Commit of the following:

- Change phantom-format file to pure markdown
- Try `execute=true` option for Literate.markdown function
- Change `plot_phantom_map` example to display T1
- Remove buildkite test to avoid overloading

.buildkite/pipeline.yml

@@ -1,39 +1,39 @@
 steps:
-  - label: ":pipeline: Upload NoMotion Tests"
-    env:
-      TEST_GROUP: "nomotion"
-    command: buildkite-agent pipeline upload .buildkite/runtests.yml
-    agents:
-      queue: "juliagpu"
+  # - label: ":pipeline: Upload NoMotion Tests"
+  #   env:
+  #     TEST_GROUP: "nomotion"
+  #   command: buildkite-agent pipeline upload .buildkite/runtests.yml
+  #   agents:
+  #     queue: "juliagpu"
 
-  - label: ":pipeline: Upload Motion Tests"
-    env:
-      TEST_GROUP: "motion"
-    command: buildkite-agent pipeline upload .buildkite/runtests.yml
-    agents:
-      queue: "juliagpu"
+  # - label: ":pipeline: Upload Motion Tests"
+  #   env:
+  #     TEST_GROUP: "motion"
+  #   command: buildkite-agent pipeline upload .buildkite/runtests.yml
+  #   agents:
+  #     queue: "juliagpu"
 
-  - label: ":pipeline: Launch Benchmarks"
-    if: build.message !~ /skip benchmarks/
-    agents:
-      queue: "juliagpu"
-    plugins:
-      - monorepo-diff#v1.0.1:
-          diff: "git diff --name-only HEAD~1"
-          interpolation: false
-          watch:
-            - path:
-                - "KomaMRICore/src/**/*"
-                - "KomaMRICore/ext/**/*"
-                - "KomaMRICore/Project.toml"
-                - "KomaMRIBase/src/**/*"
-                - "KomaMRIBase/Project.toml"
-                - "benchmarks/**/*"
-                - ".buildkite/**/*"
-                - ".github/workflows/Benchmark.yml"
-                - "Project.toml"
-              config:
-                command: "buildkite-agent pipeline upload .buildkite/runbenchmarks.yml"
-                agents:
-                  queue: "juliagpu"
+  # - label: ":pipeline: Launch Benchmarks"
+  #   if: build.message !~ /skip benchmarks/
+  #   agents:
+  #     queue: "juliagpu"
+  #   plugins:
+  #     - monorepo-diff#v1.0.1:
+  #         diff: "git diff --name-only HEAD~1"
+  #         interpolation: false
+  #         watch:
+  #           - path:
+  #               - "KomaMRICore/src/**/*"
+  #               - "KomaMRICore/ext/**/*"
+  #               - "KomaMRICore/Project.toml"
+  #               - "KomaMRIBase/src/**/*"
+  #               - "KomaMRIBase/Project.toml"
+  #               - "benchmarks/**/*"
+  #               - ".buildkite/**/*"
+  #               - ".github/workflows/Benchmark.yml"
+  #               - "Project.toml"
+  #             config:
+  #               command: "buildkite-agent pipeline upload .buildkite/runbenchmarks.yml"
+  #               agents:
+  #                 queue: "juliagpu"
 

docs/src/explanation/3-phantom-format.md

@@ -0,0 +1,40 @@
+# Phantom File Format
+
+## Introduction
+
+While there is already an open and fairly standardised format for MRI sequences 
+such as [Pulseq](https://pulseq.github.io/index.html), this is not the case for digital phantoms.
+That's why we defined a new ''.phantom'' format, which relies on the [HDF5 standard](https://www.hdfgroup.org/solutions/hdf5/).
+HDF5 is specially designed to store large amounts of heterogeneous data and to make it readable 
+and writable quickly and easily. In addition, it allows the storage of metadata. 
+For all these reasons, it is the ideal file format for storing phantoms. 
+
+## File Format Specification
+
+### Phantom File Tree
+
+```@raw html
+<p><img class="docs-light-only" width="80%" src="assets/ph-phantom-file-format-light.svg"/></p>
+<p><img class="docs-dark-only"  width="80%" src="assets/ph-phantom-file-format-dark.svg"/></p>
+```
+
+### Action types
+
+```@raw html
+<p><img class="docs-light-only" width="80%" src="assets/ph-action-types-light.svg"/></p>
+<p><img class="docs-dark-only"  width="80%" src="assets/ph-action-types-dark.svg"/></p>
+```
+
+### TimeSpan types
+
+```@raw html
+<p><img class="docs-light-only" width="80%" src="assets/ph-timespan-types-light.svg"/></p>
+<p><img class="docs-dark-only"  width="80%" src="assets/ph-timespan-types-dark.svg"/></p>
+```
+
+### SpinSpan types
+
+```@raw html
+<p><img class="docs-light-only" width="80%" src="assets/ph-spinspan-types-light.svg"/></p>
+<p><img class="docs-dark-only"  width="80%" src="assets/ph-spinspan-types-dark.svg"/></p>
+```

docs/src/explanation/lit-1-phantom.jl

@@ -63,9 +63,9 @@ obj = brain_phantom2D()
 # You can visualize the **Phantom** struct using the [`plot_phantom_map`](@ref) function, 
 # which is part of the **KomaMRIPlots** subdependency. This function plots the magnitude of a property for 
 # each magnetization at a specific spatial position. You can observe properties such as proton density 
-# and relaxation times, so feel free to replace the `:ρ` symbol with another property of the phantom in the example below:
+# and relaxation times, so feel free to replace the `:T1` symbol with another property of the phantom in the example below:
 
-p1 = plot_phantom_map(obj, :ρ; height=450)
+p1 = plot_phantom_map(obj, :T1; height=450)
 
 #md savefig(p1, "../assets/doc-1-phantom.html") # hide
 #jl display(p1)

docs/src/index.md

@@ -6,7 +6,7 @@
 
 ```@raw html
 <p align="center"><img class="docs-light-only" width="100%" src="assets/koma-schema.svg"/></p>
-<p align="center"><img class="docs-dark-only"  width="100%" src="assets/koma-schema-dark.svg""/></p>
+<p align="center"><img class="docs-dark-only"  width="100%" src="assets/koma-schema-dark.svg"/></p>
 ```
 We organized the documentation following the philosophy presented by [David Laing](https://documentation.divio.com/).
 

docs/utils.jl

@@ -65,7 +65,8 @@ function literate_doc_folder(input_folder, output_doc_section; lit_pattern="lit-
                 input_folder;
                 repo_root_url,
                 preprocess=_link_example(filename_gen),
-                name=filename_gen
+                name=filename_gen,
+                execute=true
             )
             Literate.script(tutorial_src, input_folder; name=filename_gen, repo_root_url)
             Literate.notebook(tutorial_src, input_folder; name=filename_gen, execute=false)