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pass tests #80

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14 changes: 14 additions & 0 deletions REQUIRE
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
julia 1
LightGraphs
MetaGraphs
DataFrames
CSV
BigArrays
DataStructures
LsqFit
OffsetArrays
ImageFiltering
Query
JSON
NearestNeighbors
ProgressMeter
2 changes: 1 addition & 1 deletion src/Utils/SynapseTables.jl
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Expand Up @@ -18,7 +18,7 @@ function preprocess(self::SynapseTable, voxelSize::Tuple)
# this is not working due to a DataFrames bug
# https://github.com/JuliaData/DataFrames.jl/issues/1862
# we need to add true to make it work as old ways...
@showprogress 1 "transform datatype to Float32..." for (key, value) in DataFrames.eachcol(self, true)
@showprogress 1 "transform datatype to Float32..." for (key, value) in DataFrames.eachcol(self)
#if key!=:presyn_wt && key!=:postsyn_wt
# self[key] = round.(Int, value)
#end
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4 changes: 2 additions & 2 deletions test/Neurons.jl
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Expand Up @@ -142,7 +142,7 @@ end
println("\nattaching presynapses in DataFrame...")
# the default reading of CSV is immutable and the dropmissing will fail!
# https://github.com/JuliaData/DataFrames.jl/issues/1393#issuecomment-500019773
preSynapses = CSV.read( joinpath(ASSET_DIR, "$(NEURON_ID).pre.synapses.csv"); copycols=true)
preSynapses = CSV.read( joinpath(ASSET_DIR, "$(NEURON_ID).pre.synapses.csv"), DataFrame; copycols=true)
@time preSynapses = SynapseTables.preprocess(preSynapses, (5,5,45))
println("get ", DataFrames.nrow(preSynapses), " synapses.")
@time Neurons.attach_pre_synapses!(neuron, preSynapses)
Expand All @@ -152,7 +152,7 @@ end
@test numPreSynapses > 2

println("\nattaching postsynapses in DataFrame...")
postSynapses = CSV.read( joinpath(ASSET_DIR, "$(NEURON_ID).post.synapses.csv"); copycols=true)
postSynapses = CSV.read( joinpath(ASSET_DIR, "$(NEURON_ID).post.synapses.csv"), DataFrame; copycols=true)
@time postSynapses = SynapseTables.preprocess(postSynapses, (5,5,45))
println("get ", DataFrames.nrow(postSynapses), " synapses.")
@time Neurons.attach_post_synapses!(neuron, postSynapses)
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2 changes: 1 addition & 1 deletion test/Synapses.jl
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Expand Up @@ -5,7 +5,7 @@ using RealNeuralNetworks.Neurons.Segments.Synapses

@testset "test Synapses module" begin
df = CSV.read(joinpath(Base.@__DIR__,
"../asset/77625.pre.synapses.csv"))
"../asset/77625.pre.synapses.csv"), DataFrame)
synapseList = Vector{Synapse{Float32}}()
for row in DataFrames.eachrow(df)
push!(synapseList, Synapse(row))
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