failed to run `@example` block in src/man/basics.md:63-67 ```@example ischia mdata = readh5mu(joinpath(pkgdir(ISCHIA), "docs", "src", "assets", "mudata.h5mu")) lr_network = load(joinpath(pkgdir(ISCHIA), "docs", "src", "assets", "lr_network.rds")) size(lr_network) ``` exception = The file is not an HDF5 file Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] readh5mu(filename::String; backed::Bool) @ Muon ~/.julia/packages/Muon/OxkVO/src/mudata.jl:150 [3] readh5mu(filename::String) @ Muon ~/.julia/packages/Muon/OxkVO/src/mudata.jl:144 [4] top-level scope @ basics.md:64 [5] eval @ ./boot.jl:385 [inlined] [6] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [7] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [8] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [9] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [10] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [11] with_logger @ ./logging.jl:627 [inlined] [12] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [13] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/basics.md:71-92 ```@example ischia gene_names = mdata["Spatial"].var.name mdata["Spatial"].var_names = gene_names # Create LR_Pairs column lr_network[!, :LR_Pairs] = string.(lr_network.from, "_", lr_network.to); lr_network = lr_network[:, [:from, :to, :LR_Pairs]] # Filter lr_network based on conditions from_filter = in.(lr_network[:, :from], Ref(gene_names)) to_filter = in.(lr_network[:, :to], Ref(gene_names)) all_LR_network = lr_network[from_filter .& to_filter, :]; # Extract unique genes and common genes all_LR_genes = unique(vcat(all_LR_network[:, :from], all_LR_network[:, :to])) all_LR_genes_comm = intersect(all_LR_genes, collect(gene_names)); # Create LR.pairs and LR.pairs.AllCombos LR_pairs = all_LR_network[:, :LR_Pairs] all_combos = [join(combo, "_") for combo in combinations(all_LR_genes_comm, 2)]; length(all_combos) ``` exception = UndefVarError: `mdata` not defined Stacktrace: [1] top-level scope @ basics.md:72 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/basics.md:96-107 ```@example ischia spatial_object = mdata["Spatial"] spatial_object.var_names = spatial_object.var.name Condition = unique(spatial_object.obs[!, "orig.ident"]) LR_list = all_LR_genes_comm LR_pairs = LR_pairs exp_th = 1 corr_th = 0.2 cc4_enriched_lr = find_enriched_LR_pairs(spatial_object, ["CC4"], Condition, LR_list, LR_pairs, exp_th, corr_th); cc7_enriched_lr = find_enriched_LR_pairs(spatial_object, ["CC7"], Condition, LR_list, LR_pairs, exp_th, corr_th); ``` exception = UndefVarError: `mdata` not defined Stacktrace: [1] top-level scope @ basics.md:97 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/basics.md:111-113 ```@example ischia first(cc4_enriched_lr["enriched_LRs"], 5) ``` exception = UndefVarError: `cc4_enriched_lr` not defined Stacktrace: [1] top-level scope @ basics.md:112 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/basics.md:115-117 ```@example ischia first(cc7_enriched_lr["enriched_LRs"], 5) ``` exception = UndefVarError: `cc7_enriched_lr` not defined Stacktrace: [1] top-level scope @ basics.md:116 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/basics.md:121-124 ```@example ischia diff_df47 = find_differentially_cooccurring_LR_pairs(cc7_enriched_lr, cc4_enriched_lr, 0.05, 0.1) first(diff_df47, 10) ``` exception = UndefVarError: `cc7_enriched_lr` not defined Stacktrace: [1] top-level scope @ basics.md:122 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752

Process completed with exit code 1.

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/cache@4d4ae6ae148a43d0fd1eda1800170683e9882738, pyTooling/Actions/with-post-step@adef08d3bdef092282614f3b683897cefae82ee3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Codecov: Failed to properly create commit: The process '/home/runner/work/_actions/codecov/codecov-action/v4/dist/codecov' failed with exit code 1

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/cache@4d4ae6ae148a43d0fd1eda1800170683e9882738, pyTooling/Actions/with-post-step@adef08d3bdef092282614f3b683897cefae82ee3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Codecov: Failed to properly create commit: The process '/home/runner/work/_actions/codecov/codecov-action/v4/dist/codecov' failed with exit code 1

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/cache@4d4ae6ae148a43d0fd1eda1800170683e9882738, pyTooling/Actions/with-post-step@adef08d3bdef092282614f3b683897cefae82ee3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Codecov: Failed to properly create commit: The process '/home/runner/work/_actions/codecov/codecov-action/v4/dist/codecov' failed with exit code 1