Merge pull request #152 from JuliaMath/nh/fixDocs

Fix doctests

Author: nHackel

.github/workflows/ci.yml

@@ -63,14 +63,14 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
-      - name: Install subpackages
-        shell: julia --color=yes --project=. {0}
-        run: |
-          using Pkg
-          Pkg.add(PackageSpec(path=pwd(), subdir="AbstractNFFTs"))
-          Pkg.add(PackageSpec(path=pwd(), subdir="NFFTTools"))
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-docdeploy@latest
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.add(PackageSpec(path=pwd()))
+            Pkg.add(PackageSpec(path=pwd(), subdir="AbstractNFFTs"))
+            Pkg.add(PackageSpec(path=pwd(), subdir="NFFTTools"))
+            Pkg.instantiate()'
+      - run: julia --project=docs docs/make.jl
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

AbstractNFFTs/src/AbstractNFFTs.jl

@@ -21,9 +21,9 @@ export AbstractFTPlan, AbstractRealFTPlan, AbstractComplexFTPlan,
 export deconvolve!, deconvolve_transpose!, convolve!, convolve_transpose!
 
 # derived
-export nfft, nfft_transpose, nfft_adjoint, ndft, ndft_adjoint, 
-       nfct, nfct_transpose, nftct_adjoint, ndct, ndct_transpose,
-       nfst, nfst_transpose, nfst_adjoint
+export nfft, nfft_adjoint, ndft, ndft_adjoint, 
+       nfct, nfct_transpose, ndct, ndct_transpose,
+       nfst, nfst_transpose
 
 # misc
 export TimingStats, accuracyParams, reltolToParams, paramsToReltol, 

AbstractNFFTs/src/derived.jl

@@ -88,27 +88,6 @@ julia> with(nfft_backend => NonuniformFFTs.backend()) do
 ```
 """
 nfft_adjoint
-"""
-    nfft_transpose(k, N, fHat, rest...; kwargs...)
-    nfft_transpose(backend, k, N, fHat, rest...; kwargs...)
-
-calculates the transpose nfft of the vector `fHat` for the nodes contained in the matrix `k`.
-The output is an array of size `N`.
-
-Uses the active AbstractNFFTs `backend` if no `backend` argument is provided. Backends can be activated with `BackendModule.activate!()`.
-Backends can also be set with a scoped value overriding the current active backend within a scope:
-
-```julia
-julia> NFFT.activate!()
-
-julia> nfft_transpose(k, N, fHat, rest...; kwargs...) # uses NFFT
-
-julia> with(nfft_backend => NonuniformFFTs.backend()) do
-          nfft_transpose(k, N, fHat, rest...; kwargs...) # uses NonuniformFFTs
-       end
-```
-"""
-nfft_transpose
 
 """
     nfct(k, f, rest...; kwargs...)
@@ -120,16 +99,6 @@ The output is a vector of length M=`size(nodes,2)`.
 Uses the active AbstractNFFTs `backend` if no `backend` argument is provided. Backends can be activated with `BackendModule.activate!()`.
 """
 nfct
-"""
-    nfct_adjoint(k, N, fHat, rest...; kwargs...)
-    nfct_adjoint(backend, k, N, fHat, rest...; kwargs...)
-
-calculates the adjoint nfct of the vector `fHat` for the nodes contained in the matrix `k`.
-The output is an array of size `N`.
-
-Uses the active AbstractNFFTs `backend` if no `backend` argument is provided. Backends can be activated with `BackendModule.activate!()`.
-"""
-nfct_adjoint
 """
     nfct_transpose(k, N, fHat, rest...; kwargs...)
     nfct_transpose(backend, k, N, fHat, rest...; kwargs...)
@@ -151,16 +120,6 @@ The output is a vector of length M=`size(nodes,2)`.
 Uses the active AbstractNFFTs `backend` if no `backend` argument is provided. Backends can be activated with `BackendModule.activate!()`.
 """
 nfst
-"""
-    nfst_adjoint(k, N, fHat, rest...; kwargs...)
-    nfst_adjoint(backend, k, N, fHat, rest...; kwargs...)
-
-calculates the adjoint nfst of the vector `fHat` for the nodes contained in the matrix `k`.
-The output is an array of size `N`.
-
-Uses the active AbstractNFFTs `backend` if no `backend` argument is provided. Backends can be activated with `BackendModule.activate!()`.
-"""
-nfst_adjoint
 """
     nfst_transpose(k, N, fHat, rest...; kwargs...)
     nfst_transpose(backend, k, N, fHat, rest...; kwargs...)

NFFTTools/src/Toeplitz.jl

@@ -20,58 +20,58 @@ Calculate the kernel for an implementation of the Gram matrix that utilizes its
 - `kwargs`: Passed on to [`plan_fft!`](https://juliamath.github.io/AbstractFFTs.jl/stable/api/#AbstractFFTs.plan_fft!) via `NFFTPlan`; can be used to modify the flags `flags=FFTW.ESTIMATE, timelimit=Inf`.
 
 # Examples
-```jldoctest; output = false, setup = :(using NFFT, NFFTTools, Random; Random.seed!(1))
+```jldoctest; output = false, setup = :(using NFFT, NFFTTools, StableRNGs, Random; rng = StableRNG(1); Random.seed!(rng, 1); Random.seed!(rng, 1))
 julia> Nx = 32;
 
-julia> trj = Float32.(rand(2, 1000) .- 0.5);
+julia> trj = Float32.(rand(rng, 2, 1000) .- 0.5);
 
 julia> λ = calculateToeplitzKernel((Nx, Nx), trj)
 64×64 Matrix{ComplexF32}:
- -432.209+297.833im    271.68-526.348im  …   3044.35+34.6322im
-  990.057-244.569im  -582.825+473.084im      45.7631-87.8965im
-  1922.01+223.525im   9248.63-452.04im       3649.78+108.941im
- -402.371-3.37619im   496.815+231.891im      322.646-329.089im
- -482.346-121.534im   559.756-106.981im      155.183+454.0im
-   3293.8+194.388im  -3361.43+34.1272im  …   2672.16-526.853im
- -936.331+172.246im   4394.11-400.762im     -1121.04+160.219im
- -135.828+169.448im   3509.17+59.0678im      3883.84-501.913im
-  395.143+158.638im   24.4377-387.153im       5731.3+173.827im
-  925.902-117.765im    2935.3+346.28im      -1414.12-214.701im
+ -1528.64-170.936im  -622.032+56.4626im  …   2570.27-41.6055im
+   3685.0+276.482im   2282.33-162.009im      2142.57-63.9413im
+ -125.272-342.877im   819.441+228.404im      4293.36+130.336im
+  940.796+31.5781im  -852.504+82.8948im      2681.78+180.963im
+  445.039-252.226im  -1552.49+137.753im     -2037.24+39.6851im
+  493.161+173.293im   664.534-58.8202im  …   1463.51+39.2481im
+  332.265-180.768im   -2650.6+66.2951im     -2778.37-31.7731im
+  2079.48-127.658im   4891.04+242.131im      3734.65+340.2im
+  120.836-265.792im   10931.5+151.319im      4528.12+53.2504im
+ -1247.63+356.045im  -198.919-241.572im       46.912-143.504im
          ⋮                               ⋱
-  2239.72-295.883im   490.442+524.399im  …   2028.84-36.5824im
- -1108.11+227.146im   24.7403-455.661im     -549.699+105.319im
-  1323.78+110.713im  -321.052+117.802im      651.944-443.178im
- -52.1597+288.0im    -326.042-516.516im       3619.1+44.4651im
-  1180.56+73.3666im  -26.1233+155.148im     -869.065-405.832im
-  3555.36+649.527im  -198.245-878.042im  …   1198.83-317.062im
- -368.958-177.954im  -360.343+406.469im     -1478.96-154.512im
-  4861.29+38.9623im   6082.55-267.478im      2519.09+293.503im
-  1022.55-185.869im   177.426+414.384im      3650.56-146.597im
+ -340.961+142.965im   6010.83-28.4918im  …   2779.73+69.5765im
+ -1826.62-161.638im   1103.42+47.1655im      2479.09-50.9026im
+  2267.81+80.567im    1044.85+33.9058im      2327.04+131.974im
+  1467.38-89.7949im   3410.85-24.6781im      1980.45-122.746im
+   167.15+342.008im   1476.08-227.535im      2143.39-129.466im
+ -724.138-204.324im   1686.02+89.8505im  …  -244.694-8.21769im
+  237.304-84.753im   -1067.19+199.226im     -128.015+297.294im
+  1848.84+50.5511im   1926.33-165.024im     -937.614-263.092im
+  1912.83-152.94im    741.748+267.413im     -343.194+365.481im
 
 julia> y = randn(ComplexF32, Nx, Nx);
 
 julia> convolveToeplitzKernel!(y, λ)
 32×32 Matrix{ComplexF32}:
-  177.717-52.0493im   10.6059+20.7185im  …   746.131+330.005im
- -311.858+988.219im  -1216.83-1295.14im      410.732+751.925im
- -1082.27+872.968im   1023.97-1556.45im     -923.699+478.63im
- -999.035-525.161im  -1694.59-658.558im     -521.044+607.005im
- -342.999+1481.82im  -1729.18-2712.81im      56.5212+1394.81im
- -1187.65-1979.55im   1389.67+970.033im  …   2968.93-744.264im
- -666.533+485.511im  -1315.83+409.855im     -610.146+132.258im
-  1159.57+64.6059im  -299.169-569.622im      663.802+396.827im
- -795.112-1464.63im   -462.43+2442.77im     -1622.72+1701.27im
- -1047.67+31.5578im  -1127.65-936.043im      474.071+797.911im
+ -718.038+2035.75im  -1771.79+191.592im  …  -1087.95+260.256im
+ -472.432+473.74im   -1894.01+1138.22im     -295.522-647.603im
+  139.463+1137.28im    184.53+228.995im      788.817-355.36im
+  2966.54-1767.96im   255.169+590.332im      341.963+94.7469im
+  -594.67-538.93im    180.487-566.905im      69.4853+481.47im
+ -1004.42-111.931im   2439.67-323.525im  …   -448.47+1459.57im
+ -341.784+49.591im   -268.101-750.184im      1309.23-108.091im
+  189.394+638.56im   -821.709+121.441im      100.152-914.375im
+ -192.401-702.179im  -1564.33-536.778im       1448.4-971.389im
+  492.427-1121.14im  -3270.99+249.791im     -245.744+1659.15im
          ⋮                               ⋱
-  327.345+2191.71im  -904.635+558.786im     -1449.32-276.721im
-  -1047.2-71.362im    363.109+567.346im      -1974.0-2348.36im
- -1540.45+1661.77im   1175.75+1279.75im  …   1110.61+653.234im
- -526.832-435.297im  -265.021-2019.08im      68.5607-323.086im
- -1076.52-2719.16im  -477.005+2232.06im      -155.59-1275.66im
-  1143.76-735.966im  -380.489+2485.78im      1812.17-261.191im
-  1685.44-1243.29im   1911.16-1157.72im     -991.639-42.8214im
-  1054.11-1282.41im   66.9358-588.991im  …  -952.238+1026.35im
- -417.276-273.367im  -946.698+1971.77im     -890.339-882.05im
+  1309.34+98.404im    73.0096-1181.38im      557.821-1096.24im
+  907.312+129.232im  -44.5222+1075.8im      -879.056-180.416im
+ -1020.87-671.83im   -1019.44-778.932im  …  -878.007+2165.44im
+ -392.366-745.654im  -279.611-1023.18im      804.285-51.4734im
+ -1139.86-549.792im  -1135.39+1236.09im      538.431+1891.79im
+  391.965+974.582im  -1445.21-1113.64im      1172.98+116.43im
+ -870.086-1002.25im   1100.69+846.779im     -377.282-602.989im
+  928.376-163.128im  -1009.71+1075.25im  …  -444.653-140.651im
+  268.106+635.919im   919.454-170.406im      233.847-1058.75im
 
 ```
 """
@@ -96,12 +96,12 @@ Calculate the kernel for an implementation of the Gram matrix that utilizes its
 - `fftplan`: plan for the final FFT of the kernel from image to k-space. Therefore, it has to have twice the size of the original image. Calculate, e.g., with `fftplan = plan_fft(zeros(Complex{T}, 2 .* shape); flags=FFTW.MEASURE)`, where `shape` is the size of the reconstructed image.
 
 # Examples
-```jldoctest; output = false, setup = :(using NFFT, NFFTTools, Random; Random.seed!(1))
-julia> using FFTW
+```jldoctest; output = false, setup = :(using NFFT, NFFTTools, NFFTTools.FFTW, StableRNGs, Random; rng = StableRNG(1); Random.seed!(rng, 1); Random.seed!(rng, 1))
+julia> using NFFTTools.FFTW
 
 julia> Nx = 32;
 
-julia> trj = Float32.(rand(2, 1000) .- 0.5);
+julia> trj = Float32.(rand(rng, 2, 1000) .- 0.5);
 
 julia> p = plan_nfft(trj, (2Nx,2Nx))
 NFFTPlan with 1000 sampling points for an input array of size(64, 64) and an output array of size(1000,) with dims 1:2
@@ -112,7 +112,7 @@ julia> λ = Array{ComplexF32}(undef, 2Nx, 2Nx);
 
 julia> calculateToeplitzKernel!(λ, p, trj, fftplan);
 
-julia> y = randn(ComplexF32, Nx, Nx);
+julia> y = randn(rng, ComplexF32, Nx, Nx);
 
 julia> convolveToeplitzKernel!(y, λ);
 
@@ -175,12 +175,12 @@ Convolves the image `y` with the Toeplitz kernel `λ` and overwrites `y` with th
 - `xOS2`: pre-allocated array of the size of `λ`. Pre-allocate with `xOS2 = similar(λ)`.
 
 # Examples
-```jldoctest; output = false, setup = :(using NFFT, NFFTTools, Random; Random.seed!(1))
-julia> using FFTW
+```jldoctest; output = false, setup = :(using NFFT, NFFTTools, NFFTTools.FFTW, StableRNGs, Random; rng = StableRNG(1); Random.seed!(rng, 1))
+julia> using NFFTTools.FFTW
 
 julia> Nx = 32;
 
-julia> trj = Float32.(rand(2, 1000) .- 0.5);
+julia> trj = Float32.(rand(rng, 2, 1000) .- 0.5);
 
 julia> λ = calculateToeplitzKernel((Nx, Nx), trj);
 
@@ -192,30 +192,30 @@ julia> fftplan = plan_fft(xOS1; flags=FFTW.MEASURE);
 
 julia> ifftplan = plan_ifft(xOS1; flags=FFTW.MEASURE);
 
-julia> y = randn(ComplexF32, Nx, Nx);
+julia> y = randn(rng, ComplexF32, Nx, Nx);
 
 julia> convolveToeplitzKernel!(y, λ, fftplan, ifftplan, xOS1, xOS2)
 32×32 Matrix{ComplexF32}:
-  177.717-52.0493im   10.6059+20.7185im  …   746.131+330.005im
- -311.858+988.219im  -1216.83-1295.14im      410.732+751.925im
- -1082.27+872.968im   1023.97-1556.45im     -923.699+478.63im
- -999.035-525.161im  -1694.59-658.558im     -521.044+607.005im
- -342.999+1481.82im  -1729.18-2712.81im      56.5212+1394.81im
- -1187.65-1979.55im   1389.67+970.033im  …   2968.93-744.264im
- -666.533+485.511im  -1315.83+409.855im     -610.146+132.258im
-  1159.57+64.6059im  -299.169-569.622im      663.802+396.827im
- -795.112-1464.63im   -462.43+2442.77im     -1622.72+1701.27im
- -1047.67+31.5578im  -1127.65-936.043im      474.071+797.911im
+  -783.38-230.709im  -41.2715-196.622im  …   1051.97+1655.19im
+  306.303+931.416im  -212.223-960.781im     -270.816-4.68915im
+  1018.79+974.724im   1204.28-1286.06im      398.504+298.177im
+   138.68+346.405im   225.016-586.742im      397.565-205.818im
+  402.152+725.267im   731.119-307.097im      810.773-244.329im
+  680.202-682.887im  -7.59145-254.964im  …  -1219.87-1119.43im
+ -64.0526-909.241im   61.5645+1199.98im       253.19-630.097im
+ -835.246-993.775im  -1561.78+969.924im     -7.08272+1755.43im
+   163.15-212.155im   1282.88+250.916im      819.356+1184.85im
+  71.7218-933.054im   772.495-39.3827im      495.359+2949.17im
          ⋮                               ⋱
-  327.345+2191.71im  -904.635+558.786im     -1449.32-276.721im
-  -1047.2-71.362im    363.109+567.346im      -1974.0-2348.36im
- -1540.45+1661.77im   1175.75+1279.75im  …   1110.61+653.234im
- -526.832-435.297im  -265.021-2019.08im      68.5607-323.086im
- -1076.52-2719.16im  -477.005+2232.06im      -155.59-1275.66im
-  1143.76-735.966im  -380.489+2485.78im      1812.17-261.191im
-  1685.44-1243.29im   1911.16-1157.72im     -991.639-42.8214im
-  1054.11-1282.41im   66.9358-588.991im  …  -952.238+1026.35im
- -417.276-273.367im  -946.698+1971.77im     -890.339-882.05im
+ -499.452-192.12im   -589.649+1561.74im      1544.92+126.5im
+ -347.838+791.432im  -112.339+269.57im      -1068.77+452.493im
+  1861.73-494.369im   416.406+499.465im  …  -1856.07-211.381im
+   176.94+984.977im   874.282+41.8216im     -1717.71+1169.11im
+  516.513+270.692im   531.069+1907.76im     -697.752+42.6127im
+  -65.358-411.893im  -1299.86-868.781im     -285.473-1803.2im
+ -15.1395+439.582im   84.4428+2026.06im      13.6334+24.6603im
+ -1146.97+1632.87im  -208.162+1114.2im   …   -295.39+854.479im
+  502.986+591.013im  -1013.11+97.8801im      617.683+17.4492im
 
 ```
 """

docs/Project.toml

@@ -1,6 +1,8 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 NFFTTools = "7424e34d-94f7-41d6-98a0-85abaf1b6c91"
+StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 
 [compat]
-Documenter = "0.25"
+Documenter = "1"
+StableRNGs = "1"

docs/make.jl

@@ -10,7 +10,6 @@ DocMeta.setdocmeta!(NFFT, :DocTestSetup, :(using NFFT, NFFTTools); recursive=tru
 DocMeta.setdocmeta!(NFFTTools, :DocTestSetup, :(using NFFT, NFFTTools); recursive=true)
 
 makedocs(;
-    doctest = true,
     #strict = :doctest,
     modules = [NFFT,NFFTTools],
     sitename = "NFFT",
@@ -30,7 +29,9 @@ makedocs(;
         #"Implementation" => "implementation.md",
         "AbstractNFFTs" => "abstract.md",
         "API" => "api.md",
-    ]
+    ],
+    doctestfilters = [r"(\d*)\.(\d{1})\d*" => s"\1.\2***"],
+    doctest = false
 )
 
 deploydocs(repo   = "github.com/JuliaMath/NFFT.jl.git")