Fix actions

.github/workflows/CI.yml

@@ -17,12 +17,12 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1.9.0
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v3
         env:
           cache-name: cache-artifacts
         with:
@@ -32,18 +32,18 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-buildpkg@v1.4.0
+      - uses: julia-actions/julia-runtest@v1.9.0
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         with:
           file: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1.9.0
         with:
           version: '1'
       - run: |

.github/workflows/TagBot.yml

@@ -9,7 +9,7 @@ jobs:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
-      - uses: JuliaRegistries/TagBot@v1
+      - uses: JuliaRegistries/TagBot@v1.10.0
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           ssh: ${{ secrets.DOCUMENTER_KEY }}

docs/src/diffusion/examples.md

@@ -97,12 +97,9 @@ fig[1:2, 4] = Legend(fig,
     "Molecular States"
 )
 
-save("diffusion_basic_simulation.png", fig)
 fig
-# output
 
 ```
-![Basic Diffusion Simulation](diffusion_basic_simulation.png)
 
 ## Frame Integration for Time-Lapse Imaging
 
@@ -162,12 +159,8 @@ ax = Axis(fig[1, 1],
 frame_to_show = 3  # Changed from 15 to a valid frame index (between 1 and 6)
 heatmap!(ax, transpose(images[:, :, frame_to_show]), colormap=:inferno)
 
-save("diffusion_frame_integration.png", fig)
 fig
-# output
-
 ```
-![Frame Integration for Time-Lapse Imaging](diffusion_frame_integration.png)
 
 The `frame_integration` parameter is crucial for realistic diffusion imaging:
 
@@ -228,12 +221,9 @@ lines!(ax, time_unstable, frac_unstable, linewidth=3, color=:red,
 
 axislegend(ax)
 
-save("diffusion_dimer_formation.png", fig)
 fig
-# output
 
 ```
-![Analyzing Dimer Formation](diffusion_dimer_formation.png)
 
 ## Generating Microscope Images
 
@@ -317,12 +307,7 @@ end
 # Show frames 10, 20, 30
 frame_indices = [10, 20, 30]
 fig = display_frames(images_all, images_dimers, frame_indices)
-save("diffusion_microscope_images.png", fig)
-fig
-# output
-
 ```
-![Generating Microscope Images](diffusion_microscope_images.png)
 
 ## Two Interacting Particles
 
@@ -428,10 +413,7 @@ Legend(fig[1, 2], legend_elements, legend_labels, "States")
 # Set axis limits with some padding
 limits!(ax, -0.05, 1.05, -0.05, 1.05)
 
-save("diffusion_two_particles.png", fig)
 fig
-# output
 
 ```
-![Two Interacting Particles](diffusion_two_particles.png)