Merge pull request #620 from LCSB-BioCore/develop

Develop→master for 1.3.1

.github/workflows/pr-cmd-format.yml

@@ -0,0 +1,53 @@
+
+on:
+  issue_comment:
+    types: [created]
+
+name: PR auto-formatting command
+
+jobs:
+  format:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.issue.user.id == github.event.comment.user.id) && startsWith(github.event.comment.body, '/format') }}
+    name: auto-format
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone the repository
+        uses: actions/checkout@v2
+      - name: Checkout the pull request code
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh pr checkout ${{ github.event.issue.number }}
+      - name: Install JuliaFormatter and format
+        run: |
+          julia -e 'import Pkg; Pkg.add("JuliaFormatter")'
+          julia -e 'using JuliaFormatter; format(".")'
+      - name: Remove trailing whitespace
+        run: |
+          find -name '*.jl' -or -name '*.md' -or -name '*.toml' -or -name '*.yml' | while read filename ; do
+            # remove any trailing spaces
+            sed --in-place -e 's/\s*$//' "$filename"
+            # add a final newline if missing
+            if [[ -s "$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: Commit and push the changes
+        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
+            echo "No changes, all good!"
+          fi

.github/workflows/pr-formatcheck.yml

@@ -0,0 +1,41 @@
+
+on:
+  pull_request:
+
+name: Formatting check
+
+jobs:
+  formatcheck:
+    name: check-code-format
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the code
+        uses: actions/checkout@v2
+      - name: Install JuliaFormatter and format
+        run: |
+          julia -e 'import Pkg; Pkg.add("JuliaFormatter")'
+          julia -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: Report any problems
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          if [ `git status -s | wc -l` -ne 0 ]
+          then gh pr comment ${{ github.event.number }} --body \
+          ":red_square:  Commit ${{ github.event.pull_request.head.sha }} requires formatting!\
+          "$'\n\n'"Required formatting changes summary:\
+          "$'\n```\n'"`git diff --stat`"$'\n```'
+          else gh pr comment ${{ github.event.number }} --body \
+          ":green_circle:  Commit ${{ github.event.pull_request.head.sha }} is formatted properly."
+          fi

.gitlab-ci.yml

@@ -189,44 +189,6 @@ mac:julia1.6:
   <<: *global_julia16
   <<: *global_env_mac
 
-#
-# CODE FORMAT CHECKER
-#
-
-format:
-  stage: test
-  script:
-    - |
-      docker run -v "$PWD":/project $CI_REGISTRY/r3/docker/julia-custom julia -e 'using JuliaFormatter; format("/project", verbose=true);'
-    - |
-      if [ `docker run -i -v "$PWD":/git alpine/git status -s | wc -l` -ne 0 ] ; then
-        GITHUB_COMMENT=":red_square: &nbsp;Commit ${CI_COMMIT_SHORT_SHA} requires formatting!\
-      "$'\n\n'"Required formatting changes summary:\
-      "$'\n```\n'"`docker run -i -v \"$PWD\":/git alpine/git diff --stat`"$'\n```'
-      else
-        GITHUB_COMMENT=":green_circle: &nbsp;Commit ${CI_COMMIT_SHORT_SHA} is formatted properly."
-      fi
-    - |
-      export GITHUB_TOKEN="${GITHUB_ACCESS_TOKEN_FORMATTER}"
-      export GITHUB_OWNER="lcsb-biocore"
-      export GITHUB_REPO="cobrexa.jl"
-      export GITHUB_COMMENT_TYPE=pr
-      export GITHUB_PR_ISSUE_NUMBER="${CI_EXTERNAL_PULL_REQUEST_IID}"
-      export GITHUB_COMMENT_FORMAT=""
-      export GITHUB_COMMENT
-    - |
-      docker run -i --rm \
-            -e GITHUB_TOKEN \
-            -e GITHUB_OWNER \
-            -e GITHUB_REPO \
-            -e GITHUB_COMMENT_TYPE \
-            -e GITHUB_PR_ISSUE_NUMBER \
-            -e GITHUB_COMMENT_FORMAT \
-            -e GITHUB_COMMENT \
-            cloudposse/github-commenter
-  <<: *global_dind
-  <<: *global_trigger_pull_request
-
 #
 # ASSETS
 #

Project.toml

@@ -1,7 +1,7 @@
 name = "COBREXA"
 uuid = "babc4406-5200-4a30-9033-bf5ae714c842"
 authors = ["The developers of COBREXA.jl"]
-version = "1.3.0"
+version = "1.3.1"
 
 [deps]
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"

docs/src/functions/types.md

@@ -12,3 +12,9 @@ Pages = map(file -> joinpath("base", "types", "abstract", file), readdir("../src
 Modules = [COBREXA]
 Pages = map(file -> joinpath("base", "types", file), readdir("../src/base/types"))
 ```
+
+## Model type wrappers
+```@autodocs
+Modules = [COBREXA]
+Pages = map(file -> joinpath("base", "types", "wrappers", file), readdir("../src/base/types/wrappers"))
+```

src/analysis/gecko.jl

@@ -147,24 +147,15 @@ function make_gecko_model(
         push!(coupling_row_mass_group, _gecko_capacity(grp, idxs, mms, gmgb_(grp)))
     end
 
-    # create model with dummy objective
-    gm = GeckoModel(
-        spzeros(length(columns) + length(coupling_row_gene_product)),
+    GeckoModel(
+        [
+            _gecko_reaction_column_reactions(columns, model)' * objective(model)
+            spzeros(length(coupling_row_gene_product))
+        ],
         columns,
         coupling_row_reaction,
         collect(zip(coupling_row_gene_product, gpb_.(gids[coupling_row_gene_product]))),
         coupling_row_mass_group,
         model,
     )
-
-    #=
-    Set objective. This is a separate field because gene products can also be objectives. 
-    This way they can be set as objectives by the user.
-    =#
-    gm.objective .= [
-        _gecko_reaction_column_reactions(gm)' * objective(gm.inner)
-        spzeros(length(coupling_row_gene_product))
-    ]
-
-    return gm
 end

src/analysis/sampling/warmup_variability.jl

@@ -71,7 +71,7 @@ function warmup_from_variability(
         end
     )
 
-    map(fetch, save_at.(workers, :cobrexa_sampling_warmup_optmodel, Ref(save_model)))
+    asyncmap(fetch, save_at.(workers, :cobrexa_sampling_warmup_optmodel, Ref(save_model)))
 
     fluxes = hcat(
         dpmap(
@@ -92,7 +92,7 @@ function warmup_from_variability(
     )
 
     # free the data on workers
-    map(fetch, remove_from.(workers, :cobrexa_sampling_warmup_optmodel))
+    asyncmap(fetch, remove_from.(workers, :cobrexa_sampling_warmup_optmodel))
 
     return fluxes, lbs, ubs
 end

src/analysis/screening.jl

@@ -129,9 +129,9 @@ function _screen_impl(
     workers = [myid()],
 )::Array where {V<:AbstractVector,A,N}
 
-    map(fetch, save_at.(workers, :cobrexa_screen_variants_model, Ref(model)))
-    map(fetch, save_at.(workers, :cobrexa_screen_variants_analysis_fn, Ref(analysis)))
-    map(fetch, get_from.(workers, Ref(:(precache!(cobrexa_screen_variants_model)))))
+    asyncmap(fetch, save_at.(workers, :cobrexa_screen_variants_model, Ref(model)))
+    asyncmap(fetch, save_at.(workers, :cobrexa_screen_variants_analysis_fn, Ref(analysis)))
+    asyncmap(fetch, get_from.(workers, Ref(:(precache!(cobrexa_screen_variants_model)))))
 
     res = pmap(
         (vars, args)::Tuple -> screen_variant(
@@ -144,8 +144,8 @@ function _screen_impl(
         zip(variants, args),
     )
 
-    map(fetch, remove_from.(workers, :cobrexa_screen_variants_model))
-    map(fetch, remove_from.(workers, :cobrexa_screen_variants_analysis_fn))
+    asyncmap(fetch, remove_from.(workers, :cobrexa_screen_variants_model))
+    asyncmap(fetch, remove_from.(workers, :cobrexa_screen_variants_analysis_fn))
 
     return res
 end
@@ -276,7 +276,7 @@ function _screen_optmodel_modifications_impl(
     workers = [myid()],
 )::Array where {V<:AbstractVector,VF<:AbstractVector,A,N}
 
-    map(
+    asyncmap(
         fetch,
         save_at.(
             workers,
@@ -290,12 +290,15 @@ function _screen_optmodel_modifications_impl(
             ),
         ),
     )
-    map(fetch, save_at.(workers, :cobrexa_screen_optmodel_modifications_fn, Ref(analysis)))
+    asyncmap(
+        fetch,
+        save_at.(workers, :cobrexa_screen_optmodel_modifications_fn, Ref(analysis)),
+    )
 
     res = pmap(_screen_optmodel_item, CachingPool(workers), zip(modifications, args))
 
-    map(fetch, remove_from.(workers, :cobrexa_screen_optmodel_modifications_data))
-    map(fetch, remove_from.(workers, :cobrexa_screen_optmodel_modifications_fn))
+    asyncmap(fetch, remove_from.(workers, :cobrexa_screen_optmodel_modifications_data))
+    asyncmap(fetch, remove_from.(workers, :cobrexa_screen_optmodel_modifications_fn))
 
     return res
 end

src/base/solver.jl

@@ -19,16 +19,18 @@ function make_optimization_model(model::MetabolicModel, optimizer; sense = MAX_S
     xl, xu = bounds(model)
 
     optimization_model = Model(optimizer)
-    @variable(optimization_model, x[i = 1:n])
+    @variable(optimization_model, x[1:n])
     @objective(optimization_model, sense, objective(model)' * x)
     @constraint(optimization_model, mb, stoichiometry(model) * x .== balance(model)) # mass balance
     @constraint(optimization_model, lbs, xl .<= x) # lower bounds
     @constraint(optimization_model, ubs, x .<= xu) # upper bounds
 
     C = coupling(model) # empty if no coupling
-    cl, cu = coupling_bounds(model)
-    isempty(C) || @constraint(optimization_model, c_lbs, cl .<= C * x) # coupling lower bounds
-    isempty(C) || @constraint(optimization_model, c_ubs, C * x .<= cu) # coupling upper bounds
+    isempty(C) || begin
+        cl, cu = coupling_bounds(model)
+        @constraint(optimization_model, c_lbs, cl .<= C * x) # coupling lower bounds
+        @constraint(optimization_model, c_ubs, C * x .<= cu) # coupling upper bounds
+    end
 
     return optimization_model
 end

src/base/types/MetabolicModel.jl

@@ -12,7 +12,14 @@ _missing_impl_error(m, a) = throw(MethodError(m, a))
 """
     reactions(a::MetabolicModel)::Vector{String}
 
-Return a vector of reaction identifiers in a model.
+Return a vector of reaction identifiers in a model. The vector precisely
+corresponds to the columns in [`stoichiometry`](@ref) matrix.
+
+For technical reasons, the "reactions" may sometimes not be true reactions but
+various virtual and helper pseudo-reactions that are used in the metabolic
+modeling, such as metabolite exchanges, separate forward and reverse reactions,
+supplies of enzymatic and genetic material and virtual cell volume, etc. To
+simplify the view of the model contents use [`reaction_flux`](@ref).
 """
 function reactions(a::MetabolicModel)::Vector{String}
     _missing_impl_error(reactions, (a,))
@@ -21,7 +28,11 @@ end
 """
     metabolites(a::MetabolicModel)::Vector{String}
 
-Return a vector of metabolite identifiers in a model.
+Return a vector of metabolite identifiers in a model. The vector precisely
+corresponds to the rows in [`stoichiometry`](@ref) matrix.
+
+As with [`reactions`](@ref)s, some metabolites in models may be virtual,
+representing purely technical equality constraints.
 """
 function metabolites(a::MetabolicModel)::Vector{String}
     _missing_impl_error(metabolites, (a,))