Merge pull request #23 from JuliaAstro/fixup

icweaver · web-flow · commit 7ccd42da2989 · 2025-10-26T18:05:24.000-07:00
Fixup
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,10 @@
 name = "Spectra"
 uuid = "391af1a9-06f1-59d3-8d21-0be089654739"
-authors = ["Miles Lucas <mdlucas@hawaii.edu>"]
 version = "0.1.0"
+authors = ["Miles Lucas <mdlucas@hawaii.edu>"]
+
+[workspace]
+projects = ["test", "docs"]
 
 [deps]
 DustExtinction = "fb44c06c-c62f-5397-83f5-69249e0a3c8e"
@@ -11,7 +14,6 @@ PhysicalConstants = "5ad8b20f-a522-5ce9-bfc9-ddf1d5bda6ab"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAstro = "6112ee07-acf9-5e0f-b108-d242c714bf9f"
-WCS = "15f3aee2-9e10-537f-b834-a6fb8bdb944d"
 
 [compat]
 DustExtinction = ">=0.6.0"
@@ -21,5 +23,4 @@ PhysicalConstants = "0.2"
 RecipesBase = "1"
 Unitful = "1"
 UnitfulAstro = "1"
-WCS = "0.6"
 julia = "1.10"
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -7,9 +7,6 @@ Spectra = "391af1a9-06f1-59d3-8d21-0be089654739"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAstro = "6112ee07-acf9-5e0f-b108-d242c714bf9f"
 
-[sources]
-Spectra = {path = ".."}
-
 [compat]
 Documenter = "1"
 UnitfulAstro = ">=0.4.0"
diff --git a/src/Spectra.jl b/src/Spectra.jl
@@ -1,6 +1,16 @@
 module Spectra
 
-export spectrum
+# common.jl
+export AbstractSpectrum, spectrum
+# utils.jl
+export blackbody
+# transforms/redden.jl
+export redden, redden!, deredden, deredden!
+
+using RecipesBase: @recipe
+using Measurements: Measurements, Measurement
+using Unitful: Unitful, Quantity, @u_str, ustrip, unit, dimension
+using PhysicalConstants.CODATA2018: h, c_0, k_B
 
 # AbstractSpectrum and common functionality
 include("common.jl")
@@ -31,7 +41,7 @@ julia> spec.name
 "Just Noise"
 ```
 
-There is easy integration with [Unitful.jl](https://github.com/painterqubits/unitful.jl)
+There is easy integration with [Unitful.jl](https://github.com/JuliaPhysics/Unitful.jl)
 and its sub-projects and [Measurements.jl](https://github.com/juliaphysics/measurements.jl)
 
 ```jldoctest
diff --git a/src/common.jl b/src/common.jl
@@ -1,9 +1,3 @@
-using WCS
-using Unitful
-
-export AbstractSpectrum
-#--------------------------------------------------------------------------------------
-
 """
     AbstractSpectrum{W<:Number, F<:Number}
 
diff --git a/src/fitting/fitting.jl b/src/fitting/fitting.jl
@@ -1,4 +1,4 @@
-using LinearAlgebra
+using LinearAlgebra: /, \, diagm, pinv
 
 export continuum, line_flux, equivalent_width
 
diff --git a/src/plotting.jl b/src/plotting.jl
@@ -1,5 +1,3 @@
-using RecipesBase, Unitful, Measurements
-
 @recipe function f(spec::Spectrum)
     seriestype --> :step
     xlabel --> "wave"
diff --git a/src/spectrum.jl b/src/spectrum.jl
@@ -1,5 +1,3 @@
-using Unitful
-
 """
     Spectrum <: AbstractSpectrum
 
diff --git a/src/transforms/redden.jl b/src/transforms/redden.jl
@@ -1,54 +1,49 @@
-using DustExtinction
-import DustExtinction: redden, deredden
+import DustExtinction
 
-export redden,
-       redden!,
-       deredden,
-       deredden!
 
 """
-    redden!(::AbstractSpectrum, Av; Rv = 3.1, law = CCM89)
+    redden!(::AbstractSpectrum, Av; Rv = 3.1, law = DustExtinction.CCM89)
 
 In-place version of [`redden`](@ref)
 """
-function redden!(spec::T, Av; Rv = 3.1, law = CCM89) where {T <: AbstractSpectrum}
-    @. spec.flux = redden(law, spec.wave, spec.flux; Rv, Av)
+function redden!(spec::T, Av; Rv = 3.1, law = DustExtinction.CCM89) where {T <: AbstractSpectrum}
+    @. spec.flux = DustExtinction.redden(law, spec.wave, spec.flux; Rv, Av)
     return spec
 end
 
 """
-    redden(::AbstractSpectrum, Av; Rv = 3.1, law = CCM89)
+    redden(::AbstractSpectrum, Av; Rv = 3.1, law = DustExtinction.CCM89)
 
 Redden a spectrum using common color laws provided by [DustExtinction.jl](https://github.com/juliaastro/dustextinction.jl).
 `Av` is the total extinction, `Rv` is the selective extinction (3.1 is a common
 value for the Milky Way) and `law` is the color law to use for determining the
 extinction.
 """
-function redden(spec::AbstractSpectrum, Av; Rv = 3.1, law = CCM89)
+function redden(spec::AbstractSpectrum, Av; Rv = 3.1, law = DustExtinction.CCM89)
     tmp_spec = deepcopy(spec)
     redden!(tmp_spec, Av; Rv, law)
     return tmp_spec
 end
 
 """
-    deredden!(::AbstractSpectrum, Av; Rv = 3.1, law = CCM89)
+    deredden!(::AbstractSpectrum, Av; Rv = 3.1, law = DustExtinction.CCM89)
 
 In-place version of [`deredden`](@ref)
 """
-function deredden!(spec::AbstractSpectrum, Av; Rv = 3.1, law = CCM89)
-    @. spec.flux = deredden(law, spec.wave, spec.flux; Rv, Av)
+function deredden!(spec::AbstractSpectrum, Av; Rv = 3.1, law = DustExtinction.CCM89)
+    @. spec.flux = DustExtinction.deredden(law, spec.wave, spec.flux; Rv, Av)
     return spec
 end
 
 """
-    deredden(::AbstractSpectrum, Av; Rv = 3.1, law = CCM89)
+    deredden(::AbstractSpectrum, Av; Rv = 3.1, law = DustExtinction.CCM89)
 
 Deredden a spectrum using common color laws provided by [DustExtinction.jl](https://github.com/juliaastro/dustextinction.jl).
 `Av` is the total extinction, `Rv` is the selective extinction (3.1 is a common
 value for the Milky Way) and `law` is the color law to use for determining the
 extinction.
 """
-function deredden(spec::AbstractSpectrum, Av; Rv = 3.1, law = CCM89)
+function deredden(spec::AbstractSpectrum, Av; Rv = 3.1, law = DustExtinction.CCM89)
     tmp_spec = deepcopy(spec)
     deredden!(tmp_spec, Av; Rv, law)
     return tmp_spec
diff --git a/src/utils.jl b/src/utils.jl
@@ -1,8 +1,3 @@
-using Unitful, UnitfulAstro
-using PhysicalConstants.CODATA2018: h, c_0, k_B
-
-export blackbody
-
 """
     blackbody(wave::Vector{<:Quantity}, T::Quantity)
     blackbody(wave::Vector{<:Real}, T::Real)
diff --git a/test/Project.toml b/test/Project.toml
@@ -2,12 +2,10 @@
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DustExtinction = "fb44c06c-c62f-5397-83f5-69249e0a3c8e"
 Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
+ParallelTestRunner = "d3525ed8-44d0-4b2c-a655-542cee43accc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Spectra = "391af1a9-06f1-59d3-8d21-0be089654739"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAstro = "6112ee07-acf9-5e0f-b108-d242c714bf9f"
-
-[sources]
-Spectra = {path = ".."}
diff --git a/test/aqua.jl b/test/aqua.jl
@@ -0,0 +1,3 @@
+using Aqua: test_all
+
+test_all(Spectra)
diff --git a/test/plotting.jl b/test/plotting.jl
@@ -1,5 +1,4 @@
-using RecipesBase, Unitful
-import Measurements: value
+using RecipesBase
 
 @testset "Plotting - Single" begin
     wave = range(1e4, 3e4, length = 1000)
@@ -15,7 +14,7 @@ import Measurements: value
         :xlabel => "wave",
         :ylabel => "flux density",
         :seriestype => :step)
-    @test rec[1].args == (ustrip.(spec.wave), value.(ustrip.(spec.flux)))
+    @test rec[1].args == (ustrip.(spec.wave), Measurements.value.(ustrip.(spec.flux)))
 
 
     strip_spec = ustrip(spec)
@@ -25,7 +24,7 @@ import Measurements: value
         :xlabel => "wave",
         :ylabel => "flux density",
         :seriestype => :step)
-    @test rec[1].args == (strip_spec.wave, value.(strip_spec.flux))
+    @test rec[1].args == (strip_spec.wave, Measurements.value.(strip_spec.flux))
 end
 
 @testset "Plotting - Echelle" begin
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,18 +1,14 @@
-using Test
-using Spectra
-using DustExtinction
-
-using Random
-using Unitful, UnitfulAstro, Measurements
-using Aqua
-
-Random.seed!(8675309)
+using ParallelTestRunner: runtests, find_tests, parse_args
+import Spectra
+
+const init_code = quote
+    using Spectra: Spectra, spectrum
+    using Measurements: Measurements, ±
+    using Unitful: @u_str, unit, ustrip
+    import Random
+end
 
-@testset "Spectra.jl" begin
-    include("spectrum.jl")
-    include("utils.jl")
-    include("transforms/transforms.jl")
-    include("plotting.jl")
+args = parse_args(Base.ARGS)
+testsuite = find_tests(@__DIR__)
 
-    Aqua.test_all(Spectra)
-end
+runtests(Spectra, args; testsuite, init_code)
diff --git a/test/spectrum.jl b/test/spectrum.jl
@@ -1,3 +1,5 @@
+Random.seed!(8675309)
+
 @testset "Spectrum - Single" begin
     wave = range(1e4, 5e4, length = 1000)
     sigma = randn(size(wave))
@@ -28,7 +30,7 @@
     flux_trimmed = flux[200:800]
     @test_throws AssertionError spectrum(wave, flux_trimmed)
     expected = """
-    Spectrum(Float64, Measurement{Float64})
+    Spectrum(Float64, Measurements.Measurement{Float64})
       name: test spectrum"""
     @test sprint(show, spec) == expected
     @test spec.name == "test spectrum"
@@ -78,7 +80,7 @@ end
     flux_trimmed = flux[:, 200:800]
     @test_throws AssertionError spectrum(wave, flux_trimmed)
     expected = """
-    EchelleSpectrum(Float64, Measurement{Float64})
+    EchelleSpectrum(Float64, Measurements.Measurement{Float64})
       # orders: 3
       name: Test Echelle Spectrum"""
     @test sprint(show, spec) == expected
@@ -123,7 +125,7 @@ end
     @test strip_spec.flux == ustrip.(spec.flux)
     @test strip_spec.meta == spec.meta
     expected = """
-    Spectrum(Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(Å^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+    Spectrum(Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Unitful.Quantity{Measurements.Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(Å^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
       name: test"""
     @test sprint(show, spec) == expected
 end
@@ -176,7 +178,7 @@ end
     @test strip_spec.meta == spec.meta
     sprint(show, spec)
     expected = """
-    EchelleSpectrum(Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(Å^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+    EchelleSpectrum(Unitful.Quantity{Float64, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Unitful.Quantity{Measurements.Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(Å^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
       # orders: 3
       name: test echelle"""
     @test sprint(show, spec) == expected
diff --git a/test/transforms/redden.jl b/test/transforms/redden.jl
@@ -1,46 +1,68 @@
-# Custom law
-struct CustomLaw <: DustExtinction.ExtinctionLaw
-    Rv::Float64
+using Spectra:
+    redden,
+    redden!,
+    deredden,
+    deredden!
+
+using DustExtinction: DustExtinction
+
+function mock_spectrum(n::Int = Int(1e3); use_units::Bool = false)
+    wave = range(1e4, 3e4, length = n)
+    sigma = 0.1 .* sin.(wave)
+    T = 6700
+    flux = @. 1e14 / (wave^5 * (exp(1 / (wave * T)) - 1)) ± sigma
+    if use_units
+        wave *= u"angstrom"
+        flux *= u"erg/s/cm^2/angstrom"
+    end
+    spectrum(wave, flux, name="Test Spectrum")
 end
-(law::CustomLaw)(wave) = sin(law.Rv * wave) / law.Rv
-
-@testset "Reddening Av=$Av" for Av = [0.5, 1.0, 2.0]
-    # Regression usage
-    spec = mock_spectrum()
-    spec2 = deepcopy(spec)
-    reddened = @inferred redden(spec, Av)
-    @inferred redden!(spec2, Av)
-    @test reddened.flux ≈ spec2.flux
-    @inferred deredden!(spec2, Av)
-    @test spec.flux ≈ spec2.flux
-    dereddened = @inferred deredden(reddened, Av)
-    @test dereddened.flux ≈ spec.flux
 
+@testset "redden" begin
     # Custom law
-    expected = @. spec.flux * 10^(-0.4 * Av * CustomLaw(π)(spec.wave))
-    @test expected ≈ redden(spec, Av; law=CustomLaw, Rv=π).flux
-
-    # Bad law
-    @test_throws MethodError redden(spec, Av, law = sin)
-
-    # Unitful
-    spec = mock_spectrum(use_units=true)
-    spec2 = deepcopy(spec)
-    reddened = @inferred redden(spec, Av)
-    @inferred redden!(spec2, Av)
-    @test reddened.flux ≈ spec2.flux
-    @inferred deredden!(spec2, Av)
-    @test spec.flux ≈ spec2.flux
-    dereddened = @inferred deredden(reddened, Av)
-    @test dereddened.flux ≈ spec.flux
-end
+    struct CustomLaw <: DustExtinction.ExtinctionLaw
+        Rv::Float64
+    end
+    (law::CustomLaw)(wave) = sin(law.Rv * wave) / law.Rv
+
+    @testset "Reddening Av=$Av" for Av = [0.5, 1.0, 2.0]
+        # Regression usage
+        spec = mock_spectrum()
+        spec2 = deepcopy(spec)
+        reddened = @inferred redden(spec, Av)
+        @inferred redden!(spec2, Av)
+        @test reddened.flux ≈ spec2.flux
+        @inferred deredden!(spec2, Av)
+        @test spec.flux ≈ spec2.flux
+        dereddened = @inferred deredden(reddened, Av)
+        @test dereddened.flux ≈ spec.flux
+
+        # Custom law
+        expected = @. spec.flux * 10^(-0.4 * Av * CustomLaw(π)(spec.wave))
+        @test expected ≈ redden(spec, Av; law=CustomLaw, Rv=π).flux
+
+        # Bad law
+        @test_throws MethodError redden(spec, Av, law = sin)
+
+        # Unitful
+        spec = mock_spectrum(use_units=true)
+        spec2 = deepcopy(spec)
+        reddened = @inferred redden(spec, Av)
+        @inferred redden!(spec2, Av)
+        @test reddened.flux ≈ spec2.flux
+        @inferred deredden!(spec2, Av)
+        @test spec.flux ≈ spec2.flux
+        dereddened = @inferred deredden(reddened, Av)
+        @test dereddened.flux ≈ spec.flux
+    end
 
-@testset "Reddening Av=0" begin
-    # Test no change when Av = 0
-    Av = 0.0
-    spec = mock_spectrum()
-    reddened = redden(spec, Av)
-    @test reddened.flux ≈ spec.flux
-    dereddened = deredden(reddened, Av)
-    @test dereddened.flux ≈ spec.flux
+    @testset "Reddening Av=0" begin
+        # Test no change when Av = 0
+        Av = 0.0
+        spec = mock_spectrum()
+        reddened = redden(spec, Av)
+        @test reddened.flux ≈ spec.flux
+        dereddened = deredden(reddened, Av)
+        @test dereddened.flux ≈ spec.flux
+    end
 end
diff --git a/test/transforms/resample.jl b/test/transforms/resample.jl
diff --git a/test/transforms/transforms.jl b/test/transforms/transforms.jl
diff --git a/test/utils.jl b/test/utils.jl

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-using LinearAlgebra`
	`1`	`+using LinearAlgebra: /, \, diagm, pinv`
`2`	`2`
`3`	`3`	`export continuum, line_flux, equivalent_width`
`4`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,3 @@`
`1`		`-using RecipesBase, Unitful, Measurements`
`2`		`-`
`3`	`1`	`@recipe function f(spec::Spectrum)`
`4`	`2`	`seriestype --> :step`
`5`	`3`	`xlabel --> "wave"`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,3 @@`
`1`		`-using Unitful`
`2`		`-`
`3`	`1`	`"""`
`4`	`2`	`Spectrum <: AbstractSpectrum`
`5`	`3`