fix skeletonization. (#79)

* upgrade to Julia 1.4; fix skeletonize by not reversing the coordinate from xyz to zyx;

* fix travis build

* fix Pkg.PackageSpec

* delete installing the package.

* fix documenter build

* drop support of julia1.0

.gitignore

@@ -1,3 +1,4 @@
 docs/build/
 Manifest.toml
 *.log
+*.dat

.travis.yml

@@ -2,7 +2,8 @@ language: julia
 os: linux
 
 julia: 
-    - 1.0
+    - 1.3
+    - 1.4
     - nightly
 
 notifications: 
@@ -14,10 +15,9 @@ install:
     - sudo apt-get install -y -qq hdf5-tools
 
 script:
-    - julia -e 'import Pkg; Pkg.clone("https://github.com/seung-lab/BigArrays.jl.git")'
-    - julia -e 'import Pkg; Pkg.clone(pwd()); Pkg.test("RealNeuralNetworks", coverage=true)'
-    - julia -e 'using Pkg; Pkg.add("Documenter")'
-    - julia -e 'using Pkg; cd(Pkg.dir("RealNeuralNetworks")); include(joinpath("docs", "make.jl"))'
+    - julia -e 'using Pkg; Pkg.develop(PackageSpec(name="BigArrays", url="https://github.com/seung-lab/BigArrays.jl.git"))'
+    - julia -e 'using Pkg; Pkg.test("RealNeuralNetworks", coverage=true)'
+    - julia -e 'using Pkg; Pkg.add("Documenter"); cd(Pkg.dir("RealNeuralNetworks")); include(joinpath("docs", "make.jl"))'
 
 
       #jobs:

Dockerfile

@@ -1,4 +1,4 @@
-FROM julia:1.3
+FROM julia:1.4
 LABEL   maintainer="Jingpeng Wu <[email protected]>" \
         function="skeletonization"
 
@@ -20,9 +20,11 @@ RUN julia -e 'using Pkg; Pkg.update(); Pkg.instantiate();'
 RUN julia -e 'using Pkg; Pkg.develop(PackageSpec(name="BigArrays", url="https://github.com/seung-lab/BigArrays.jl.git"))'
     #Pkg.resolve(); \
     #Pkg.develop(PackageSpec(url="https://github.com/seung-lab/RealNeuralNetworks.jl.git")); \
-RUN julia -e 'using Pkg; Pkg.develop(PackageSpec(name="RealNeuralNetworks", path=pwd())); \
+
+RUN julia -e 'using Pkg; Pkg.develop(PackageSpec(name="RealNeuralNetworks", path=joinpath(pwd(), "RealNeuralNetworks"))); \
         Pkg.develop("RealNeuralNetworks"); Pkg.instantiate();' 
     # install registered packages later
+
 RUN julia -e 'using Pkg; Pkg.add("LightGraphs");  \
     Pkg.add("MetaGraphs"); \
     Pkg.add("ArgParse");\

Project.toml

@@ -1,6 +1,6 @@
 name = "RealNeuralNetworks"
 uuid = "4491297b-8966-5840-8cb9-b189d60f3398"
-version = "1.0.1"
+version = "1.3.1"
 
 [deps]
 BigArrays = "c2a8506f-1b35-5b08-8aa1-bb4a7b47a05e"

docs/make.jl

@@ -1,14 +1,32 @@
-using Documenter, RealNeuralNetworks
+using Documenter
+using RealNeuralNetworks
 using RealNeuralNetworks.Neurons 
 using RealNeuralNetworks.Neurons.Segments 
 using RealNeuralNetworks.Neurons.Segments.Synapses
 using RealNeuralNetworks.SWCs
 
+# The DOCSARGS environment variable can be used to pass additional arguments to make.jl.
+# This is useful on CI, if you need to change the behavior of the build slightly but you
+# can not change the .travis.yml or make.jl scripts any more (e.g. for a tag build).
+if haskey(ENV, "DOCSARGS")
+    for arg in split(ENV["DOCSARGS"])
+        (arg in ARGS) || push!(ARGS, arg)
+    end
+end
+
 makedocs(
 	modules=[RealNeuralNetworks, Neurons, Segments, Synapses, SWCs],
 	sitename="RealNeuralNetworks.jl",
 	authors="Jingpeng Wu",
-	format=:html,
+    format = Documenter.HTML(
+        # Use clean URLs, unless built as a "local" build
+        prettyurls = !("local" in ARGS),
+        canonical = "https://seung-lab.github.io/RealNeuralNetworks.jl/latest/",
+        assets = ["assets/favicon.ico"],
+        analytics = "UA-136089579-2",
+        highlights = ["yaml"],
+    ),
+    linkcheck = !("skiplinks" in ARGS),
     pages = [
         "Home" => "index.md",
         "Manual" => Any[
@@ -26,15 +44,11 @@ makedocs(
         ],
         "man/contributing.md",
     ],
-    # use clean URLs, unless built as a "local" build 
-    html_prettyurls = !("local" in ARGS),
-    html_canonical = "https://seung-lab.github.io/RealNeuralNetworks.jl/latest",
 )
 
 deploydocs(
 	repo="github.com/seung-lab/RealNeuralNetworks.jl",
 	target="build",
-	julia="0.7",
 	deps=nothing,
 	make=nothing
 )

scripts/skeletonize.jl

@@ -32,7 +32,7 @@ end
 
 function parse_commandline()
     s = ArgParseSettings()
-    @add_arg_table s begin 
+    @add_arg_table! s begin 
         "--neuronid", "-i"
             help = "the segment id to skeletonize"
             arg_type = Int

src/Manifests.jl

@@ -51,7 +51,7 @@ function Manifest( ranges::Vector, ba::BigArray{D,T} ) where {D,T}
     rangesList = map( BigArrays.Indexes.string2unit_range, ranges )
     # convert from z,y,x to x,y,z
     # this is due to a bug in chunkflow, we should not need this in the future
-    rangesList = map( reverse, rangesList)
+    # rangesList = map( reverse, rangesList)
     @show rangesList 
     Manifest( ba, obj_id, rangesList )
 end

src/Utils/RangeIndexingArrays.jl

@@ -45,9 +45,9 @@ function range_string_list2septa_list(rangeStringList::Vector)
     septaList
 end 
 
-@inline function range_string_list2septa_list(rangeStringList::CSV.Column{String, String})
-    range_string_list2septa_list(map(string, rangeStringList))
-end 
+#@inline function range_string_list2septa_list(rangeStringList::CSV.Column{String, String})
+#    range_string_list2septa_list(map(string, rangeStringList))
+#end 
 
 
 """