Merge pull request #34 from divital-coder/main

Documentation setup for deployment.

.github/workflows/docx.yml

@@ -0,0 +1,24 @@
+name: Documenter
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.10'  # Use the appropriate Julia version
+      - name: Install dependencies
+        run: julia --project=docs -e 'using Pkg; Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # GitHub automatically provides this
+        run: julia --project=docs docs/make.jl

docs/make.jl

@@ -4,25 +4,27 @@ using DocumenterVitepress
 
 DocMeta.setdocmeta!(MedImages, :DocTestSetup, :(using MedImages); recursive=true)
 
-makedocs(;
-    modules=[MedImages],
-    repo=Remotes.GitHub("JuliaHealth", "MedImage.jl"),
-    authors="Jakub-Mitura <[email protected]>, Divyansh-Goyal <[email protected]> and contributors",
-    sitename="MedImages.jl",
-    format=DocumenterVitepress.MarkdownVitepress(
-        repo="https://github.com/JuliaHealth/MedImage.jl",
-    ),
-    pages=[
-        "Home" => "index.md",
+pgs = [ "Home" => "index.md",
         "Tutorials" => "tutorials.md",
         "Contributing" => "contributing.md"
-    ],
-)
+       ]
+
+fmt = DocumenterVitepress.MarkdownVitepress(
+      repo = "https://github.com/Juliahealth/MedImages.jl",)
 
+
+makedocs(;
+    modules=[MedImages],
+    repo=Remotes.GitHub("JuliaHealth", "MedImages.jl"),
+    authors="Jakub-Mitura <[email protected]>, Divyansh-Goyal <[email protected]>, Jan-Zubik and contributors",
+    sitename="MedImages.jl",
+    format=fmt,
+    pages=pgs
+   )    
 deploydocs(;
-    repo="github.com/JuliaHealth/MedImage.jl",
+    repo="github.com/JuliaHealth/MedImages.jl",
     target="build", # this is where Vitepress stores its output
     devbranch="main",
     branch="gh-pages",
     push_preview=true
-)
+)

docs/src/index.md

@@ -1,34 +1,33 @@
 ```@docs
-MedImages.string_intent
-MedImages.Mode_mi
-MedImages.calculate_inverse_44_matrix
-MedImages.formulate_sto_xyz
-MedImages.Image_type
-MedImages.formulate_qto_xyz
-MedImages.calculate_qfac
-MedImages.interpolate_point
-MedImages.Interpolator_enum
-MedImages.get_pixel_data
-MedImages.get_base_indicies_arr
-MedImages.interpolate_my
-MedImages.formulate_xform_string
-MedImages.CoordinateTerms
-MedImages.formulate_string
-MedImages.cast_to_array_b_type
-MedImages.Image_subtype
-MedImages.check_sform_qform_similarity
-MedImages.formulate_timing_scale_for_xyzt_time
-MedImages.set_spacing_for_nifti_files
-MedImages.resample_to_image
-MedImages.scale_mi
-MedImages.set_direction_for_nifti_file
-MedImages.set_origin_for_nifti_file
-MedImages.pad_mi
-MedImages.unique_series_id_within_dicom_files
-MedImages.formulate_nifti_image_struct
-MedImages.formulate_header_data_dict
-MedImages.formulate_spacing_scale_for_xyzt_space
-MedImages.crop_mi
-MedImages.scale
-MedImages.translate_mi
-```
+MedImages.MedImage
+MedImages.Utils.create_nii_from_medimage
+MedImages.Load_and_save.load_image
+MedImages.save_med_image
+MedImages.Basic_transformations.crop_mi
+MedImages.Basic_transformations.translate_mi
+MedImages.Brute_force_orientation.brute_force_find_perm_rev
+MedImages.Utils.interpolate_my
+MedImages.Spatial_metadata_change.change_orientation
+MedImages.Load_and_save.unique_series_id_within_dicom_files
+MedImages.Resample_to_target.scale
+MedImages.Basic_transformations.pad_mi
+MedImages.Resample_to_target.resample_to_image
+MedImages.Basic_transformations.computeIndexToPhysicalPointMatrices_Julia
+MedImages.Basic_transformations.scale_mi
+MedImages.Utils.cast_to_array_b_type
+MedImages.Load_and_save.get_pixel_data
+MedImages.Spatial_metadata_change.scale
+MedImages.Utils.interpolate_point
+MedImages.load_med_image
+MedImages.Utils.get_base_indicies_arr
+MedImages.MedImage_data_struct.Interpolator_enum
+MedImages.MedImage_data_struct.Mode_mi
+MedImages.MedImage_data_struct.Image_subtype
+MedImages.MedImage_data_struct.current_device_enum
+MedImages.MedImage_data_struct.Image_type
+MedImages.MedImage_data_struct.CoordinateMajornessTerms
+MedImages.MedImage_data_struct.Orientation_code
+MedImages.MedImage_data_struct.CoordinateTerms
+MedImages.Load_and_save.infer_modality
+```
+