .net file. This is necessary as BioNetGen can generate exceptionally long
+  species names, involving characters that lead to malformed species names when
+  used with `Catalyst`.
+- `groupstoids`, a `Dict` mapping the `Symbol`s (i.e. names) for any species
+  groups defined in the .net file to a vector of indices into `u₀` where the
+  corresponding species are stored.
 
-Given `prnbng`, we can construct and solve the corresponding ODE model for the reaction system by
+Given `prnbng`, we can construct and solve the corresponding ODE model for the
+reaction system by
 ```julia
 using OrdinaryDiffEq, Catalyst
 rn = prnbng.rn
@@ -85,8 +102,8 @@ prn = loadrxnetwork(MatrixNetwork(),
                     rateexprs::AbstractVector, 
                     substoich::AbstractMatrix, 
                     prodstoich::AbstractMatrix; 
-                    species=Symbol[], 
-                    params=Symbol[])
+                    species::AbstractVector=Operation[], 
+                    params::AbstractVector=Operation[])
 ```
 Here `MatrixNetwork()` is the dispatch type, which selects that we are
 constructing a matrix-based stoichiometric representation as input. The other
@@ -102,8 +119,10 @@ parameters are:
 - `prodstoich` - A number of species by number of reactions matrix with entry
   `(i,j)` giving the stoichiometric coefficient of species `i` as a product in
   reaction `j`.
-- `species` - Optional `ModelingToolkit.Operation`s representing each species in the network.
-- `parameters` - Optional `ModelingToolkit.Operation`s representing each parameter in the network.
+- `species` - Optional `ModelingToolkit.Operation`s representing each species in
+  the network.
+- `parameters` - Optional `ModelingToolkit.Operation`s representing each
+  parameter in the network.
 
 `prn` is again a `ParsedReactionNetwork`, with only the `reaction_network`
 field, `prn.rn`, defined.
@@ -114,7 +133,7 @@ A dispatch is added if `substoich` and `prodstoich` both have the type
 
 If the keyword argument `species` is not set, the resulting reaction network
 will simply name the species `S1`, `S2`,..., `SN` for a system with `N` total
-species. `params` defaults to an empty vector of `Symbol`s, so that it does not
+species. `params` defaults to an empty vector of `Operation`s, so that it does not
 need to be set for systems with no parameters.
 
 <!-- ### Loading a RSSA format network file

examples/test_bcr_odes.jl

@@ -6,7 +6,7 @@ using ReactionNetworkImporters
 using TimerOutputs
 
 # parameters
-doplot = true
+doplot = false
 networkname = "testbcrbng"
 tf = 10000.
 build_jac = false
@@ -31,7 +31,7 @@ show(to)
 rnbng = prnbng.rn; u0 = prnbng.u₀; p = prnbng.p; 
 @timeit to "bODESystem" bosys = convert(ODESystem, rnbng)
 show(to)
-@timeit to "bODEProb" boprob = ODEProblem(bosys, Pair.(species(rnbng,u0), (0.,tf), Pair.(params(rnbng),p))
+@timeit to "bODEProb" boprob = ODEProblem(bosys, Pair.(species(rnbng),u0), (0.,tf), Pair.(params(rnbng),p))
 show(to)
 u = copy(u0);
 du = similar(u);
@@ -47,8 +47,8 @@ show(to)
 println()
 
 # BNG simulation results for Activated Syk
-asykgroups = prnbng.groupstoids[!,:Activated_Syk]
-asyksyms = findall(x -> x ∈ asykgroups, rnbng.syms_to_ints)
+asykgroups = prnbng.groupstoids[:Activated_Syk]
+#asyksyms = findall(x -> x ∈ asykgroups, rnbng.syms_to_ints)
 # asynbng = zeros(length(gdatdf[:time]))
 # for sym in asyksyms
 #     global asynbng
@@ -72,14 +72,14 @@ basyk = sum(bsol[asykgroups,:], dims=1)
 
 if doplot
     plotlyjs()
-    plot(gdatdf[!,:time][2:end], gdatdf[!,:Activated_Syk][2:end], xscale=:log10, label=:AsykGroup, linestyle=:dot)
+    plot(gdatdf[!,:time][2:end], gdatdf[!,:Activated_Syk][2:end], xscale=:log10, label="AsykGroup", linestyle=:dot)
 #     # plot!(cdatdf[:time][2:end], asynbng[2:end], xscale=:log10, label=:AsykSum)
-    plot!(bsol.t[2:end], basyk'[2:end], label=:AsykDEBio, xscale=:log10)
+    plot!(bsol.t[2:end], basyk'[2:end], label="AsykDEBio", xscale=:log10)
 end
 
 # test the error, note may be large in abs value though small relatively
 # #norm(gdatdf[:Activated_Syk] - asynbng, Inf)
 # #norm(asynbng - basyk', Inf)
 norm(gdatdf[!,:Activated_Syk] - basyk', Inf)
 
-@assert all(abs.(gdatdf[:Activated_Syk] - asynbng) .< 1e-6 * abs.(gdatdf[:Activated_Syk]))
+#@assert all(abs.(gdatdf[!,:Activated_Syk] - basyk') .< 1e-6 * abs.(gdatdf[:Activated_Syk]))

src/parsing_routines_matrixnetworks.jl

@@ -70,8 +70,8 @@ function loadrxnetwork(ft::MatrixNetwork,
                         rateexprs::AbstractVector, 
                         substoich::SparseMatrixCSC, 
                         prodstoich::SparseMatrixCSC; 
-                        species=Symbol[], 
-                        params=Symbol[])
+                        species::AbstractVector=Operation[], 
+                        params::AbstractVector=Operation[])
 
     sz = size(substoich)
     @assert sz == size(prodstoich)