Process completed with exit code 1.

┌ Error: ERROR: Test Summary: | Pass Fail Error Total Time MetaManifold | 825 1 9 835 1m16.8s CladeCumulus & Phylogenetic Integration | 74 1 8 83 18.2s Strict raw jplace evidence reader, edge projection, and independent LWR threshold | 9 1 10 7.1s Dual-hierarchy CladeCumulus, polyphyly detection, drag-and-drop, and HTTP routes | 3 1 7 11 8.4s ERROR: LoadError: Some tests did not pass: 825 passed, 1 failed, 9 errored, 0 broken.

Dual-hierarchy CladeCumulus, polyphyly detection, drag-and-drop, and HTTP routes: Error During Test at /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:340 Test threw exception Expression: length(comb.diversity.samples) == 2 KeyError: key :diversity not found Stacktrace: [1] getindex(h::Dict{Symbol, Int64}, key::Symbol) @ Base ./dict.jl:477 [2] get(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, key::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:87 [3] getproperty(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, prop::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:127 [4] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:27 [5] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:279 [inlined] [7] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:340 [inlined] [9] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined]

Dual-hierarchy CladeCumulus, polyphyly detection, drag-and-drop, and HTTP routes: Error During Test at /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:339 Test threw exception Expression: comb.diversity !== nothing KeyError: key :diversity not found Stacktrace: [1] getindex(h::Dict{Symbol, Int64}, key::Symbol) @ Base ./dict.jl:477 [2] get(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, key::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:87 [3] getproperty(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, prop::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:127 [4] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:27 [5] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:279 [inlined] [7] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:339 [inlined] [9] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined]

Dual-hierarchy CladeCumulus, polyphyly detection, drag-and-drop, and HTTP routes: Error During Test at /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:338 Test threw exception Expression: EP.verify_receipt(JSON3.read(JSON3.write(comb.receipt), Dict{String, Any})) KeyError: key :receipt not found Stacktrace: [1] getindex(h::Dict{Symbol, Int64}, key::Symbol) @ Base ./dict.jl:477 [2] get(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, key::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:87 [3] getproperty(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, prop::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:127 [4] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:27 [5] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:279 [inlined] [7] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:338 [inlined] [9] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] [10] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:338 [inlined]

Dual-hierarchy CladeCumulus, polyphyly detection, drag-and-drop, and HTTP routes: Error During Test at /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:337 Test threw exception Expression: any((dt->begin #= /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:337 =# dt.taxon == "SplitGenus" && dt.monophyletic == false end), comb.concordance.dispersed_taxa) KeyError: key :concordance not found Stacktrace: [1] getindex(h::Dict{Symbol, Int64}, key::Symbol) @ Base ./dict.jl:477 [2] get(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, key::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:87 [3] getproperty(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, prop::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:127 [4] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:27 [5] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:279 [inlined] [7] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:337 [inlined] [9] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] [10] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:337 [inlined]

Dual-hierarchy CladeCumulus, polyphyly detection, drag-and-drop, and HTTP routes: Error During Test at /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:336 Test threw exception Expression: all((ch->begin #= /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:336 =# ch.cumulative_count <= comb.root.cumulative_count end), comb.root.children) KeyError: key :root not found Stacktrace: [1] getindex(h::Dict{Symbol, Int64}, key::Symbol) @ Base ./dict.jl:477 [2] get(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, key::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:87 [3] getproperty(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, prop::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:127 [4] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:27 [5] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:279 [inlined] [7] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:336 [inlined] [9] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] [10] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:336 [inlined]

Dual-hierarchy CladeCumulus, polyphyly detection, drag-and-drop, and HTTP routes: Error During Test at /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:335 Test threw exception Expression: ≈(comb.root.cumulative_count, 110.0, atol = 1.0e-9) KeyError: key :root not found Stacktrace: [1] getindex(h::Dict{Symbol, Int64}, key::Symbol) @ Base ./dict.jl:477 [2] get(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, key::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:87 [3] getproperty(obj::JSON3.Object{Base.CodeUnits{UInt8, String}, Vector{UInt64}}, prop::Symbol) @ JSON3 ~/.julia/packages/JSON3/rT1w2/src/JSON3.jl:127 [4] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:27 [5] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:279 [inlined] [7] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:335 [inlined] [9] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined]

Dual-hierarchy CladeCumulus, polyphyly detection, drag-and-drop, and HTTP routes: Test Failed at /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:333 Expression: r_comb.status == 200 Evaluated: 500 == 200 Stacktrace: [1] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:27 [2] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [3] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:279 [inlined] [4] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [5] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:333 [inlined] [6] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:680 [inlined]

Strict raw jplace evidence reader, edge projection, and independent LWR threshold: Error During Test at /home/runner/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:129 Got exception outside of a @test FieldError: type MetaManifold.CladeCumulus.PhyloNode has no field `edge_num`, available fields: `id`, `name`, `branch_length`, `support`, `edge_number`, `children` Stacktrace: [1] getproperty @ ./Base_compiler.jl:54 [inlined] [2] (::MetaManifold.CladeCumulus.var"#walk#_graft_jplace_queries##2"{Base.RefValue{Int64}, Dict{Int64, Vector{MetaManifold.CladeCumulus._GraftedQuerySpec}}})(u::MetaManifold.CladeCumulus.PhyloNode) @ MetaManifold.CladeCumulus ~/work/MetaManifold-WebUI/MetaManifold-WebUI/src/analysis/clade_cumulus.jl:1032 [3] (::MetaManifold.CladeCumulus.var"#walk#_graft_jplace_queries##2"{Base.RefValue{Int64}, Dict{Int64, Vector{MetaManifold.CladeCumulus._GraftedQuerySpec}}})(u::MetaManifold.CladeCumulus.PhyloNode) (repeats 2 times) @ MetaManifold.CladeCumulus ~/work/MetaManifold-WebUI/MetaManifold-WebUI/src/analysis/clade_cumulus.jl:1031 [4] _graft_jplace_queries(base_root::MetaManifold.CladeCumulus.PhyloNode, jd::MetaManifold.CladeCumulus.JplaceDocument, asv_reads::OrderedDict{String, Float64}, asv_deepest_taxon::Dict{String, Union{Nothing, String}}, asv_tax_conf::Dict{String, Float64}, query_lwr::Dict{String, Float64}) @ MetaManifold.CladeCumulus ~/work/MetaManifold-WebUI/MetaManifold-WebUI/src/analysis/clade_cumulus.jl:1054 [5] build_clade_tree(df::DataFrame; mode::Symbol, newick::Nothing, jplace_json::String, sample_cols::Nothing, rank_cols::Nothing, support_threshold::Float64, lwr_threshold::Float64, tree_method::Symbol, max_asvs::Int64, seed::Int64) @ MetaManifold.CladeCumulus ~/work/MetaManifold-WebUI/MetaManifold-WebUI/src/analysis/clade_cumulus.jl:1109 [6] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:27 [7] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:130 [inlined] [9] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [10] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/unit/test_clade_cumulus.jl:162 [inlined] [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:307 [12] top-level scope @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/runtests.jl:96 [13] macro expansion @ ~/work/_temp/julia-1.12.5/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [14] macro expansion @ ~/work/MetaManifold-WebUI/MetaManifold-WebUI/test/runtests.jl:97 [inlined] [15] include(mod::Module, _path::String) @ Base ./Base.jl:306 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [17] _start() @ Base ./client.jl:550 ┌ Error: ERROR: │ exception = │ MethodError: no method matching _valid_tree_file(::SubString{String}) │ The function `_valid_tree_file` exists, but no method is defined for this combination of argument types. │ │ Closest candidates are: │ _valid_tree_file(!Matched::String) │ @ MetaManifold ~/work/MetaManifold-WebUI/MetaManifold-WebUI/src/server/routes/trees.jl:22 │ │ Stacktrace:

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@11d5960a326750d5838078e36cf38b85af677262. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@11d5960a326750d5838078e36cf38b85af677262. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@11d5960a326750d5838078e36cf38b85af677262. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/