Merge pull request #29 from open-AIMS/julia-format

JuliaFormatter config, reformat project, doc improvements.

.JuliaFormatter.toml

@@ -0,0 +1,20 @@
+style="blue"
+indent=4
+margin=92
+always_for_in="nothing"
+for_in_replacement="∈"
+whitespace_typedefs=false
+import_to_using=true
+align_struct_field=true
+align_assignment=false
+align_conditional=true
+align_pair_arrow=false
+normalize_line_endings="unix"
+align_matrix=true
+join_lines_based_on_source=true
+indent_submodule=true
+surround_whereop_typeparameters=false
+yas_style_nesting=true
+trailing_comma=false
+short_to_long_function_def=false
+conditional_to_if=false

.github/workflows/Format.yml

@@ -0,0 +1,13 @@
+name: Format suggestions
+on:
+  pull_request:
+    # this argument is not required if you don't use the `suggestion-label` input
+    types: [ opened, reopened, synchronize, labeled, unlabeled ]
+jobs:
+  code-style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: julia-actions/julia-format@v3
+        with:
+          version: '1' # Set `version` to '1.0.54' if you need to use JuliaFormatter.jl v1.0.54 (default: '1')
+          suggestion-label: 'format-suggest' # leave this unset or empty to show suggestions for all PRs

docs/make.jl

@@ -14,10 +14,10 @@ makedocs(;
     modules=[ReefGuideAPI],
     clean=true,
     doctest=true,
-    format=DocumenterVitepress.MarkdownVitepress(
+    format=DocumenterVitepress.MarkdownVitepress(;
         repo="github.com/open-AIMS/ReefGuideAPI.jl",
         devbranch="main",
-        devurl = "dev"
+        devurl="dev"
     ),
     draft=false,
     source="src",

docs/makelocal.jl

@@ -12,11 +12,11 @@ makedocs(;
     doctest=true,
     authors="Iwanaga et al.",
     checkdocs=:all,
-    format=DocumenterVitepress.MarkdownVitepress(
+    format=DocumenterVitepress.MarkdownVitepress(;
         repo="github.com/open-AIMS/ReefGuideAPI.jl", # this must be the full URL!
         devbranch="main",
         devurl="dev",
-        build_vitepress=false;
+        build_vitepress=false
     ),
     remotes=nothing,
     draft=true,
@@ -31,7 +31,7 @@ makedocs(;
 deploydocs(;
     repo="github.com/open-AIMS/ReefGuideAPI.jl.git",
     target="build", # this is where Vitepress stores its output
-    branch = "gh-pages",
+    branch="gh-pages",
     devbranch="main",
-    push_preview = true
+    push_preview=true
 )

src/Middleware.jl

@@ -12,10 +12,10 @@ const CORS_HEADERS = [
 
 # https://juliaweb.github.io/HTTP.jl/stable/examples/#Cors-Server
 function CorsMiddleware(handler)
-    return function(req::HTTP.Request)
+    return function (req::HTTP.Request)
         @debug "CORS middleware"
         # determine if this is a pre-flight request from the browser
-        if HTTP.method(req)=="OPTIONS"
+        if HTTP.method(req) == "OPTIONS"
             return HTTP.Response(200, CORS_HEADERS)
         else
             # passes the request to the AuthMiddleware and route function.
@@ -28,7 +28,6 @@ function CorsMiddleware(handler)
     end
 end
 
-
 function setup_jwt_middleware(config::Dict)
     if !get(config["jwt_auth"], "JWT_ENABLED", false)
         return identity  # Return a pass-through middleware if JWT is not enabled
@@ -46,10 +45,12 @@ function setup_jwt_middleware(config::Dict)
     rsa_public = JSONWebTokens.RS256(public_key)
 
     return function jwt_auth_middleware(handler)
-        return function(req::HTTP.Request)
+        return function (req::HTTP.Request)
             auth_header = HTTP.header(req, "Authorization", "")
             if !startswith(auth_header, "Bearer ")
-                return HTTP.Response(401, "Unauthorized: Missing or invalid Authorization header.")
+                return HTTP.Response(
+                    401, "Unauthorized: Missing or invalid Authorization header."
+                )
             end
 
             token = strip(auth_header[8:end])  # Remove "Bearer " prefix
@@ -77,7 +78,9 @@ function setup_jwt_middleware(config::Dict)
                     return HTTP.Response(401, "Unauthorized: Invalid token format")
                 else
                     # Log the error for debugging
-                    @error "Unexpected error during JWT validation" exception=(e, catch_backtrace())
+                    @error "Unexpected error during JWT validation" exception = (
+                        e, catch_backtrace()
+                    )
                     return HTTP.Response(500, "Internal Server Error")
                 end
             end

src/ReefGuideAPI.jl

@@ -30,7 +30,6 @@ include("site_assessment/best_fit_polygons.jl")
 
 include("Middleware.jl")
 
-
 function get_regions()
     # TODO: Comes from config?
     regions = String[
@@ -75,7 +74,7 @@ function setup_regional_data(config::Dict)
 
     reef_data_path = config["prepped_data"]["PREPPED_DATA_DIR"]
 
-    regional_assessment_data = OrderedDict{String, RegionalCriteria}()
+    regional_assessment_data = OrderedDict{String,RegionalCriteria}()
     for reg in get_regions()
         data_paths = String[]
         data_names = String[]
@@ -93,7 +92,7 @@ function setup_regional_data(config::Dict)
             push!(data_names, string(k))
             if occursin("valid", string(dp))
                 # Load up Parquet files
-                parq_file = replace(first(g), ".tif"=>"_lookup.parq")
+                parq_file = replace(first(g), ".tif" => "_lookup.parq")
 
                 if occursin("slope", string(dp))
                     slope_table = GeoParquet.read(parq_file)
@@ -197,10 +196,9 @@ Invokes warm up of regional data cache to reduce later spin up times.
 """
 function warmup_cache(config_path::String)
     config = TOML.parsefile(config_path)
-    setup_regional_data(config)
+    return setup_regional_data(config)
 end
 
-
 function start_server(config_path)
     @info "Launching server... please wait"
 
@@ -219,7 +217,7 @@ function start_server(config_path)
     port = 8000
     @info "Initialisation complete, starting server on port $(port) with $(Threads.nthreads()) threads."
 
-    serve(
+    return serve(;
         middleware=[CorsMiddleware],
         host="0.0.0.0",
         port=port,

src/criteria_assessment/_generators_dev.jl

@@ -1,5 +1,4 @@
 
-
 abstract type DeploymentCriteria end
 
 """
@@ -48,4 +47,4 @@ function generate_criteria_structs()::Nothing
 end
 
 # function generate_criteria_state()::Nothing
-# end
+# end

src/criteria_assessment/criteria.jl

@@ -16,7 +16,6 @@ const COG_HEADERS = [
     "Cache-Control" => "max-age=86400, no-transform"
 ]
 
-
 function criteria_data_map()
     # TODO: Load from config?
     return OrderedDict(
@@ -59,6 +58,7 @@ function Base.show(io::IO, ::MIME"text/plain", z::RegionalCriteria)
     Number of valid slope locations: $(nrow(z.valid_slopes))
     Number of valid flat locations: $(nrow(z.valid_flats))
     """)
+    return nothing
 end
 
 struct CriteriaBounds{F<:Function}
@@ -79,17 +79,16 @@ end
 # Define struct type definition to auto-serialize/deserialize to JSON
 StructTypes.StructType(::Type{CriteriaBounds}) = StructTypes.Struct()
 
-
 """
     criteria_middleware(handle)
 
 Creates middleware that parses a criteria query before reaching an endpoint
 
 # Example
-https:://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40
+`https://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40`
 """
 function criteria_middleware(handle)
-    function(req)
+    function (req)
         fd = queryparams(req)
 
         criteria_names = string.(split(fd["criteria_names"], ","))
@@ -110,10 +109,10 @@ function setup_region_routes(config, auth)
         qp = queryparams(req)
         file_id = string(hash(qp))
         mask_temp_path = _cache_location(config)
-        mask_path = joinpath(mask_temp_path, file_id*".tiff")
+        mask_path = joinpath(mask_temp_path, file_id * ".tiff")
 
         if isfile(mask_path)
-            return file(mask_path, headers=COG_HEADERS)
+            return file(mask_path; headers=COG_HEADERS)
         end
 
         criteria_names, lbs, ubs = remove_rugosity(reg, parse_criteria_query(qp)...)
@@ -137,16 +136,16 @@ function setup_region_routes(config, auth)
             source="gdal",
             driver="COG",
             options=Dict{String,String}(
-                "COMPRESS"=>"DEFLATE",
-                "SPARSE_OK"=>"TRUE",
-                "OVERVIEW_COUNT"=>"5",
-                "BLOCKSIZE"=>"256",
-                "NUM_THREADS"=>n_gdal_threads(config)
+                "COMPRESS" => "DEFLATE",
+                "SPARSE_OK" => "TRUE",
+                "OVERVIEW_COUNT" => "5",
+                "BLOCKSIZE" => "256",
+                "NUM_THREADS" => n_gdal_threads(config)
             ),
             force=true
         )
 
-        return file(mask_path, headers=COG_HEADERS)
+        return file(mask_path; headers=COG_HEADERS)
     end
 
     @get auth("/bounds/{reg}") function (req::Request, reg::String)
@@ -157,25 +156,25 @@ function setup_region_routes(config, auth)
 
     # Form for testing/dev
     # https:://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40
-    @get "/" function()
-        html("""
-        <form action="/assess/Cairns-Cooktown/slopes" method="post">
-            <label for="criteria_names">Criteria Names:</label><br>
-            <input type="text" id="criteria_names" name="criteria"><br>
+    @get "/" function ()
+        return html("""
+               <form action="/assess/Cairns-Cooktown/slopes" method="post">
+                   <label for="criteria_names">Criteria Names:</label><br>
+                   <input type="text" id="criteria_names" name="criteria"><br>
 
-            <label for="lb">Lower Bound:</label><br>
-            <input type="text" id="lb" name="lower_bound"><br><br>
+                   <label for="lb">Lower Bound:</label><br>
+                   <input type="text" id="lb" name="lower_bound"><br><br>
 
-            <label for="ub">Upper Bound:</label><br>
-            <input type="text" id="ub" name="upper_bound"><br><br>
+                   <label for="ub">Upper Bound:</label><br>
+                   <input type="text" id="ub" name="upper_bound"><br><br>
 
-            <input type="submit" value="Submit">
-        </form>
-        """)
+                   <input type="submit" value="Submit">
+               </form>
+               """)
     end
 
     # Parse the form data and return it
-    @post auth("/form") function(req)
+    @post auth("/form") function (req)
         data = formdata(req)
         return data
     end

src/criteria_assessment/query_parser.jl

@@ -39,7 +39,6 @@ Remove rugosity layer from consideration if region is not Townsville.
 Rugosity data currently only exists for the Townsville region.
 """
 function remove_rugosity(reg, criteria_names, lbs, ubs)
-
     if !Base.contains(reg, "Townsville")
         # Remove rugosity layer from consideration as it doesn't exist for regions
         # outside of Townsville.

src/criteria_assessment/query_thresholds.jl

@@ -109,8 +109,7 @@ end
 
 Obtain the pixel positions of valid data.
 
-Intended for use in something like:
-https://developers.arcgis.com/javascript/latest/sample-code/layers-imagery-pixelvalues/
+Intended for use in applications similar to [ImageryLayer - client side pixel filter](https://developers.arcgis.com/javascript/latest/sample-code/layers-imagery-pixelvalues/).
 
 # Arguments
 - `data` :
@@ -200,7 +199,7 @@ Generate mask for a given region and reef type (slopes or flats) according to th
 applied to a set of criteria.
 
 # Notes
-- Zero values indicate locations to mask **out**.
+- Zeros indicate locations to mask **out**.
 - Ones indicate locations to **keep**.
 
 # Arguments
@@ -260,7 +259,7 @@ Generate mask file for a given region and reef type (slopes or flats) according
 applied to a set of criteria.
 
 # Notes
-- Zero values indicate locations to mask **out**.
+- Zeros indicate locations to mask **out**.
 - Ones indicate locations to **keep**.
 
 # Arguments
@@ -272,7 +271,12 @@ applied to a set of criteria.
 # Returns
 Nothing
 """
-function generate_criteria_mask!(fn::String, rst_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Nothing
+function generate_criteria_mask!(
+    fn::String,
+    rst_stack::RasterStack,
+    lookup::DataFrame,
+    ruleset::Vector{CriteriaBounds{Function}}
+)::Nothing
     # Create the geotiff
     res = spzeros(size(rst_stack))
     tmp_rst = Raster(
@@ -291,14 +295,14 @@ function generate_criteria_mask!(fn::String, rst_stack::RasterStack, lookup::Dat
 
     write(
         fn,
-        UInt8.(tmp_rst),
+        UInt8.(tmp_rst);
         ext=".tiff",
         source="gdal",
         driver="COG",  # GTiff
         options=Dict{String,String}(
-            "COMPRESS"=>"LZW",
-            "SPARSE_OK"=>"TRUE",
-            "OVERVIEW_COUNT"=>"5"
+            "COMPRESS" => "LZW",
+            "SPARSE_OK" => "TRUE",
+            "OVERVIEW_COUNT" => "5"
         )
     )