various small things

.github/workflows/CompatHelper.yml

@@ -0,0 +1,43 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -0,0 +1,42 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1' # This is always the latest stable release in the 1.X series
+          #- '1.6' # LTS
+          #- 'nightly'
+        os:
+          - ubuntu-latest
+          #- macOS-latest
+          #- windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@latest
+      - run: |
+          git config --global user.name Tester
+          git config --global user.email [email protected]
+      - uses: julia-actions/julia-runtest@latest
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/pr-format.yml

@@ -0,0 +1,62 @@
+on:
+  pull_request:
+  issue_comment:
+    types: [created]
+
+name: Formatting
+
+jobs:
+  formatting:
+    if: github.event_name == 'pull_request' || (github.event_name == 'issue_comment' && github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'OWNER' || github.event.issue.user.id == github.event.comment.user.id) && startsWith(github.event.comment.body, '/format') )
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone the repository
+        uses: actions/checkout@v4
+      - name: Checkout the pull request code # this checks out the actual branch so that one can commit into it
+        if: github.event_name == 'issue_comment'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh pr checkout ${{ github.event.issue.number }}
+      - name: Install JuliaFormatter and format
+        run: |
+          julia --color=yes -e 'import Pkg; Pkg.add("JuliaFormatter")'
+          julia --color=yes -e 'using JuliaFormatter; format(".")'
+      - name: Remove trailing whitespace
+        run: |
+          find -name '*.jl' -or -name '*.md' -or -name '*.toml' -or -name '*.yml' | while read filename ; do
+            # remove any trailing spaces
+            sed --in-place -e 's/\s*$//' "$filename"
+            # add a final newline if missing
+            if [[ -s "$filename" && $(tail -c 1 "$filename" |wc -l) -eq 0 ]] ; then
+              echo >> "$filename"
+            fi
+            # squash superfluous final newlines
+            sed -i -e :a -e '/^\n*$/{$d;N;};/\n$/ba' "$filename"
+          done
+      - name: Fail on formatting problems
+        if: github.event_name == 'pull_request'
+        run: |
+          if git diff --exit-code --quiet
+          then echo "Looks OK"
+          else echo "Formatting fixes required!"; git diff -p ; exit 1
+          fi
+      - name: Commit fixes
+        if: github.event_name == 'issue_comment'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          if [ `git status -s | wc -l` -ne 0 ] ; then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "[email protected]"
+            git commit -a -m "automatic formatting" -m "triggered by @$GITHUB_ACTOR on PR #${{ github.event.issue.number }}"
+            if git push
+            then gh pr comment ${{ github.event.issue.number }} --body \
+              ":heavy_check_mark: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) succeeded, commited as `git rev-parse HEAD`"
+            else gh pr comment ${{ github.event.issue.number }} --body \
+              ":x: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) failed, perhaps someone pushed to the PR in the meantime?"
+            fi
+          else
+            gh pr comment ${{ github.event.issue.number }} --body \
+              ":sunny: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) succeeded, but the code was already formatted correctly."
+          fi

.gitignore

@@ -1,7 +1,10 @@
-/.vscode
-/vscode
-*.code-workspace
+/docs/build/
 Manifest.toml
 
-downloaded/*
-test/downloaded/*
+*.cov
+.*.swp
+
+.vscode
+*.code-workspace
+
+/test/test-models

Project.toml

@@ -11,8 +11,8 @@ ReadableRegex = "cbbcb084-453d-4c4c-b292-e315607ba6a4"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
-AbstractFBCModels = "0.2"
-DocStringExtensions = "0.9"
+AbstractFBCModels = "0.1, 0.2"
+DocStringExtensions = "0.8, 0.9"
 JSON = "0.21"
 
 [extras]

README.md

@@ -18,18 +18,19 @@ The primary purpose of this is to provide JSON loading functionality for
 [FBCModelTests.jl](https://github.com/LCSB-BioCore/FBCModelTests.jl), but is
 otherwise completely generic and can be used independently of these packages.
 
-You should be able to load JSON models (called `JSONFBCModel`) via the
+You should be able to load JSON models (of type  `JSONFBCModel`) via the
 AbstractFBCModels interface:
 
 ```julia
-import AbstractFBCModels as A
+import AbstractFBCModels as M
 import JSONFBCModels
 
-model = A.load("my_model.json")
-A.reactions(model) # accessors defined by the interface (NB: access through the overloads: A.xyz)
+model = M.load("my_model.json")
 ```
-See the docstrings of all the accessors available by entering `A.accessors()` in
-the REPL. For example:
+
+Documentation of
+[AbstractFBCModels.jl](https://github.com/COBREXA/AbstractFBCModels.jl)
+provides details on the use of the loaded model.
 
 #### Acknowledgements
 

src/interface.jl

@@ -47,28 +47,28 @@ JSONFBCModel(json::Dict{String,Any}) = begin
 
     JSONFBCModel(
         json,
-        Dict(_json_rxn_name(r, i) => i for (i, r) in enumerate(rs)),
+        Dict(extract_json_reaction_id(r, i) => i for (i, r) in enumerate(rs)),
         rs,
-        Dict(_json_met_name(m, i) => i for (i, m) in enumerate(ms)),
+        Dict(extract_json_metabolite_id(m, i) => i for (i, m) in enumerate(ms)),
         ms,
-        Dict(_json_gene_name(g, i) => i for (i, g) in enumerate(gs)),
+        Dict(extract_json_gene_id(g, i) => i for (i, g) in enumerate(gs)),
         gs,
     )
 end
 
 # model
 A.reactions(model::JSONFBCModel) =
-    String[_json_rxn_name(r, i) for (i, r) in enumerate(model.reactions)]
+    String[extract_json_reaction_id(r, i) for (i, r) in enumerate(model.reactions)]
 
 A.n_reactions(model::JSONFBCModel) = length(model.reactions)
 
 A.metabolites(model::JSONFBCModel) =
-    String[_json_met_name(m, i) for (i, m) in enumerate(model.metabolites)]
+    String[extract_json_metabolite_id(m, i) for (i, m) in enumerate(model.metabolites)]
 
 A.n_metabolites(model::JSONFBCModel) = length(model.metabolites)
 
 A.genes(model::JSONFBCModel) =
-    String[_json_gene_name(g, i) for (i, g) in enumerate(model.genes)]
+    String[extract_json_gene_id(g, i) for (i, g) in enumerate(model.genes)]
 
 A.n_genes(model::JSONFBCModel) = length(model.genes)
 
@@ -169,16 +169,12 @@ A.metabolite_name(model::JSONFBCModel, mid::String) =
 A.gene_name(model::JSONFBCModel, gid::String) =
     parse_name(get(model.genes[model.gene_index[gid]], "name", nothing))
 
-A.reaction_stoichiometry(model::JSONFBCModel, rid::String) =
+A.reaction_stoichiometry(model::JSONFBCModel, rid::String)::Dict{String,Float64} =
     model.reactions[model.reaction_index[rid]]["metabolites"]
 
 function A.metabolite_compartment(model::JSONFBCModel, mid::String)
     x = get(model.metabolites[model.metabolite_index[mid]], "compartment", nothing)
-    if isa(x, String)
-        return x
-    else
-        return nothing
-    end
+    return isa(x, String) ? x : nothing
 end
 
 function Base.convert(::Type{JSONFBCModel}, mm::A.AbstractFBCModel)

src/utils.jl

@@ -1,14 +1,14 @@
 
-_json_rxn_name(r, i) = string(get(r, "id", "rxn$i"))
+extract_json_reaction_id(r, i) = string(get(r, "id", "rxn$i"))
 
-_json_met_name(m, i) = string(get(m, "id", "met$i"))
+extract_json_metabolite_id(m, i) = string(get(m, "id", "met$i"))
 
-_json_gene_name(g, i) = string(get(g, "id", "gene$i"))
+extract_json_gene_id(g, i) = string(get(g, "id", "gene$i"))
 
 function parse_grr(str::Maybe{String})
     isnothing(str) && return nothing
     isempty(str) && return nothing
-    
+
     dnf = A.GeneAssociationDNF()
     for isozyme in string.(split(str, " or "))
         push!(
@@ -31,15 +31,17 @@ function parse_formula(x::Maybe{String})
     return res
 end
 
-function parse_charge(x)
+function parse_charge(x)::Maybe{Int}
     if isa(x, Int)
-        return x
+        x
     elseif isa(x, Float64)
-        return Int(x)::Int
+        Int(x)
     elseif isa(x, String)
-        return parse(Int, x)
-    else
+        Int(parse(Float64, x))
+    elseif isnothing(x)
         nothing
+    else
+        throw(DomainError(x, "cannot parse charge"))
     end
 end
 
@@ -53,7 +55,7 @@ function parse_annotations_or_notes(x)
         if isa(vs, String)
             a_or_n[k] = String[vs]
         else
-            a_or_n[k] = String[v for v in vs]    
+            a_or_n[k] = String[v for v in vs]
         end
     end
     return a_or_n

test/misc.jl

@@ -0,0 +1,25 @@
+
+@testset "Miscellaneous tests" begin
+    # the path is inherited from the main testset
+    model = A.load(JSONFBCModel, joinpath(@__DIR__, "test-models", "iML1515.json"))
+    # test that no superfluous keys are generated
+    @test all(
+        key in ["metabolites", "id", "compartments", "reactions", "version", "genes"] for
+        key in keys(model.json)
+    )
+
+    # caps suffix is quite common
+    @test all(suffix in A.filename_extensions(JSONFBCModel) for suffix in ["json", "JSON"])
+end
+
+@testset "Corner cases" begin
+    import JSONFBCModels: parse_charge
+
+    @test parse_charge(1) == 1
+    @test parse_charge(2.0) == 2
+    @test parse_charge("3") == 3
+    @test parse_charge("4.0") == 4
+    @test parse_charge(nothing) == nothing
+    @test_throws ArgumentError parse_charge("totally positive charge")
+    @test_throws DomainError parse_charge(["very charged"])
+end