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Merged
merged 3 commits into from
Dec 11, 2018
Merged

Fix doctests #153

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9299244
Fix AxisArray type pretty printing with Base.summary
Dec 11, 2018
da07848
Fix doctests
Dec 11, 2018
28fdd4e
Keep coverage stable by using a fixed juila version.
Dec 11, 2018
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6 changes: 4 additions & 2 deletions .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ script:
jobs:
include:
- stage: deploy
julia: 0.7
julia: 1.0
os: linux
script:
- julia -e 'import Pkg; Pkg.clone(pwd()); Pkg.build("AxisArrays")'
Expand All @@ -29,4 +29,6 @@ jobs:

after_success:
# - julia -e 'Pkg.add("Unitful")' ?
- julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Coveralls.submit(process_folder())'
- if [ $TRAVIS_JULIA_VERSION = "1.0" ] && [ $TRAVIS_OS_NAME = "linux" ]; then
julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Coveralls.submit(process_folder())'
fi
1 change: 1 addition & 0 deletions docs/make.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ using Documenter, AxisArrays

makedocs(
modules = [AxisArrays],
sitename = "AxisArrays",
)

deploydocs(
Expand Down
97 changes: 48 additions & 49 deletions docs/src/index.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
```@meta
DocTestSetup = quote
using AxisArrays, Unitful
using AxisArrays, Unitful, Random
import Unitful: s, ms, µs
rng = MersenneTwister(123)
fs = 40000
Expand Down Expand Up @@ -33,7 +33,7 @@ Collaboration is welcome! This is still a work-in-progress. See [the roadmap](ht

```julia
julia> Pkg.add("AxisArrays")
julia> using AxisArrays, Unitful
julia> using AxisArrays, Unitful, Random
julia> import Unitful: s, ms, µs

julia> rng = MersenneTwister(123) # Seed a random number generator for repeatable examples
Expand All @@ -51,7 +51,6 @@ julia> for spk = (sin.(0.8:0.2:8.6) .* [0:0.01:.1; .15:.1:.95; 1:-.05:.05] .* 50

```jldoctest
julia> A = AxisArray([y 2y], Axis{:time}(0s:1s/fs:60s), Axis{:chan}([:c1, :c2]))

2-dimensional AxisArray{Float64,2,...} with axes:
:time, 0.0 s:2.5e-5 s:60.0 s
:chan, Symbol[:c1, :c2]
Expand Down Expand Up @@ -88,18 +87,18 @@ julia> A[Axis{:time}(4)]
1-dimensional AxisArray{Float64,1,...} with axes:
:chan, Symbol[:c1, :c2]
And data, a 2-element Array{Float64,1}:
1.37825
2.75649
1.378246861221241
2.756493722442482

julia> A[Axis{:chan}(:c2), Axis{:time}(1:5)]
1-dimensional AxisArray{Float64,1,...} with axes:
:time, 0.0 s:2.5e-5 s:0.0001 s
And data, a 5-element Array{Float64,1}:
7.14161
12.2891
6.85591
2.75649
-2.38007
7.141607285917661
12.28907824673544
6.855905417203194
2.756493722442482
-2.380074475771338

```

Expand All @@ -113,16 +112,16 @@ julia> A[40µs .. 220µs, :c1]
1-dimensional AxisArray{Float64,1,...} with axes:
:time, 5.0e-5 s:2.5e-5 s:0.0002 s
And data, a 7-element Array{Float64,1}:
3.42795
1.37825
-1.19004
-1.99414
2.9429
-0.226449
0.821446
3.427952708601597
1.378246861221241
-1.190037237885669
-1.994137635575063
2.9429034802756004
-0.22644919919326786
0.8214461136364685

julia> AxisArrays.axes(ans, 1)
AxisArrays.Axis{:time,StepRangeLen{Quantity{Float64, Dimensions:{𝐓}, Units:{s}},Base.TwicePrecision{Quantity{Float64, Dimensions:{𝐓}, Units:{s}}},Base.TwicePrecision{Quantity{Float64, Dimensions:{𝐓}, Units:{s}}}}}(5.0e-5 s:2.5e-5 s:0.0002 s)
Axis{:time,StepRangeLen{Unitful.Quantity{Float64,𝐓,Unitful.FreeUnits{(s,),𝐓,nothing}},Base.TwicePrecision{Unitful.Quantity{Float64,𝐓,Unitful.FreeUnits{(s,),𝐓,nothing}}},Base.TwicePrecision{Unitful.Quantity{Float64,𝐓,Unitful.FreeUnits{(s,),𝐓,nothing}}}}}(5.0e-5 s:2.5e-5 s:0.0002 s)

```

Expand All @@ -138,7 +137,7 @@ julia> A[2.5e-5s..2.5e-5s, :c1]
1-dimensional AxisArray{Float64,1,...} with axes:
:time, 2.5e-5 s:2.5e-5 s:2.5e-5 s
And data, a 1-element Array{Float64,1}:
6.14454
6.14453912336772

```

Expand All @@ -147,7 +146,7 @@ You can even index by multiple values by broadcasting `atvalue` over an array:
```jldoctest
julia> A[atvalue.([2.5e-5s, 75.0µs])]
2-dimensional AxisArray{Float64,2,...} with axes:
:time, Quantity{Float64, Dimensions:{𝐓}, Units:{s}}[2.5e-5 s, 7.5e-5 s]
:time, Unitful.Quantity{Float64,𝐓,Unitful.FreeUnits{(s,),𝐓,nothing}}[2.5e-5 s, 7.5e-5 s]
:chan, Symbol[:c1, :c2]
And data, a 2×2 Array{Float64,2}:
6.14454 12.2891
Expand All @@ -166,13 +165,13 @@ julia> A[atindex(-90µs .. 90µs, 5), :c2]
1-dimensional AxisArray{Float64,1,...} with axes:
:time_sub, -7.5e-5 s:2.5e-5 s:7.5e-5 s
And data, a 7-element Array{Float64,1}:
12.2891
6.85591
2.75649
-2.38007
-3.98828
5.88581
-0.452898
12.28907824673544
6.855905417203194
2.756493722442482
-2.380074475771338
-3.988275271150126
5.885806960551201
-0.4528983983865357

```

Expand All @@ -187,28 +186,28 @@ julia> idxs = findall(diff(A[:,:c1] .< -15) .> 0);
julia> spks = A[atindex(-200µs .. 800µs, idxs), :c1]
2-dimensional AxisArray{Float64,2,...} with axes:
:time_sub, -0.0002 s:2.5e-5 s:0.0008 s
:time_rep, Quantity{Float64, Dimensions:{𝐓}, Units:{s}}[0.162 s, 0.20045 s, 0.28495 s, 0.530325 s, 0.821725 s, 1.0453 s, 1.11967 s, 1.1523 s, 1.22085 s, 1.6253 s … 57.0094 s, 57.5818 s, 57.8716 s, 57.8806 s, 58.4353 s, 58.7041 s, 59.1015 s, 59.1783 s, 59.425 s, 59.5657 s]
And data, a 41×247 Array{Float64,2}:
-1.82238 2.3315 -1.56147 … 4.33751 4.77713 -1.81713
0.672063 7.25649 0.633375 1.54583 5.81194 -4.706
-1.65182 2.57487 0.477408 3.09505 3.52478 4.13037
4.46035 2.11313 4.78372 1.23385 7.2525 3.57485
5.25651 -2.19785 3.05933 0.965021 6.78414 5.94854
7.8537 0.345008 0.960533 … 0.812989 0.336715 0.303909
0.466816 0.643649 -3.67087 3.92978 -3.1242 0.789722
-6.0445 -13.2441 -4.60716 0.265144 -4.50987 -8.84897
-9.21703 -13.2254 -14.4409 -8.6664 -13.3457 -11.6213
-16.1809 -22.7037 -25.023 -15.9376 -28.0817 -16.996
⋮ ⋱ ⋮
1.72728 4.77428 -10.3922 -2.08555 1.19198 -1.94365
-0.301629 0.0683982 -4.36574 1.92362 -5.12333 -3.4431
4.7182 1.18615 4.40717 -4.51757 -8.64314 0.0800021
-2.43775 -0.151882 -1.40817 … -3.38555 -2.23418 0.728549
3.2482 -0.60967 0.471288 2.53395 0.468817 -3.65905
-4.26967 2.24747 -3.13758 1.74967 4.5052 -0.145357
-0.752487 1.69446 -1.20491 1.71429 1.81936 0.290158
4.64348 -3.94187 -1.59213 7.15428 -0.539748 4.82309
1.09652 -2.66999 0.521931 … -3.80528 1.70421 3.40583
:time_rep, Unitful.Quantity{Float64,𝐓,Unitful.FreeUnits{(s,),𝐓,nothing}}[0.161275 s, 0.489925 s, 0.957175 s, 1.1457 s, 1.40185 s, 1.84193 s, 2.07365 s, 2.32947 s, 2.7763 s, 2.79275 s … 57.6724 s, 57.7152 s, 57.749 s, 58.1109 s, 58.3783 s, 58.4178 s, 58.921 s, 59.1693 s, 59.6546 s, 59.7824 s]
And data, a 41×273 Array{Float64,2}:
-2.47171 -1.72242 4.54491 … 2.74969 3.1869 -2.00435
6.78576 3.65903 5.14183 -0.98535 3.96603 -5.74065
1.56584 1.88131 0.470257 2.66664 5.27674 0.0610194
4.78242 3.20142 3.28502 5.20484 -3.66085 1.16247
3.23148 -1.24878 -0.0252124 5.46585 4.88651 3.64283
6.5714 0.572557 3.038 … -0.974689 2.61297 7.3496
4.46643 -0.444754 -4.52857 0.304449 -1.54659 -2.53197
-9.57806 -1.29114 -2.23969 -9.10793 -6.35711 -5.06038
-12.2567 -5.06283 -8.53581 -11.9826 -14.868 -14.0543
-24.5458 -19.9823 -20.0798 -20.3065 -18.5437 -25.3609
⋮ ⋱ ⋮
2.14059 -0.365031 1.36771 -4.23763 5.9211 -3.84708
3.58157 2.87076 0.835568 -2.27752 1.18686 2.3412
6.7953 -1.32384 -3.0897 0.464151 -1.12327 -2.14844
1.19649 2.44709 -5.16029 … -0.965397 2.37465 -2.36185
-1.57253 0.526027 0.831144 0.6505 3.61602 1.93462
0.739684 -1.74925 -6.18072 -7.36229 -0.187708 1.97774
0.645211 1.04006 -1.33676 4.30262 -4.46544 -0.278097
1.32901 -1.74821 1.94781 0.780325 3.22951 -0.436806
0.387814 0.128453 -0.00287742 … -1.51196 -2.10081 -2.26663

```

Expand Down
8 changes: 1 addition & 7 deletions src/core.jl
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Expand Up @@ -476,7 +476,7 @@ dropax(ax) = ()
# A simple display method to include axis information. It might be nice to
# eventually display the axis labels alongside the data array, but that is
# much more difficult.
function summaryio(io::IO, A::AxisArray)
function Base.summary(io::IO, A::AxisArray)
_summary(io, A)
for (name, val) in zip(axisnames(A), axisvalues(A))
print(io, " :$name, ")
Expand All @@ -487,12 +487,6 @@ function summaryio(io::IO, A::AxisArray)
end
_summary(io, A::AxisArray{T,N}) where {T,N} = println(io, "$N-dimensional AxisArray{$T,$N,...} with axes:")

function Base.summary(A::AxisArray)
io = IOBuffer()
summaryio(io, A)
String(take!(io))
end

# Custom methods specific to AxisArrays
"""
axisvalues(A::AxisArray) -> (AbstractVector...)
Expand Down