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Bump DimensionalData dependency to 0.27 (#390)
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* Fix to_dataset kwarg in docs

* Bump DimensionalData to 0.27 and replace dim2key and name2dim

* Force update of registry in docs action

* Bump codecov action to version 4
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@felixcremer
felixcremer authored May 2, 2024
1 parent 0d0a874 commit b4bf448
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Showing 12 changed files with 31 additions and 31 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/CI.yml
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Expand Up @@ -42,7 +42,7 @@ jobs:
env:
JULIA_NUM_THREADS: '4'
- uses: julia-actions/julia-processcoverage@v1
- uses: codecov/codecov-action@v1
- uses: codecov/codecov-action@v4
with:
file: lcov.info
- uses: coverallsapp/github-action@master
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2 changes: 1 addition & 1 deletion .github/workflows/Documenter.yml
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Expand Up @@ -43,7 +43,7 @@ jobs:
- name: Install documentation dependencies # for GLMakie plots
run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev
- name: Install documentation dependencies
run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs -e 'using Pkg; pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs -e 'using Pkg; Pkg.Registry.update(); pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
#- name: Creating new mds from src
- name: Build and deploy docs
env:
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4 changes: 2 additions & 2 deletions Project.toml
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@@ -1,7 +1,7 @@
name = "YAXArrays"
uuid = "c21b50f5-aa40-41ea-b809-c0f5e47bfa5c"
authors = ["Fabian Gans <fgans@bgc-jena.mpg.de>"]
version = "0.5.5"
version = "0.5.6"

[deps]
CFTime = "179af706-886a-5703-950a-314cd64e0468"
Expand Down Expand Up @@ -34,7 +34,7 @@ YAXArrayBase = "90b8fcef-0c2d-428d-9c56-5f86629e9d14"
[compat]
CFTime = "0.0, 0.1"
DataStructures = "0.17, 0.18"
DimensionalData = "0.26"
DimensionalData = "0.27"
DiskArrayTools = "0.1"
DiskArrays = "0.3,0.4"
DocStringExtensions = "0.8, 0.9"
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12 changes: 6 additions & 6 deletions src/Cubes/Cubes.jl
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Expand Up @@ -163,9 +163,9 @@ end
# because getproperty is overloaded, propertynames should be as well
function Base.propertynames(a::YAXArray, private::Bool=false)
if private
(DD.dim2key.(DD.dims(a))..., :axes, :data, :properties)
(DD.name.(DD.dims(a))..., :axes, :data, :properties)
else
(DD.dim2key.(DD.dims(a))..., :axes, :data)
(DD.name.(DD.dims(a))..., :axes, :data)
end
end

Expand Down Expand Up @@ -340,9 +340,9 @@ function outaxis_from_column(tab,icol)
axname = schema(tab).names[icol]
if eltype(axdata) <: AbstractString ||
(!issorted(axdata) && !issorted(axdata, rev = true))
DD.rebuild(DD.key2dim(Symbol(axname)), axdata)
DD.rebuild(DD.name2dim(Symbol(axname)), axdata)
else
DD.rebuild(DD.key2dim(Symbol(axname)), axdata)
DD.rebuild(DD.name2dim(Symbol(axname)), axdata)
end
end

Expand All @@ -356,13 +356,13 @@ function outaxis_from_data(cax,axinds,indlist)
ax.values[i[ai-minai+1]]
end
end
DD.rebuild(DD.key2dim(Symbol(newname)), mergevals)
DD.rebuild(DD.name2dim(Symbol(newname)), mergevals)
end
chunkoffset(c) = grid_offset(eachchunk(c))

# Implementation for YAXArrayBase interface
YAXArrayBase.dimvals(x::YAXArray, i) = caxes(x)[i].val
YAXArrayBase.dimname(x::YAXArray, i) = DD.dim2key(DD.dims(x)[i])
YAXArrayBase.dimname(x::YAXArray, i) = DD.name(DD.dims(x)[i])
YAXArrayBase.getattributes(x::YAXArray) = x.properties
YAXArrayBase.iscontdim(x::YAXArray, i) = isa(caxes(x)[i], RangeAxis)
YAXArrayBase.getdata(x::YAXArray) = getfield(x, :data)
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2 changes: 1 addition & 1 deletion src/Cubes/Slices.jl
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Expand Up @@ -23,7 +23,7 @@ end
dimvals(x::YAXSlice, i) = x.c.axes[x.otheraxes[1][i]].values

function dimname(x::YAXSlice, i)
DD.dim2key(x.otheraxes[2][i])
DD.name(x.otheraxes[2][i])
end

getattributes(x::YAXSlice) = x.c.properties
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4 changes: 2 additions & 2 deletions src/DAT/DAT.jl
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Expand Up @@ -170,7 +170,7 @@ function getworkarray(c::InOutCube, ntr)
i1 = findfirst(isequal(i), c.icolon)
i1 === nothing || return caxes(c.cube)[c.icolon[i1]]
i2 = findfirst(isequal(i), c.iwindow)
DD.rebuild(DD.key2dim(DD.dim2key(caxes(c.cube)[c.iwindow[i2]])),UnitRange(-c.window[i2][1], c.window[i2][2]))
DD.rebuild(DD.key2dim(DD.name(caxes(c.cube)[c.iwindow[i2]])),UnitRange(-c.window[i2][1], c.window[i2][2]))
end
wrapWorkArray(c.desc.artype, w, axes)
end
Expand Down Expand Up @@ -735,7 +735,7 @@ struct AllLoopAxes{S,V} <: AxValCreator
loopsyms::S
loopaxvals::V
end
AllLoopAxes(a) = AllLoopAxes(map(DD.dim2key, a), map(i -> i.val, a))
AllLoopAxes(a) = AllLoopAxes(map(DD.name, a), map(i -> i.val, a))
getlaxvals(::NoLoopAxes, cI, offscur) = ()
getlaxvals(a::AllLoopAxes, cI, offscur) = (
NamedTuple{a.loopsyms}(
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2 changes: 1 addition & 1 deletion src/DAT/dciterators.jl
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Expand Up @@ -195,7 +195,7 @@ function CubeIterator(
eltype(ic.cube)
end
et = (et..., map(i->eltype(i.val), loopaxes)...)
axnames = DD.dim2key.(loopaxes)
axnames = DD.name.(loopaxes)
colnames = (map(Symbol, varnames)..., axnames...)
CubeIterator(
dc,
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2 changes: 1 addition & 1 deletion src/DAT/registration.jl
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Expand Up @@ -27,7 +27,7 @@ findAxis(m::MovingWindow, c) = findAxis(m.desc, c)

wrapWorkArray(::Type{Array}, a, axes) = a
wrapWorkArray(T, a, axes) =
yaxcreate(T, a, map(DD.dim2key, axes), map(i -> i.values, axes), Dict{String, Any}())
yaxcreate(T, a, map(DD.name, axes), map(i -> i.values, axes), Dict{String, Any}())

abstract type ProcFilter end
struct AllMissing <: ProcFilter end
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12 changes: 6 additions & 6 deletions src/DAT/tablestats.jl
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Expand Up @@ -139,11 +139,11 @@ function tooutaxis(
if haskey(bycube.properties, "labels")
idict = bycube.properties["labels"]
axname = get(bycube.properties, "name", "Label")
outAxis = DD.rebuild(DD.key2dim(Symbol(axname)), collect(String, values(idict)))
outAxis = DD.rebuild(DD.name2dim(Symbol(axname)), collect(String, values(idict)))
convertdict = Dict(k => i for (i, k) in enumerate(keys(idict)))
else
sort!(k)
outAxis = DD.rebuild(DD.key2dim(Symbol(s)), k)
outAxis = DD.rebuild(DD.name2dim(Symbol(s)), k)
convertdict = Dict(k => i for (i, k) in enumerate(k))
end
else
Expand All @@ -155,7 +155,7 @@ function tooutaxis(
end
function tooutaxis(f, iter::CubeIterator, k, ibc)
sort!(k)
outAxis = DD.rebuild(DD.key2dim(Symbol("Category$(ibc)")), k)
outAxis = DD.rebuild(DD.name2dim(Symbol("Category$(ibc)")), k)
convertdict = Dict(k => i for (i, k) in enumerate(k))
outAxis, convertdict
end
Expand All @@ -173,7 +173,7 @@ getStatType(t::Type{<:Dict{<:Any,T}}) where {T} = T
getStatOutAxes(tab, agg) = getStatOutAxes(tab, agg, getStatType(agg))
getStatOutAxes(tab, agg, ::Type{<:OnlineStat}) = ()
function getStatOutAxes(tab, agg, ::Type{<:Extrema})
(DD.rebuild(DD.key2dim(:Extrema), ["min", "max"]),)
(DD.rebuild(DD.name2dim(:Extrema), ["min", "max"]),)
end
function getStatOutAxes(tab, agg, ::Type{<:WeightedCovMatrix})
varn = tab.schema.names
Expand All @@ -189,8 +189,8 @@ function getStatOutAxes(tab, agg, ::Type{<:WeightedCovMatrix})
end
function getStatOutAxes(tab,agg,::Type{<:Union{Ash,HistogramStat, WeightedAdaptiveHist}})
nbin = getnbins(agg)
a1 = DD.rebuild(DD.key2dim(Symbol("Bin")), 1:nbin)
a2 = DD.rebuild(DD.key2dim(Symbol("Hist")), ["MidPoints", "Frequency"])
a1 = DD.rebuild(DD.name2dim(Symbol("Bin")), 1:nbin)
a2 = DD.rebuild(DD.name2dim(Symbol("Hist")), ["MidPoints", "Frequency"])
(a1, a2)
end
function getByAxes(iter, agg::GroupedOnlineAggregator)
Expand Down
14 changes: 7 additions & 7 deletions src/DatasetAPI/Datasets.jl
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Expand Up @@ -43,13 +43,13 @@ function Dataset(; properties = Dict{String,Any}(), cubes...)
end

"""
to_dataset(c;datasetaxis = "Variable", name = "layer")
to_dataset(c;datasetaxis = "Variable", layername = "layer")
Convert a Data Cube into a Dataset. It is possible to treat one of
the Cube's axes as a "DatasetAxis" i.e. the cube will be split into
different parts that become variables in the Dataset. If no such
axis is specified or found, there will only be a single variable
in the dataset with the name `name`
in the dataset with the name `layername`
"""
function to_dataset(c;datasetaxis = "Variable", layername = get(c.properties,"name","layer"))
axlist = DD.dims(c)
Expand Down Expand Up @@ -219,7 +219,7 @@ end
function toaxis(dimname, g, offs, len)
axname = Symbol(dimname)
if !haskey(g, dimname)
return DD.rebuild(DD.key2dim(axname), 1:len)
return DD.rebuild(DD.name2dim(axname), 1:len)
end
ar = get_var_handle(g, dimname)
aratts = get_var_attrs(g, dimname)
Expand All @@ -232,15 +232,15 @@ function toaxis(dimname, g, offs, len)
DD.Ti(tsteps[offs+1:end])
elseif haskey(aratts, "_ARRAYVALUES")
vals = identity.(aratts["_ARRAYVALUES"])
DD.rebuild(DD.key2dim(axname),(vals))
DD.rebuild(DD.name2dim(axname),(vals))
else
axdata = cleanaxiselement.(ar[offs+1:end])
axdata = testrange(axdata)
if eltype(axdata) <: AbstractString ||
(!issorted(axdata) && !issorted(axdata, rev = true))
DD.rebuild(DD.key2dim(axname), axdata)
DD.rebuild(DD.name2dim(axname), axdata)
else
DD.rebuild(DD.key2dim(axname), axdata)
DD.rebuild(DD.name2dim(axname), axdata)
end
end
end
Expand Down Expand Up @@ -367,7 +367,7 @@ function Cube(ds::Dataset; joinname = "Variable", target_type = nothing)
if length(newkeys) == 1
return ds.cubes[first(newkeys)]
else
varax = DD.rebuild(DD.key2dim(Symbol(joinname)), string.(newkeys))
varax = DD.rebuild(DD.name2dim(Symbol(joinname)), string.(newkeys))
cubestomerge = map(newkeys) do k
if eltype(ds.cubes[k]) <: prom_type
ds.cubes[k]
Expand Down
2 changes: 1 addition & 1 deletion src/helpers.jl
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
using DimensionalData: DimensionalData as DD
const VecOrTuple{S} = Union{Vector{<:S},Tuple{Vararg{<:S}}} where {S}
const VecOrTuple{S} = Union{Vector{<:S},Tuple{Vararg{S}}} where {S}

abstract type AxisDescriptor end

Expand Down
4 changes: 2 additions & 2 deletions test/Datasets/datasets.jl
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Expand Up @@ -219,7 +219,7 @@ end
ar = Cube(ds)
@test ar isa YAXArray
@test size(ar) == (10, 5, 2, 2)
@test DD.name.(ar.axes) == (:Time, :d2, :d3, :Variable)
@test DD.name.(ar.axes) == (:Ti, :d2, :d3, :Variable)
@test DD.lookup(ar.axes[4]) == ["Var1", "Var3"]
end
@testset "Dataset creation" begin
Expand All @@ -230,7 +230,7 @@ end
)
# Basic
newds, newds2 = YAXArrays.Datasets.createdataset(MockDataset, al)
@test DD.dim2key.(newds2.axes) == (:Time, :Xvals, :Variable)
@test DD.name.(newds2.axes) == (:Time, :Xvals, :Variable)
@test DD.lookup(newds2.axes[1]) == Date(2001):Month(1):Date(2001, 12, 31)
@test DD.lookup(newds2.axes[3]) == ["A", "B"]
@test DD.lookup(newds2.axes[2]) == 1:10
Expand Down

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Registration pull request created: JuliaRegistries/General/106016

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.5.6 -m "<description of version>" b4bf44866fbd9c5fe1a78f42d3ff0b454a4102a2
git push origin v0.5.6

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