test/test_plot_diagnostics.jl: Additional tests for plotting.

src/LineageCollapse.jl

@@ -12,9 +12,12 @@ module LineageCollapse
     export compute_distance, compute_pairwise_distance, perform_clustering
 
     function plot_diagnostics(args...; opts...)
-        error(isdefined(Main, :CairoMakie) ? "Invalid method call" : "Import CairoMakie to enable plotting")
+        if !isdefined(@__MODULE__, :CairoMakie)
+            error("Import CairoMakie to enable plotting")
+        else
+            error("Invalid method call")
+        end
     end
-
     include("data_loading.jl")
     include("preprocessing.jl")
     include("lineage_processing.jl")

src/data_loading.jl

@@ -3,12 +3,12 @@
               delimiter::Char='\t', 
               required_columns=[:sequence_id, :sequence, :v_sequence_end, :j_sequence_start, :cdr3, :v_call, :j_call, :stop_codon])::DataFrame
 
-Load data from a file and return a DataFrame.
+Load data from a file (compressed or uncompressed) and return a DataFrame.
 
 # Arguments
 - `filepath::String`: Path to the data file.
 - `delimiter::Char='\t'`: Delimiter used in the data file (default: tab).
-- `required_columns::Vector{Symbol}`: Required columns in the data file.
+- `required_columns::Vector{Symbol}`: Required columns to select from the data file.
 
 # Returns
 - `DataFrame`: DataFrame containing the loaded data.
@@ -19,14 +19,10 @@ Load data from a file and return a DataFrame.
 function load_data(filepath::String; 
                    delimiter::Char='\t', 
                    required_columns=[:sequence_id, :sequence, :v_sequence_end, :j_sequence_start, :cdr3, :v_call, :j_call, :stop_codon])::DataFrame
-    # First, read the header to check for required columns
-    header = String.(split(readline(filepath), delimiter))
-    missing_columns = setdiff(String.(required_columns), header)
-
-    if !isempty(missing_columns)
-        throw(ArgumentError("Missing required columns: $(join(missing_columns, ", "))"))
+    try
+        df = CSV.File(filepath, delim=delimiter, select=required_columns) |> DataFrame
+        df = df[!, required_columns]  # This is to ensure exception is thrown if any column is missing
+    catch e
+        rethrow(e)
     end
-
-    # If all required columns are present, load the data
-    return CSV.File(filepath, delim=delimiter, select=required_columns) |> DataFrame
 end

test/runtests.jl

@@ -5,4 +5,5 @@ using LineageCollapse
     include("test_data_loading.jl")
     include("test_preprocessing.jl")
     include("test_lineage_processing.jl")
+    include("test_plot_diagnostics.jl")
 end

test/test_plot_diagnostics.jl

@@ -0,0 +1,35 @@
+using Test
+using LineageCollapse
+
+@testset "Plot Diagnostics" begin
+    @testset "CairoMakie not imported" begin
+        # Ensure CairoMakie is not imported
+        if isdefined(Main, :CairoMakie)
+            @warn "CairoMakie is already imported, which may affect the test results"
+        end
+
+        # Test that the function throws an error with the correct message
+        @test_throws ErrorException("Import CairoMakie to enable plotting") plot_diagnostics()
+
+        # Test with arguments
+        @test_throws ErrorException("Import CairoMakie to enable plotting") plot_diagnostics(rand(10))
+
+        # Test with keyword arguments
+        @test_throws ErrorException("Import CairoMakie to enable plotting") plot_diagnostics(color="red")
+    end
+
+    @testset "CairoMakie imported" begin
+        # Create a temporary module to simulate CairoMakie being imported
+        @eval Main module TestPlotDiagnostics
+            using LineageCollapse
+
+            # Simulate CairoMakie being imported
+            LineageCollapse.eval(:(CairoMakie = 1))
+
+            using Test
+            @test_throws ErrorException("Invalid method call") plot_diagnostics()
+            @test_throws ErrorException("Invalid method call") plot_diagnostics(rand(10))
+            @test_throws ErrorException("Invalid method call") plot_diagnostics(color="red")
+        end
+    end
+end