update readme, format benchmark dir

sumiya11 · Sep 17, 2024 · 249dab4 · 249dab4
1 parent 3649358
commit 249dab4
Show file tree

Hide file tree

Showing 30 changed files with 188 additions and 718 deletions.
diff --git a/README.md b/README.md
@@ -38,17 +38,13 @@ It works with polynomials from AbstractAlgebra.jl, DynamicPolynomials.jl, and Ne
 
 ### with AbstractAlgebra.jl
 
-We create a ring of polynomials in 3 variables
+We create a ring of polynomials in 3 variables and a simple polynomial system
 
 ```julia
 using AbstractAlgebra
 
 R, (x1, x2, x3) = QQ["x1", "x2", "x3"]
-```
-
-Then, we can define a simple polynomial system
 
-```julia
 system = [
   x1 + x2 + x3,
   x1*x2 + x1*x3 + x2*x3,
@@ -66,9 +62,9 @@ G = groebner(system)
 ```julia
 # result
 3-element Vector{AbstractAlgebra.Generic.MPoly{Rational{BigInt}}}:
- x1 + x2 + x3
- x2^2 + x2*x3 + x3^2
  x3^3 - 1
+ x2^2 + x2*x3 + x3^2
+ x1 + x2 + x3
 ```
 
 ### with DynamicPolynomials.jl
@@ -86,10 +82,10 @@ G = groebner(system)
 ```
 ```julia
 # result
-3-element Vector{Polynomial{DynamicPolynomials.Commutative{DynamicPolynomials.CreationOrder}, Graded{LexOrder}, Int64}}:
- 10x2 - 10x1 - 11x2² + 11x1²
- 110 - 121x2 - 100x2² + 100x1x2 + 110x2³
- 10 - 11x1 + 10x1x2²
+3-element Vector{Polynomial{DynamicPolynomials.Commutative{DynamicPolynomials.CreationOrder}, Graded{LexOrder}, Rational{BigInt}}}:
+ 10//11x2 - 10//11x1 - x2² + x1²
+ 1//1 - 11//10x2 - 10//11x2² + 10//11x1x2 + x2³
+ 1//1 - 11//10x1 + x1x2²
 ```
 
 ## Contacts

diff --git a/benchmark/CI-scripts/run_benchmarks.jl b/benchmark/CI-scripts/run_benchmarks.jl
@@ -112,10 +112,7 @@ push!(
     (
         problem_name="groebner,AA,2^30+3,yang1",
         type=:time,
-        result=compute_gb(
-            Groebner.Examples.yang1(internal_ordering=:degrevlex, k=GF(2^30 + 3)),
-            2
-        )
+        result=compute_gb(Groebner.Examples.yang1(internal_ordering=:degrevlex, k=GF(2^30 + 3)), 2)
     )
 )
 push!(
@@ -148,11 +145,7 @@ push!(
         result=[
             sum(
                 compute_gb(
-                    Groebner.Examples.cyclicn(
-                        6,
-                        internal_ordering=:degrevlex,
-                        k=GF(2^30 + 3)
-                    ),
+                    Groebner.Examples.cyclicn(6, internal_ordering=:degrevlex, k=GF(2^30 + 3)),
                     2000
                 )
             )
@@ -165,12 +158,7 @@ push!(
         problem_name="groebner,AA,QQ,100xchandra 7",
         type=:time,
         result=[
-            sum(
-                compute_gb(
-                    Groebner.Examples.chandran(7, internal_ordering=:degrevlex, k=QQ),
-                    100
-                )
-            )
+            sum(compute_gb(Groebner.Examples.chandran(7, internal_ordering=:degrevlex, k=QQ), 100))
         ]
     )
 )
@@ -221,9 +209,7 @@ push!(
     (
         problem_name="groebner,AA,100 vars drl",
         type=:time,
-        result=compute_gb(
-            n_variable_set(100, internal_ordering=:degrevlex, k=GF(2^31 - 1))
-        )
+        result=compute_gb(n_variable_set(100, internal_ordering=:degrevlex, k=GF(2^31 - 1)))
     )
 )
 
@@ -343,19 +329,15 @@ push!(
     (
         problem_name="groebner,AA,QQ,katsura 8",
         type=:time,
-        result=compute_gb(
-            Groebner.Examples.katsuran(8, internal_ordering=:degrevlex, k=QQ)
-        )
+        result=compute_gb(Groebner.Examples.katsuran(8, internal_ordering=:degrevlex, k=QQ))
     )
 )
 push!(
     suite,
     (
         problem_name="groebner,Nemo,QQ,katsura 8",
         type=:time,
-        result=compute_gb(
-            Groebner.Examples.katsuran(8, internal_ordering=:degrevlex, k=Nemo.QQ)
-        )
+        result=compute_gb(Groebner.Examples.katsuran(8, internal_ordering=:degrevlex, k=Nemo.QQ))
     )
 )
 push!(
@@ -379,10 +361,7 @@ push!(
     (
         problem_name="groebner,AA,QQ,noon 8",
         type=:time,
-        result=compute_gb(
-            Groebner.Examples.noonn(8, internal_ordering=:degrevlex, k=QQ),
-            3
-        )
+        result=compute_gb(Groebner.Examples.noonn(8, internal_ordering=:degrevlex, k=QQ), 3)
     )
 )
 push!(

diff --git a/benchmark/benchmark_systems.jl b/benchmark/benchmark_systems.jl
@@ -68,18 +68,9 @@ function benchmark_set_1()
         ("NFkB (w.)", NFkB_with_weights(k=ground_field)),
         ("Goodwin (w.)", Goodwin_with_weights(k=ground_field)),
         ("yang1", Groebner.Examples.yang1(internal_ordering=:degrevlex, k=ground_field)),
-        (
-            "bayes148",
-            Groebner.Examples.bayes148(internal_ordering=:degrevlex, k=ground_field)
-        ),
-        (
-            "gametwo2",
-            Groebner.Examples.gametwo2(internal_ordering=:degrevlex, k=ground_field)
-        ),
-        (
-            "jason210",
-            Groebner.Examples.jason210(internal_ordering=:degrevlex, k=ground_field)
-        ),
+        ("bayes148", Groebner.Examples.bayes148(internal_ordering=:degrevlex, k=ground_field)),
+        ("gametwo2", Groebner.Examples.gametwo2(internal_ordering=:degrevlex, k=ground_field)),
+        ("jason210", Groebner.Examples.jason210(internal_ordering=:degrevlex, k=ground_field)),
         ("alea6", Groebner.Examples.alea6(internal_ordering=:degrevlex, k=ground_field)),
         ("mayr42", Groebner.Examples.mayr42(internal_ordering=:degrevlex, k=ground_field)),
         ("BIOMD0000000103", BIOMD0000000103(k=ground_field)),
@@ -150,10 +141,7 @@ function benchmark_set_3()
         ("reimer 6", Groebner.Examples.reimern(6, k=ground_field)),
         ("reimer 7", Groebner.Examples.reimern(7, k=ground_field)),
         ("reimer 8", Groebner.Examples.reimern(8, k=ground_field)),
-        (
-            "chandra 9",
-            Groebner.Examples.chandran(9, k=ground_field, internal_ordering=:degrevlex)
-        ),
+        ("chandra 9", Groebner.Examples.chandran(9, k=ground_field, internal_ordering=:degrevlex)),
         (
             "chandra 10",
             Groebner.Examples.chandran(10, k=ground_field, internal_ordering=:degrevlex)
@@ -170,10 +158,7 @@ function benchmark_set_3()
             "chandra 13",
             Groebner.Examples.chandran(13, k=ground_field, internal_ordering=:degrevlex)
         ),
-        (
-            "ipp",
-            Groebner.Examples.ipp(k=ground_field, tol=0.0, internal_ordering=:degrevlex)
-        )
+        ("ipp", Groebner.Examples.ipp(k=ground_field, tol=0.0, internal_ordering=:degrevlex))
     ]
 
     (name="The rationals", field=ground_field, systems=systems)
@@ -253,8 +238,7 @@ end
 
 function benchmark_set_9()
     ground_field = AbstractAlgebra.QQ
-    systems =
-        [("BIOMD0000000103", BIOMD0000000103()), ("BIOMD0000000123", BIOMD0000000123())]
+    systems = [("BIOMD0000000103", BIOMD0000000103()), ("BIOMD0000000123", BIOMD0000000123())]
     (name="BIOMD, the rationals", field=ground_field, systems=systems)
 end
 

diff --git a/benchmark/generate/benchmark_generators.jl b/benchmark/generate/benchmark_generators.jl
@@ -1,12 +1,5 @@
 
-function generate_benchmark_source_for_groebner(
-    name,
-    system,
-    dir,
-    validate,
-    nruns,
-    time_filename
-)
+function generate_benchmark_source_for_groebner(name, system, dir, validate, nruns, time_filename)
     ring = parent(system[1])
     field = base_ring(ring)
     vars_repr = join(map(string, gens(ring)), ", ")
@@ -33,32 +26,11 @@ function generate_benchmark_source_for_groebner(
     String(take!(buf))
 end
 
-function generate_benchmark_source_for_singular(
-    name,
-    system,
-    dir,
-    validate,
-    nruns,
-    time_filename
-)
-    generate_benchmark_source_for_groebner(
-        name,
-        system,
-        dir,
-        validate,
-        nruns,
-        time_filename
-    )
+function generate_benchmark_source_for_singular(name, system, dir, validate, nruns, time_filename)
+    generate_benchmark_source_for_groebner(name, system, dir, validate, nruns, time_filename)
 end
 
-function generate_benchmark_source_for_maplefgb(
-    name,
-    system,
-    dir,
-    validate,
-    nruns,
-    time_filename
-)
+function generate_benchmark_source_for_maplefgb(name, system, dir, validate, nruns, time_filename)
     ring = parent(system[1])
     field = base_ring(ring)
     buf = IOBuffer()
@@ -84,10 +56,7 @@ function generate_benchmark_source_for_maplefgb(
     println(buf, "")
     println(buf, "timings_fn := \"$time_filename\":")
     println(buf, "FileTools[Text][WriteLine](timings_fn, \"$name\");")
-    println(
-        buf,
-        "FileTools[Text][WriteLine](timings_fn, cat(\"total_time, \", String(runtime))):"
-    )
+    println(buf, "FileTools[Text][WriteLine](timings_fn, cat(\"total_time, \", String(runtime))):")
     if validate
         println(buf)
         output_fn = output_filename()
@@ -106,14 +75,7 @@ function generate_benchmark_source_for_maplefgb(
     String(take!(buf))
 end
 
-function generate_benchmark_source_for_mgb(
-    name,
-    system,
-    dir,
-    validate,
-    nruns,
-    time_filename
-)
+function generate_benchmark_source_for_mgb(name, system, dir, validate, nruns, time_filename)
     ring = parent(system[1])
     field = base_ring(ring)
     buf = IOBuffer()
@@ -136,10 +98,7 @@ function generate_benchmark_source_for_mgb(
     println(buf, "")
     println(buf, "timings_fn := \"$time_filename\":")
     println(buf, "FileTools[Text][WriteLine](timings_fn, \"$name\");")
-    println(
-        buf,
-        "FileTools[Text][WriteLine](timings_fn, cat(\"total_time, \", String(runtime))):"
-    )
+    println(buf, "FileTools[Text][WriteLine](timings_fn, cat(\"total_time, \", String(runtime))):")
     if validate
         println(buf)
         output_fn = output_filename()
@@ -158,14 +117,7 @@ function generate_benchmark_source_for_mgb(
     String(take!(buf))
 end
 
-function generate_benchmark_source_for_msolve(
-    name,
-    system,
-    dir,
-    validate,
-    nruns,
-    time_filename
-)
+function generate_benchmark_source_for_msolve(name, system, dir, validate, nruns, time_filename)
     ring = parent(system[1])
     field = base_ring(ring)
     vars_repr = join(map(string, gens(ring)), ", ")
@@ -177,14 +129,7 @@ function generate_benchmark_source_for_msolve(
     String(take!(buf))
 end
 
-function generate_benchmark_source_for_openf4(
-    name,
-    system,
-    dir,
-    validate,
-    nruns,
-    time_filename
-)
+function generate_benchmark_source_for_openf4(name, system, dir, validate, nruns, time_filename)
     ring = parent(system[1])
     field = base_ring(ring)
     buf = IOBuffer()
@@ -203,10 +148,8 @@ function generate_benchmark_source_for_openf4(
         {
         """
     )
-    vars_repr =
-        join(map(s -> "\tvariableName.push_back(\"$s\");", map(repr, gens(ring))), "\n")
-    system_repr =
-        join(map(s -> "\tpolynomialArray.emplace_back(\"$s\");", map(repr, system)), "\n")
+    vars_repr = join(map(s -> "\tvariableName.push_back(\"$s\");", map(repr, gens(ring))), "\n")
+    system_repr = join(map(s -> "\tpolynomialArray.emplace_back(\"$s\");", map(repr, system)), "\n")
     println(
         buf,
         """

diff --git a/benchmark/generate/benchmark_systems/SI/SI.jl b/benchmark/generate/benchmark_systems/SI/SI.jl
@@ -6,13 +6,11 @@ include((@__DIR__) * "/parser.jl")
 function load_SI_problem(name; k=AbstractAlgebra.QQ)
     if name == "SIWR"
         sys = read_SIWR(k=k)[2]
-        @assert AbstractAlgebra.internal_ordering(AbstractAlgebra.parent(sys[1])) ==
-                :degrevlex
+        @assert AbstractAlgebra.internal_ordering(AbstractAlgebra.parent(sys[1])) == :degrevlex
         return sys
     elseif name == "SEAIJRC"
         sys = read_SEAIJRC(k=k)[2]
-        @assert AbstractAlgebra.internal_ordering(AbstractAlgebra.parent(sys[1])) ==
-                :degrevlex
+        @assert AbstractAlgebra.internal_ordering(AbstractAlgebra.parent(sys[1])) == :degrevlex
         return sys
     else
         throw("Beda beda ogorchenie")

diff --git a/benchmark/generate/benchmark_systems/biomodels/BIOMD.jl b/benchmark/generate/benchmark_systems/biomodels/BIOMD.jl
@@ -14,17 +14,14 @@ function BIOMD0000000123(; k=AbstractAlgebra.QQ, internal_ordering=:degrevlex)
         2 // k(78125) * x5 +
         21 // k(12500) * x6 +
         807 // k(226000) * x9,
-        x1^3 * x8 - 663 // k(100) * x3 * x4 - 663 // k(100) * x4 * x5 -
-        25023 // k(25000) * x4 +
+        x1^3 * x8 - 663 // k(100) * x3 * x4 - 663 // k(100) * x4 * x5 - 25023 // k(25000) * x4 +
         21 // k(12500) * x6 +
         21 // k(12500) * x7 +
         5111 // k(1130000) * x10,
         8 // k(3125) * x3 - 663 // k(100) * x4 * x5 - 78129 // k(156250) * x5 +
         21 // k(12500) * x7 +
         269 // k(22600) * x11,
-        663 // k(100) * x3 * x4 - 231 // k(25000) * x6 +
-        1 // k(2) * x7 +
-        269 // k(226) * x12,
+        663 // k(100) * x3 * x4 - 231 // k(25000) * x6 + 1 // k(2) * x7 + 269 // k(226) * x12,
         663 // k(100) * x4 * x5 + 8 // k(3125) * x6 - 12521 // k(12500) * x7 +
         269 // k(22600) * x13,
         -x1^3 * x8 + x4 - 23 // k(25000) * x8 + 5111 // k(1130000) * x14,
@@ -37,8 +34,7 @@ function BIOMD0000000123(; k=AbstractAlgebra.QQ, internal_ordering=:degrevlex)
         21 // k(12500) * x13,
         113 // k(538) * x5 + 8 // k(3125) * x9 - 663 // k(100) * x10 * x11 -
         3141 // k(625000) * x11 + 21 // k(12500) * x13,
-        113 // k(53800) * x6 + 663 // k(100) * x9 * x10 - 6303 // k(12500) * x12 +
-        1 // k(2) * x13,
+        113 // k(53800) * x6 + 663 // k(100) * x9 * x10 - 6303 // k(12500) * x12 + 1 // k(2) * x13,
         113 // k(538) * x7 + 663 // k(100) * x10 * x11 + 8 // k(3125) * x12 -
         12667 // k(25000) * x13,
         -x2^3 * x14 + 2599 // k(6725000) * x8 + x10 - 19 // k(10000) * x14
@@ -102,8 +98,7 @@ function BIOMD0000000103(; k=AbstractAlgebra.QQ, internal_ordering=:degrevlex)
         1 // k(500) * x1 * x3 + 1 // k(1000) * x4 * x6 - 3 // k(1000) * x5 * x8 -
         51 // k(500) * x5 + 1 // k(1000) * x15,
         1 // k(500) * x1 * x2 - 1 // k(1000) * x4 * x6 + 1 // k(1000) * x5 -
-        1 // k(5000) * x6 * x8 - 1 // k(1000) * x6 * x9 - 101 // k(1000) * x6 +
-        1 // k(1000) * x15,
+        1 // k(5000) * x6 * x8 - 1 // k(1000) * x6 * x9 - 101 // k(1000) * x6 + 1 // k(1000) * x15,
         -1 // k(200000) * x2 * x7 - 7 // k(20000) * x6 * x7 - 1 // k(20000) * x7 * x11 -
         7 // k(2000) * x7 * x12 - 1 // k(1000) * x7 + 1 // k(5),
         1 // k(200000) * x2 * x7 - 3 // k(1000) * x3 * x8 - 3 // k(1000) * x4 * x8 -

diff --git a/benchmark/generate/benchmark_systems/biomodels/parser.jl b/benchmark/generate/benchmark_systems/biomodels/parser.jl
@@ -36,9 +36,7 @@ function read_BIOMDs(nspecies)
 
         symvs = map(x -> Symbol(x), vs)
         expvs = Meta.parse(join(symvs, ","))
-        R, xs = eval(
-            :((R, $expvs) = AbstractAlgebra.polynomial_ring(AbstractAlgebra.QQ, $symvs))
-        )
+        R, xs = eval(:((R, $expvs) = AbstractAlgebra.polynomial_ring(AbstractAlgebra.QQ, $symvs)))
 
         for p in params
             p = eval(Meta.parse(p))