Cleanup type annotations.

tanaylab · May 29, 2024 · 4602846 · 4602846
1 parent 06a5342
commit 4602846
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Showing 7 changed files with 36 additions and 10 deletions.
diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-05-23T13:18:35","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-05-29T08:17:40","documenter_version":"1.4.1"}}
diff --git a/docs/v0.1.0/anndata_format.html b/docs/v0.1.0/anndata_format.html
@@ -175,7 +175,7 @@ <h1 id="AnnData-Format">
     type_property::Maybe{AbstractString} = nothing,
     rename_type::Maybe{AbstractString} = &quot;type&quot;,
     type_colors_csv::Maybe{AbstractString} = nothing,
-    type_properties::Maybe{AbstractStringSet} = nothing,
+    type_properties::Maybe{AbstractSet{&lt;:AbstractString}} = nothing,
     properties_defaults::Maybe{Dict} = nothing,
 )::Nothing
 </code>

diff --git a/docs/v0.1.0/search_index.js b/docs/v0.1.0/search_index.js
diff --git a/docs/v0.1.0/spheres.html b/docs/v0.1.0/spheres.html
@@ -166,6 +166,7 @@ <h1 id="Spheres">
     max_sphere_diameter::AbstractFloat = 2.0,
     max_neighborhood_diameter::AbstractFloat = 2.0,
     noisy_gene_fold::AbstractFloat = 1.0,
+    min_gene_correlation::AbstractFloat = 0.5,
     max_deviant_genes_fraction::AbstractFloat = 0.01,
     overwrite::Bool = false,
 )::Nothing

diff --git a/improved_spheres.auto.log b/improved_spheres.auto.log
@@ -0,0 +1,24 @@
+ERROR: SystemError: opening file "/Users/obk/projects/Metacells.jl/scripts/improved_spheres.jl": No such file or directory
+Stacktrace:
+  [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
+    @ Base ./error.jl:176
+  [2] systemerror
+    @ Base ./error.jl:175 [inlined]
+  [3] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing)
+    @ Base ./iostream.jl:293
+  [4] open
+    @ Base ./iostream.jl:275 [inlined]
+  [5] open(f::Base.var"#433#434"{String}, args::String; kwargs::@Kwargs{})
+    @ Base ./io.jl:394
+  [6] open
+    @ Base ./io.jl:393 [inlined]
+  [7] read
+    @ Base ./io.jl:486 [inlined]
+  [8] _include(mapexpr::Function, mod::Module, _path::String)
+    @ Base ./loading.jl:2126
+  [9] include(mod::Module, _path::String)
+    @ Base ./Base.jl:495
+ [10] exec_options(opts::Base.JLOptions)
+    @ Base ./client.jl:318
+ [11] _start()
+    @ Base ./client.jl:552
diff --git a/src/anndata_format.jl b/src/anndata_format.jl
@@ -102,7 +102,7 @@ METACELLS_SQUARE_DATA = CopyAnnData(["obs_outgoing_weights" => ("outgoing_weight
         type_property::Maybe{AbstractString} = nothing,
         rename_type::Maybe{AbstractString} = "type",
         type_colors_csv::Maybe{AbstractString} = nothing,
-        type_properties::Maybe{AbstractStringSet} = nothing,
+        type_properties::Maybe{AbstractSet{<:AbstractString}} = nothing,
         properties_defaults::Maybe{Dict} = nothing,
     )::Nothing
 
@@ -186,7 +186,7 @@ to the raw-only genes or cells.
     rename_type::Maybe{AbstractString} = "type",
     empty_type::Maybe{AbstractString} = nothing,
     type_colors_csv::Maybe{AbstractString} = nothing,
-    type_properties::Maybe{AbstractStringSet} = nothing,
+    type_properties::Maybe{AbstractSet{<:AbstractString}} = nothing,
     properties_defaults::Maybe{Dict} = nothing,
 )::Nothing
     metacells_daf =  # NOJET
@@ -279,7 +279,7 @@ function import_metacells(
     rename_type::Maybe{AbstractString},
     empty_type::Maybe{AbstractString},
     type_colors_csv::Maybe{AbstractString},
-    type_properties::Maybe{AbstractStringSet},
+    type_properties::Maybe{AbstractSet{<:AbstractString}},
     properties_defaults::Maybe{Dict},
 )::Nothing
     copy_axis!(; destination = destination, source = metacells_daf, axis = "metacell")
@@ -325,7 +325,7 @@ function import_metacell_types(
     rename_type::Maybe{AbstractString},
     empty_type::Maybe{AbstractString},
     type_colors_csv::Maybe{AbstractString},
-    type_properties::Maybe{AbstractStringSet},
+    type_properties::Maybe{AbstractSet{<:AbstractString}},
     properties_defaults::Maybe{Dict},
 )::Nothing
     if rename_type === nothing
@@ -510,7 +510,7 @@ function import_mask_matrix(
     destination::DafWriter,
     source::DafReader,
     rename_type::AbstractString,
-    type_names::AbstractStringVector,
+    type_names::AbstractVector{<:AbstractString},
     prefix::AbstractString,
 )::Nothing
     any_exist = false

diff --git a/src/spheres.jl b/src/spheres.jl
@@ -29,6 +29,7 @@ using Statistics
         max_sphere_diameter::AbstractFloat = 2.0,
         max_neighborhood_diameter::AbstractFloat = 2.0,
         noisy_gene_fold::AbstractFloat = 1.0,
+        min_gene_correlation::AbstractFloat = 0.5,
         max_deviant_genes_fraction::AbstractFloat = 0.01,
         overwrite::Bool = false,
     )::Nothing
@@ -254,8 +255,8 @@ end
 
 @logged function write_data(  # untested
     daf::DafWriter;
-    sphere_names::AbstractStringVector,
-    neighborhood_names::AbstractStringVector,
+    sphere_names::AbstractVector{<:AbstractString},
+    neighborhood_names::AbstractVector{<:AbstractString},
     spheres_of_metacells::Vector{UInt32},
     main_neighborhoods_of_spheres::Vector{UInt32},
     is_member_of_spheres_in_neighborhoods::AbstractMatrix{Bool},