Unify XSpectrum types

README.md

@@ -20,3 +20,33 @@ Currently this package can only be installed from github. To do so, either clone
     pkg> add https://github.com/JuliaAstro/Spectra.jl
 
 from the `pkg` command line (Press `]` from Julia REPL)
+
+## Developer documentation
+
+Below we show the commands to run from the package root level to develop the tests and documentation.
+
+### Tests
+
+```julia-repl
+julia --proj
+
+julia> import Pkg
+
+# List tests
+julia> Pkg.test("Spectra"; test_args = `--list`)
+
+# Run specific testsets by name. Will match with `startswith`
+julia> Pkg.test("Spectra"; test_args = `--verbose <testset name>`)
+```
+
+### Docs
+
+Assuming `LiveServer.jl` is in your global environment:
+
+```julia-repl
+julia --proj=docs/
+
+julia> using LiveServer
+
+julia> servedocs(; include_dirs = ["src/"])
+```

docs/Project.toml

@@ -3,6 +3,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FITSIO = "525bcba6-941b-5504-bd06-fd0dc1a4d2eb"
 Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Spectra = "391af1a9-06f1-59d3-8d21-0be089654739"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAstro = "6112ee07-acf9-5e0f-b108-d242c714bf9f"

docs/make.jl

@@ -2,12 +2,15 @@ using Documenter
 using Spectra
 using Unitful
 using Measurements
+using Revise
+
+Revise.revise()
 
 DocMeta.setdocmeta!(Spectra, :DocTestSetup, :(using Spectra); recursive = true)
 
 makedocs(sitename = "Spectra.jl",
     format = Documenter.HTML(;
-        prettyurls = get(ENV, "CI", nothing) == "true",
+        prettyurls = true,
         canonical = "https://juliaastro.org/Spectra/stable/",
     ),
     authors = "Miles Lucas and contributors.",
@@ -17,8 +20,8 @@ makedocs(sitename = "Spectra.jl",
         "Home" => "index.md",
         "spectrum.md",
         "transforms.md",
-        "fitting.md",
-        "analysis.md",
+        #"fitting.md",
+        #"utils.md",
         "contrib.md",
     ],
     warnonly = [:missing_docs],
@@ -27,5 +30,7 @@ makedocs(sitename = "Spectra.jl",
 
 deploydocs(;
     repo = "github.com/JuliaAstro/Spectra.jl.git",
-    versions = ["stable" => "v^", "v#.#"] # Restrict to minor releases
+    devbranch = "main",
+    push_preview = true,
+    versions = ["stable" => "v^", "v#.#"], # Restrict to minor releases
 )

docs/src/analysis.md → docs/old_docs/utils.md

@@ -1,6 +1,7 @@
-# Analysis
+# Utilities
 
 ```@docs
+Spectra.blackbody
 Spectra.equivalent_width
 Spectra.line_flux
-```
+```

docs/src/index.md

@@ -18,7 +18,9 @@ julia> using Spectra
 
 ## Quick Start
 
-Here is a quick demo of some of our features
+Here is a quick demo of some of our features.
+
+### Spectrum construction
 
 ```jldoctest guide
 julia> using Spectra, FITSIO, Unitful, UnitfulAstro, Plots
@@ -41,23 +43,17 @@ julia> wave = (10 .^ read(f[2], "loglam"))u"angstrom";
 julia> flux = (read(f[2], "flux") .* 1e-17)u"erg/s/cm^2/angstrom";
 
 julia> spec = spectrum(wave, flux)
-Spectrum(Quantity{Float32, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Quantity{Float64, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(Å^-1, erg, cm^-2, s^-1), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+SingleSpectrum(Quantity{Float32, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Quantity{Float64, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(Å^-1, erg, cm^-2, s^-1), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+  spectral axis (3827,): 3815.0483f0 Å .. 9206.613f0 Å
+  flux axis (3827,): 2.182261505126953e-15 erg Å^-1 cm^-2 s^-1 .. 1.7559197998046877e-15 erg Å^-1 cm^-2 s^-1
+  meta: Dict{Symbol, Any}()
 
 julia> plot(spec);
 ```
 
 ![](assets/sdss.svg)
 
-```jldoctest guide
-julia> cont_fit = continuum(spec)
-Spectrum(Quantity{Float32, 𝐋, Unitful.FreeUnits{(Å,), 𝐋, nothing}}, Quantity{Float64, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(Å^-1, erg, cm^-2, s^-1), 𝐌 𝐋^-1 𝐓^-3, nothing}})
-  coeffs: Quantity{Float64, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(Å^-1, erg, cm^-2, s^-1), 𝐌 𝐋^-1 𝐓^-3, nothing}}[1.983152216046405e-15 erg Å^-1 cm^-2 s^-1, -1.8822245369267038e-16 erg Å^-1 cm^-2 s^-1, -1.0422750370065006e-16 erg Å^-1 cm^-2 s^-1, 4.8112282273206135e-17 erg Å^-1 cm^-2 s^-1]
-  normalized: true
-
-julia> plot(cont_fit, xlims=(6545, 6600));
-```
-
-![](assets/sdss_cont.svg)
+For constructing higher dimensional spectra, e.g., for echelle or IFU spectra, see the docstrings for [EchelleSpectrum](@ref) and [IFUSpectrum](@ref), respectively.
 
 ## Citation
 

docs/src/spectrum.md

@@ -1,10 +1,3 @@
-```@meta
-DocTestSetup = quote
-  using Spectra, Random
-  Random.seed!(11894)
-end
-```
-
 # Spectrum
 
 Here we will go over the different spectral types and how we use them.
@@ -14,7 +7,11 @@ Here we will go over the different spectral types and how we use them.
 Spectra are defined as possible subtypes of `AbstractSpectrum`. You can use these directly for construction, or use the catch-all [`spectrum`](@ref) function, which is preferred.
 
 ```@docs
+Spectra.AbstractSpectrum
 Spectra.Spectrum
+Spectra.SingleSpectrum
+Spectra.EchelleSpectrum
+Spectra.IFUSpectrum
 ```
 
 ## Constructors
@@ -28,25 +25,37 @@ Spectra.spectrum
 
 For more advanced transformations, see [Transformations](@ref)
 
+### Getters
+```@docs
+Spectra.spectral_axis(::AbstractSpectrum)
+Spectra.flux_axis(::AbstractSpectrum)
+Spectra.meta(::AbstractSpectrum)
+```
+
+### Array interface
+
 | Function                           |
 |:-----------------------------------|
+| `Base.argmax(::AbstractSpectrum)`  |
+| `Base.argmin(::AbstractSpectrum)`  |
+| `Base.eltype(::AbstractSpectrum)`  |
+| `Base.findmax(::AbstractSpectrum)` |
+| `Base.findmin(::AbstractSpectrum)` |
+| `Base.iterate(::AbstractSpectrum)` |
 | `Base.length(::AbstractSpectrum)`  |
-| `Base.size(::AbstractSpectrum)`    |
 | `Base.maximum(::AbstractSpectrum)` |
 | `Base.minimum(::AbstractSpectrum)` |
-| `Base.argmax(::AbstractSpectrum)`  |
-| `Base.argmin(::AbstractSpectrum)`  |
-| `Base.findmax(::AbstractSpectrum)`  |
-| `Base.findmin(::AbstractSpectrum)`  |
+| `Base.size(::AbstractSpectrum)`    |
 
 ### Arithmetic
 
-| Function                           |
-|:-----------------------------------|
-| `+(::AbstractSpectrum, A)`         |
-| `-(::AbstractSpectrum, A)`         |
-| `*(::AbstractSpectrum, A)`         |
-| `/(::AbstractSpectrum, A)`         |
+| Function                                            |
+|:----------------------------------------------------|
+| `+(::AbstractSpectrum, A)`                          |
+| `-(::AbstractSpectrum, A)`                          |
+| `*(::AbstractSpectrum, A)`                          |
+| `/(::AbstractSpectrum, A)`                          |
+| `Base.(==)(::AbstractSpectrum, ::AbstractSpectrum)` |
 
 ## Unitful helpers
 
@@ -76,7 +85,3 @@ savefig("spec-plot.svg"); nothing # hide
 ```@index
 Pages = ["spectrum.md"]
 ```
-
-```@meta
-DocTestSetup = nothing
-```

docs/src/transforms.md

@@ -1,31 +1,17 @@
-```@meta
-DocTestSetup = quote
-  using Spectra, Random
-  Random.seed!(11894)
-end
-```
-
 # Transformations
 
 ## Extinction
 
 By levaraging [DustExtinction.jl](https://github.com/juliaastro/dustextinction.jl) we can apply common reddening laws to our spectra.
 
 ```jldoctest
-julia> using Unitful, Measurements, Random
+julia> using Spectra, Unitful, Measurements, Random
 
 julia> rng = Random.seed!(0);
 
-julia> wave = (1:0.5:3)u"μm"
-(1.0:0.5:3.0) μm
+julia> wave = (1:0.5:3)u"μm";
 
-julia> sigma = randn(rng, size(wave))
-5-element Vector{Float64}:
-  0.942970533446119
-  0.13392275765318448
-  1.5250689085124804
-  0.12390123120559722
- -1.205772284259936
+julia> sigma = randn(rng, size(wave));
 
 julia> flux = (100 .± sigma)u"W/m^2/μm"
 5-element Vector{Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(μm^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}}}:
@@ -36,12 +22,18 @@ julia> flux = (100 .± sigma)u"W/m^2/μm"
  100.0 ± -1.2 W μm^-1 m^-2
 
 julia> spec = spectrum(wave, flux)
-Spectrum(Quantity{Float64, 𝐋, Unitful.FreeUnits{(μm,), 𝐋, nothing}}, Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(μm^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+SingleSpectrum(Quantity{Float64, 𝐋, Unitful.FreeUnits{(μm,), 𝐋, nothing}}, Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(μm^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+  spectral axis (5,): 1.0 μm .. 3.0 μm
+  flux axis (5,): 100.0 ± 0.94 W μm^-1 m^-2 .. 100.0 ± -1.2 W μm^-1 m^-2
+  meta: Dict{Symbol, Any}()
 
 julia> red = redden(spec, 0.3)
-Spectrum(Quantity{Float64, 𝐋, Unitful.FreeUnits{(μm,), 𝐋, nothing}}, Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(μm^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+SingleSpectrum(Quantity{Float64, 𝐋, Unitful.FreeUnits{(μm,), 𝐋, nothing}}, Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(μm^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+  spectral axis (5,): 1.0 μm .. 3.0 μm
+  flux axis (5,): 89.44 ± 0.84 W μm^-1 m^-2 .. 98.1 ± 1.2 W μm^-1 m^-2
+  meta: Dict{Symbol, Any}()
 
-julia> red.flux
+julia> flux_axis(red)
 5-element Vector{Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(μm^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}}}:
  89.44 ± 0.84 W μm^-1 m^-2
  94.35 ± 0.13 W μm^-1 m^-2
@@ -50,9 +42,12 @@ julia> red.flux
   98.1 ± 1.2 W μm^-1 m^-2
 
 julia> deredden!(red, 0.3)
-Spectrum(Quantity{Float64, 𝐋, Unitful.FreeUnits{(μm,), 𝐋, nothing}}, Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(μm^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+SingleSpectrum(Quantity{Float64, 𝐋, Unitful.FreeUnits{(μm,), 𝐋, nothing}}, Quantity{Measurement{Float64}, 𝐌 𝐋^-1 𝐓^-3, Unitful.FreeUnits{(μm^-1, m^-2, W), 𝐌 𝐋^-1 𝐓^-3, nothing}})
+  spectral axis (5,): 1.0 μm .. 3.0 μm
+  flux axis (5,): 100.0 ± 0.94 W μm^-1 m^-2 .. 100.0 ± 1.2 W μm^-1 m^-2
+  meta: Dict{Symbol, Any}()
 
-julia> red.flux ≈ spec.flux
+julia> flux_axis(red) ≈ flux_axis(spec)
 true
 ```
 
@@ -64,7 +59,3 @@ redden!
 deredden
 deredden!
 ```
-
-```@meta
-DocTestSetup = nothing
-```