Fix docs and update cache action (#49)

* Fix for Documenter pr2388

* Update action cache v4

* Specify using

.github/workflows/Documentation.yml

@@ -21,7 +21,7 @@ jobs:
         with:
           version: '1'
       - name: CacheArtifacts
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:

docs/lit/examples/1-overview.jl

@@ -11,7 +11,8 @@ This page gives an overview of the Julia package
 
 # Packages needed here.
 
-using SPECTrecon
+using SPECTrecon: plan_psf, psf_gauss, SPECTplan
+using SPECTrecon: project, project!, backproject, backproject!
 using MIRTjim: jim, prompt
 using LinearAlgebra: mul!
 using LinearMapsAA: LinearMapAA
@@ -218,10 +219,10 @@ mul!(tmp, A', views)
 The pixel dimensions `deltas` can (and should!) be values with units.
 
 Here is an example ... (todo)
-=#
 
-#using UnitfulRecipes
-#using Unitful: mm
+using UnitfulRecipes
+using Unitful: mm
+=#
 
 
 # ## Projection view animation

docs/lit/examples/2-rotate.jl

@@ -11,7 +11,7 @@ This page explains the image rotation portion of the Julia package
 
 # Packages needed here.
 
-using SPECTrecon
+using SPECTrecon: plan_rotate, imrotate!, imrotate_adj!
 using MIRTjim: jim, prompt
 using Plots: scatter, scatter!, plot!, default
 default(markerstrokecolor=:auto, markersize=3)

docs/lit/examples/3-psf.jl

@@ -11,7 +11,7 @@ This page explains the PSF portion of the Julia package
 
 # Packages needed here.
 
-using SPECTrecon
+using SPECTrecon: psf_gauss, plan_psf, fft_conv!, fft_conv_adj!
 using MIRTjim: jim, prompt
 using Plots: scatter, scatter!, plot!, default
 default(markerstrokecolor=:auto, markersize=3)

docs/lit/examples/4-mlem.jl

@@ -11,7 +11,7 @@ This page illustrates ML-EM reconstruction with the Julia package
 
 # Packages needed here.
 
-using SPECTrecon
+using SPECTrecon: SPECTplan, psf_gauss, project!, backproject!, mlem, mlem!
 using MIRTjim: jim, prompt
 using Plots: scatter, plot!, default; default(markerstrokecolor=:auto)
 

docs/lit/examples/5-2d.jl

@@ -12,7 +12,8 @@ using the Julia package
 
 # Packages needed here.
 
-using SPECTrecon
+using SPECTrecon: SPECTplan, psf_gauss
+using SPECTrecon: project, project!, backproject, backproject!
 using MIRTjim: jim, prompt
 using ImagePhantoms: shepp_logan, SheppLoganEmis
 using LinearAlgebra: mul!

docs/lit/examples/6-dl.jl

@@ -219,26 +219,37 @@ end
 # Initial loss
 @show loss(xhat1, xtrue)
 
-# ### Train the CNN
-# Uncomment the following code to train!
-## using Printf
-## nepoch = 200
-## for e = 1:nepoch
-##     @printf("epoch = %d, loss = %.2f\n", e, loss(xhat1, xtrue))
-##     ps = Flux.params(cnn)
-##     gs = gradient(ps) do
-##         loss(xhat1, xtrue) # we start with the 30 iteration EM reconstruction
-##     end
-##     opt = ADAMW(0.002)
-##     Flux.Optimise.update!(opt, ps, gs)
-## end
-
-# Uncomment to save your trained model.
-## file = "../data/trained-cnn-example-6-dl.bson" # adjust path/name as needed
-## @save file cnn
-
-# Load the pre-trained model (uncomment if you save your own model).
-## @load file cnn
+#=
+### Train the CNN
+Uncomment the following code to train:
+
+```
+using Printf
+nepoch = 200
+for e in 1:nepoch
+    @printf("epoch = %d, loss = %.2f\n", e, loss(xhat1, xtrue))
+    ps = Flux.params(cnn)
+    gs = gradient(ps) do
+        loss(xhat1, xtrue) # we start with the 30 iteration EM reconstruction
+    end
+    opt = ADAMW(0.002)
+    Flux.Optimise.update!(opt, ps, gs)
+end
+```
+=#
+
+#=
+Uncomment to save your trained model:
+```
+file = "../data/trained-cnn-example-6-dl.bson" # adjust path/name as needed
+@save file cnn
+```
+
+Load the pre-trained model (uncomment if you save your own model):
+```
+@load file cnn
+```
+=#
 
 #=
 The code below here works fine when run via `include` from the REPL,