Let runtests.jl handle testing

* fix bug in main.yml (tests renamed to test) * update RunSampling.jl to reference pcvct.jl
drbergman · Sep 5, 2024 · a3644d4 · a3644d4
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commit a3644d4
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Showing 5 changed files with 33 additions and 35 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -56,19 +56,19 @@ jobs:
     - uses: julia-actions/setup-julia@v2
       with:
         version: ${{ matrix.julia-version }}
+    - name: Set environment variable PHYSICELL_CPP
+      run: echo "PHYSICELL_CPP=${{ matrix.compiler }}" >> $GITHUB_ENV
     - uses: julia-actions/cache@v2
     - uses: julia-actions/julia-buildpkg@v1
     - uses: julia-actions/julia-runtest@v1 # not sure what this does yet...runs files marked as tests?
-    - name: Install julia dependencies
-      run: |
-        julia -e 'using Pkg; \
-                  Pkg.add(["DataFrames", "CSV", "SQLite", "Random", "LightXML", "LazyGrids", "Dates", "Tables", "Distributions", "Statistics", "QuasiMonteCarlo", "Sobol", "MAT", "FFTW", "GlobalSensitivity"]); \
-                  Pkg.update()'
-        echo "Julia packages added and updated"
-    - name: Set environment variable PHYSICELL_CPP
-      run: echo "PHYSICELL_CPP=${{ matrix.compiler }}" >> $GITHUB_ENV
-    - name: Run sampling
-      run: |
-        cd ./tests
-        julia -t 8 ./test-project/VCT/RunSampling.jl
-        echo "RunSampling.jl complete"
+    # - name: Install julia dependencies
+    #   run: |
+    #     julia -e 'using Pkg; \
+    #               Pkg.add(["DataFrames", "CSV", "SQLite", "Random", "LightXML", "LazyGrids", "Dates", "Tables", "Distributions", "Statistics", "QuasiMonteCarlo", "Sobol", "MAT", "FFTW", "GlobalSensitivity"]); \
+    #               Pkg.update()'
+    #     echo "Julia packages added and updated"
+    # - name: Run sampling
+    #   run: |
+    #     cd ./test
+    #     julia -t 8 ./test-project/VCT/RunSampling.jl
+    #     echo "RunSampling.jl complete"
diff --git a/src/VCTLoader.jl b/src/VCTLoader.jl
@@ -18,7 +18,7 @@ end
 
 function getLabels(xml_doc::XMLDocument)
     xml_path = ["cellular_information", "cell_populations", "cell_population", "custom", "simplified_data", "labels"]
-    labels_element = VCTModule.retrieveElement(xml_doc, xml_path; required=true)
+    labels_element = retrieveElement(xml_doc, xml_path; required=true)
 
     labels = String[]
     for label in child_elements(labels_element)
@@ -45,17 +45,17 @@ indexToFilename(index::Int) = "output$(lpad(index,8,"0"))"
 
 function PhysiCellSnapshot(folder::String, index::Union{Int, Symbol}; labels::Vector{String}=String[])
     filepath_base = "$(folder)/$(indexToFilename(index))"
-    xml_doc = VCTModule.openXML("$(filepath_base).xml")
+    xml_doc = openXML("$(filepath_base).xml")
     mat_file = "$(filepath_base)_cells.mat"
-    time = VCTModule.getField(xml_doc, ["metadata","current_time"]) |> x->parse(Float64, x)
+    time = getField(xml_doc, ["metadata","current_time"]) |> x->parse(Float64, x)
     if isempty(labels)
         labels = getLabels(xml_doc)
     end
     cells = DataFrame(matread(mat_file)["cell"]', labels)
     cells[!,:ID] = convert.(Int,cells[!,:ID])
     cells[!,:dead] = convert.(Bool,cells[!,:dead])
     cells[!,:cell_type] = convert.(Int,cells[!,:cell_type])
-    VCTModule.closeXML(xml_doc)
+    closeXML(xml_doc)
     return PhysiCellSnapshot(folder, index, time, DataFrame(cells))
 end
 

diff --git a/src/pcvct.jl b/src/pcvct.jl
@@ -1,7 +1,5 @@
 module pcvct
 
 include("VCTModule.jl")
-# using .VCTModule
-# export VCTModule
 
 end
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -3,5 +3,5 @@ using Test
 
 @testset "pcvct.jl" begin
     # Write your tests here.
-    @assert 2+2==4
+    include("./test-project/VCT/RunSampling.jl")
 end
diff --git a/test/test-project/VCT/RunSampling.jl b/test/test-project/VCT/RunSampling.jl
@@ -1,5 +1,7 @@
-include("../../../src/VCTModule.jl") # include
-using .VCTModule
+using Test, pcvct
+
+# include("../../../src/pcvct.jl") # include
+# using .pcvct
 
 path_to_physicell_folder = "./PhysiCell" # path to PhysiCell folder
 path_to_data_folder = "./test-project/data" # path to data folder
@@ -22,7 +24,7 @@ config_variation_ids, rulesets_variation_ids = addVariations(GridVariation(), co
 
 println("""
 ############################################
-##   DATABASE SUCCESSFULLY INITIALIZED!   ##
+##     DATABASE SUCCESSFULLY UPDATED!     ##
 ############################################
 """)
 
@@ -63,8 +65,8 @@ println("""
 ############################################
 """)
 
-query = VCTModule.constructSelectQuery("simulations", "")
-df = queryToDataFrame(query; is_row=true)
+query = pcvct.constructSelectQuery("simulations", "")
+df = pcvct.queryToDataFrame(query; is_row=true)
 
 println("""
 ############################################
@@ -75,19 +77,17 @@ println("""
 monad_min_length = 2
 
 EV = ElementaryVariation[]
-xml_path = [VCTModule.cyclePath("default"); "phase_durations"; "duration:index:0"]
+xml_path = [pcvct.cyclePath("default"); "phase_durations"; "duration:index:0"]
 push!(EV, ElementaryVariation(xml_path, [1.0, 2.0]))
-xml_path = [VCTModule.cyclePath("default"); "phase_durations"; "duration:index:1"]
+xml_path = [pcvct.cyclePath("default"); "phase_durations"; "duration:index:1"]
 push!(EV, ElementaryVariation(xml_path, [3.0, 4.0]))
-xml_path = [VCTModule.cyclePath("default"); "phase_durations"; "duration:index:2"]
+xml_path = [pcvct.cyclePath("default"); "phase_durations"; "duration:index:2"]
 push!(EV, ElementaryVariation(xml_path, [5.0, 6.0]))
-xml_path = [VCTModule.cyclePath("default"); "phase_durations"; "duration:index:3"]
+xml_path = [pcvct.cyclePath("default"); "phase_durations"; "duration:index:3"]
 push!(EV, ElementaryVariation(xml_path, [7.0, 8.0]))
 
-reference_config_variation_id = config_variation_id
-reference_rulesets_variation_id = rulesets_variation_id
-
-sampling = Sampling(monad_min_length, config_folder, rulesets_collection_folder, ic_cell_folder, ic_substrate_folder, ic_ecm_folder, custom_code_folder, reference_config_variation_id, reference_rulesets_variation_id)
+config_variation_ids, rulesets_variation_ids = addVariations(GridVariation(), config_folder, rulesets_collection_folder, EV; reference_variation_id=config_variation_id, reference_rulesets_variation_id=rulesets_variation_id)
+sampling = Sampling(monad_min_length, config_folder, rulesets_collection_folder, ic_cell_folder, ic_substrate_folder, ic_ecm_folder, custom_code_folder, config_variation_ids, rulesets_variation_ids)
 
 println("""
 ############################################
@@ -106,10 +106,10 @@ println("""
 simulation_ids = getSimulations(sampling)
 expected_num_sims = monad_min_length
 for ev in EV
-    expected_num_sims *= length(ev.values)
+    global expected_num_sims *= length(ev.values)
 end
 
-@assert length(simulation_ids) == expected_num_sims
+@test length(simulation_ids) == expected_num_sims
 
 println("""
 ############################################