Code quality

.gitignore

@@ -32,3 +32,4 @@ JuliaLocalPreferences.toml
 docs/src/examples/jupyter_notebooks/.ipynb_checkpoints
 docs/Manifest.toml
 benchmarks_output.json
+.codex

Project.toml

@@ -18,20 +18,21 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 
 [compat]
-# Aqua = "0.8"
-# CheckConcreteStructs = "0.1"
+Aqua = "0.8"
+CheckConcreteStructs = "0.1"
 DataInterpolations = "8"
 FunctionWrappers = "1"
 DiffEqNoiseProcess = "5.27.0"
-# ExplicitImports = "1.12"
+ExplicitImports = "1.11"
+JET = "0.9.18, 0.10, 0.11"
 LinearAlgebra = "1.10"
 ModelingToolkit = "10"
 NumericalIntegration = "0.3"
 OrdinaryDiffEq = "6"
 QuantumCumulants = "0.4"
 QuantumOptics = "1"
 QuantumOpticsBase = "0.4, 0.5"
-SecondQuantizedAlgebra = "0.4.4"
+SecondQuantizedAlgebra = "0.4.5"
 SpecialFunctions = "2"
 StaticArrays = "1"
 Symbolics = "6"
@@ -41,11 +42,12 @@ julia = "1.10"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
-# CheckConcreteStructs = "73c92db5-9da6-4938-911a-6443a7e94a58"
-# ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
+CheckConcreteStructs = "73c92db5-9da6-4938-911a-6443a7e94a58"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 QuantumCumulants = "35bcea6d-e19f-57db-af74-8011de6c7255"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"] #, "QuantumCumulants", "Aqua", "ExplicitImports", "CheckConcreteStructs"]
+test = ["Test", "Aqua", "ExplicitImports", "JET", "CheckConcreteStructs"] #, "QuantumCumulants"

TODOs.md

@@ -1,15 +1,9 @@
 # MAIN TODO - LIST:
 
-- [ ] clean up 
-  - [x] rm QC.jl 
-  - [ ] types
-  - [ ] rename translate_qo (to to_numerics ?)
-  - [ ] speed up derivation
-
 - [ ] examples
   - [ ] Multi-mode Dicke state superradiance (https://journals.aps.org/pra/abstract/10.1103/PhysRevA.103.033713)
-  - [ ] SUPER example (Johannes)
-  - [ ] pulse delay advanced example (Victor paper)
+  - [ ] SUPER example 
+  - [ ] pulse delay advanced example
   - [x] feedback reduction (see SLH paper)  
   - [ ] cumulants correlation matrix modes 
   - [ ] H_loop in example 09-1 is not simplified correctly on the docu (locally it is fine; pkg versions)
@@ -25,30 +19,24 @@
   - [ ] u_Gaussian, v_Gaussian; slower?
 
 - [ ] more functionalities
-  - [x] feedback reduction
+  - [ ] pulse delay 
   - [ ] better method for u_eff and v_eff (Victor)
-  - [ ] interaction picture (Victor paper)
-    - [ ] general expression for A(t)
-  - [ ] pulse delay (Victor paper)
-  - [x] two_time_corr_matrix for Ls const (see example 02-2)
-
-- [x] Formatter/SpellCheck
-
-- [ ] JET
-
-- [ ] Aqua
 
+- [] docu
+  - u_eff and v_eff theory 
+  - development status
 
 ## Additional TODOs
 
-- [ ] SLH more specific types
-  - [ ] AbstractVector{<:QTerm}
-- [ ] directly use gu(t) without substitution? (think about iscall)
 - [ ] u_eff and v_eff equation (PRA 2020, appendix) theory,  API, implementation
+- [ ] rename translate_qo (to to_numerics ?)
 
 
 
 ## DONE
+- [x] rm QC.jl 
+- [x] types
+- [x] speed up derivation
 
 - [x] Translate function: 
     - [x] Try TimeDependentSums again (after solving the gu(t) mistake/problem) [~factor 2 slower!]
@@ -95,3 +83,11 @@
     - [x] arg u not needed?! 
   - [x] analytic expression for u=v
   - [x] kwarg for adjoint replacement in substitute_operators
+  - [x] feedback reduction
+  - [x] interaction picture 
+    - [x] general expression for A(t)
+  - [x] two_time_corr_matrix for Ls const (see example 02-2)
+
+- [x] Formatter/SpellCheck
+- [x] JET
+- [x] Aqua

src/QuantumInputOutput.jl

@@ -1,21 +1,18 @@
 module QuantumInputOutput
 
-using SecondQuantizedAlgebra
-using QuantumOpticsBase
-using QuantumOptics
-using SymbolicUtils:
-    SymbolicUtils, substitute, BasicSymbolic, operation, arguments, iscall, simplify, expand
-using Symbolics
+using SecondQuantizedAlgebra: SecondQuantizedAlgebra, QSym, to_numeric
+using QuantumOpticsBase: QuantumOpticsBase, expect, basis, dagger, sparse
+using QuantumOptics: QuantumOptics, timeevolution
+using SymbolicUtils: SymbolicUtils, substitute, BasicSymbolic, arguments, simplify, expand
+using Symbolics: Symbolics, build_function
 using SpecialFunctions: erf
 using DataInterpolations: LinearInterpolation, ExtrapolationType
 using NumericalIntegration: cumul_integrate
 using LinearAlgebra: LinearAlgebra, I, mul!
-using OrdinaryDiffEq
-using StaticArrays
-using FunctionWrappers
+using OrdinaryDiffEq: OrdinaryDiffEq, ODEProblem, Tsit5, solve
+using StaticArrays: StaticArrays, SMatrix, SVector
+using FunctionWrappers: FunctionWrappers, FunctionWrapper
 
-import QuantumOpticsBase: expect
-import SecondQuantizedAlgebra: numeric_average
 const SQA = SecondQuantizedAlgebra
 
 export SLH,

src/SLH.jl

@@ -1,4 +1,4 @@
-using StaticArrays
+using StaticArrays: StaticArrays, SMatrix, SVector
 using FunctionWrappers: FunctionWrapper
 
 # NOTE: FunctionWrapper is callable but NOT <: Function.
@@ -451,6 +451,3 @@ function _feedback_maps(n::Int, connections)
     end
     return mapped
 end
-
-Base.length(h::SecondQuantizedAlgebra.ConcreteHilbertSpace) = 1
-Base.length(h::ProductSpace) = length(h.spaces)

src/utils.jl

@@ -1,16 +1,3 @@
-# move to SQA
-function numeric_average(op::SQA.QNumber, state::Vector; kwargs...)
-    op_num = sparse(to_numeric(op, state[1]; kwargs...))
-    return QuantumOpticsBase.expect(op_num, state)
-end
-function numeric_average(avg::Average, state::Vector; kwargs...)
-    op = undo_average(avg)
-    return numeric_average(op, state; kwargs...)
-end
-
-expect(avg::Average, state; kwargs...) = numeric_average(avg, state; kwargs...)
-expect(op::SQA.QNumber, state; kwargs...) = numeric_average(op, state; kwargs...)
-
 """
     substitute_operators(op, dict::Dict; replace_adjoint=true)
 
@@ -38,6 +25,6 @@ end
 
 function _extend_with_adjoint(dict::Dict)
     pairs_ = collect(dict)
-    adj_pairs = [SQA.adjoint(k) => SQA.adjoint(v) for (k, v) in pairs_]
+    adj_pairs = [Base.adjoint(k) => Base.adjoint(v) for (k, v) in pairs_]
     return Dict(vcat(pairs_, adj_pairs))
 end

test/runtests.jl

@@ -1,4 +1,5 @@
 names = [
+    "test_code_quality.jl",
     "test_SLH.jl",
     "test_feedback.jl",
     "test_translate.jl",

test/test_code_quality.jl

@@ -0,0 +1,37 @@
+using QuantumInputOutput, Test
+
+@testset "best practices" begin
+    using Aqua
+
+    Aqua.test_ambiguities([QuantumInputOutput]; broken = false)
+    Aqua.test_piracies(QuantumInputOutput; broken = false)
+    Aqua.test_all(QuantumInputOutput; ambiguities = false, piracies = false)
+end
+
+@testset "ExplicitImports" begin
+    using ExplicitImports
+
+    @test check_no_implicit_imports(QuantumInputOutput) == nothing
+    @test check_all_explicit_imports_via_owners(QuantumInputOutput) == nothing
+    @test check_no_stale_explicit_imports(QuantumInputOutput) == nothing
+    @test check_all_qualified_accesses_via_owners(QuantumInputOutput) == nothing
+    @test check_no_self_qualified_accesses(QuantumInputOutput) == nothing
+end
+
+if isempty(VERSION.prerelease)
+    @testset "Code linting" begin
+        using JET
+
+        rep = report_package(QuantumInputOutput)
+        @show rep
+        @test length(JET.get_reports(rep)) < 74 # TODO
+    end
+end
+
+@testset "Concretely typed" begin
+    import QuantumInputOutput as QIO
+    using CheckConcreteStructs
+
+    all_concrete(typeof(QIO.SLH(1, 0, 0))) # TODO
+    all_concrete(QIO.Gaussian)
+end