From 9e9772f78d75589cdc2e5b804a0516c7ef5ae279 Mon Sep 17 00:00:00 2001 From: CompatHelper Julia Date: Sat, 2 May 2026 00:44:44 +0000 Subject: [PATCH 1/5] CompatHelper: bump compat for Symbolics in [extras] to 7, (keep existing compat) --- Project.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index 842cef8..569e14a 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "SBML" uuid = "e5567a89-2604-4b09-9718-f5f78e97c3bb" -authors = ["The developers of SBML.jl"] version = "1.6" +authors = ["The developers of SBML.jl"] [deps] DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" @@ -16,7 +16,7 @@ ConstructionBase = "1.3" DocStringExtensions = "0.8, 0.9" IfElse = "0.1" SBML_jll = "5.19.5" -Symbolics = "5,6" +Symbolics = "5,6, 7" Unitful = "1" julia = "1.6" From 3e38a58dabd352c4b4c6228fe123993d07efd128 Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Sat, 2 May 2026 09:16:33 +0200 Subject: [PATCH 2/5] fix tests for symbolics 7 --- test/loadmodels.jl | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/test/loadmodels.jl b/test/loadmodels.jl index a843fdf..a499b3d 100644 --- a/test/loadmodels.jl +++ b/test/loadmodels.jl @@ -345,7 +345,11 @@ end m = readSBML(joinpath(@__DIR__, "data", "01565-sbml-l3v1.xml")) if TEST_SYMBOLICS - @test interpret_as_num(m.reactions["J23"].kinetic_math) == 0.0 + @variables S23 S23b + @test isequal( + interpret_as_num(m.reactions["J23"].kinetic_math), + (S23*S23b*log(1)) / log(10), + ) @variables S29 S29b @test isequal(interpret_as_num(m.reactions["J29"].kinetic_math), 2.0 * S29 * S29b) From cdc112eed04d261539d6930d8e29e6e47ca8cad8 Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Sat, 2 May 2026 09:16:47 +0200 Subject: [PATCH 3/5] push symbolics dep forward --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 569e14a..1a60996 100644 --- a/Project.toml +++ b/Project.toml @@ -16,7 +16,7 @@ ConstructionBase = "1.3" DocStringExtensions = "0.8, 0.9" IfElse = "0.1" SBML_jll = "5.19.5" -Symbolics = "5,6, 7" +Symbolics = "7" Unitful = "1" julia = "1.6" From e2a72e011df9ee6a62748a1aa32717bbfcc8d7ba Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Sat, 2 May 2026 09:30:45 +0200 Subject: [PATCH 4/5] mark broken --- test/loadmodels.jl | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/test/loadmodels.jl b/test/loadmodels.jl index a499b3d..a1ce562 100644 --- a/test/loadmodels.jl +++ b/test/loadmodels.jl @@ -345,11 +345,8 @@ end m = readSBML(joinpath(@__DIR__, "data", "01565-sbml-l3v1.xml")) if TEST_SYMBOLICS - @variables S23 S23b - @test isequal( - interpret_as_num(m.reactions["J23"].kinetic_math), - (S23*S23b*log(1)) / log(10), - ) + # TODO: some future symbolics experts are welcome to fix this + @test_broken isequal(interpret_as_num(m.reactions["J23"].kinetic_math), 0.0) @variables S29 S29b @test isequal(interpret_as_num(m.reactions["J29"].kinetic_math), 2.0 * S29 * S29b) From 9b49bed78ad6305cc7d7bcbac6428d2f3266d7ea Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Fri, 14 Aug 2026 13:56:07 +0200 Subject: [PATCH 5/5] ok let's just provide both variants --- test/loadmodels.jl | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/test/loadmodels.jl b/test/loadmodels.jl index a1ce562..7029ba8 100644 --- a/test/loadmodels.jl +++ b/test/loadmodels.jl @@ -345,8 +345,14 @@ end m = readSBML(joinpath(@__DIR__, "data", "01565-sbml-l3v1.xml")) if TEST_SYMBOLICS - # TODO: some future symbolics experts are welcome to fix this - @test_broken isequal(interpret_as_num(m.reactions["J23"].kinetic_math), 0.0) + # Older versions of symbolics somehow auto-simplify this, newer ones do not. + @variables S23 S23b + @test ( + isequal(interpret_as_num(m.reactions["J23"].kinetic_math), 0.0) || isequal( + interpret_as_num(m.reactions["J23"].kinetic_math), + S23 * S23b * log(Num(1)) / log(Num(10)), + ) + ) @variables S29 S29b @test isequal(interpret_as_num(m.reactions["J29"].kinetic_math), 2.0 * S29 * S29b)