Split packages (#198)

* Removed a lot of files * move some files * break more things * Clean up Proc module * Many fixes to get dataset creation running again * savecube to netcdf works * more improvements * Commit many more changes * Separate out API * some test fixes * switch to YAXArrayBase * read variables in a typed way * add ESDLArray export * Fixes to remap * remove NetCDF and Zarr dependency * delete some unused stuff * Do not permute cubes by default * Add concatenations * Fixes to findaxis * Tests pass again * Try to fix chunking * dont depend on reexport * remove reexport dep * dont forgegt using it * update test * Allow NamedTuples * minor changes * Finalsplit (#220) * Delete almost everything * More updates * Old tests for ESDL pass * More changes * Fix bugs in ESDL * Some fixes * Fix some warnings * tests should pass
JuliaDataCubes · Dec 7, 2020 · bd344c0 · bd344c0
1 parent e0bfb1c
commit bd344c0
Show file tree

Hide file tree

Showing 48 changed files with 479 additions and 4,425 deletions.
diff --git a/Project.toml b/Project.toml
@@ -5,56 +5,41 @@ version = "0.8.4"
 
 [deps]
 CFTime = "179af706-886a-5703-950a-314cd64e0468"
-Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DiskArrayTools = "fcd2136c-9f69-4db6-97e5-f31981721d63"
 DiskArrays = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
-IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
-IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
-NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9"
 OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e"
 Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
-ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Shapefile = "8e980c4a-a4fe-5da2-b3a7-4b4b0353a2f4"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 WeightedOnlineStats = "bbac0a1f-7c9d-5672-960b-c6ca726e5d5d"
+YAXArrays = "c21b50f5-aa40-41ea-b809-c0f5e47bfa5c"
 Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99"
 
 [compat]
-CFTime = "0.0, 0.1"
-Combinatorics = "1"
-DataFrames = "0.19, 0.20"
-DataStructures = "0.17"
 FFTW = "1"
 GeoInterface = "0.4, 0.5"
-Interpolations = "0.12"
-IntervalSets = "0.3, 0.4"
-IterTools = "1"
-NetCDF = "0.8, 0.9, 0.10"
 OnlineStats = "1"
-Polynomials = "0.6"
-ProgressMeter = "1"
+Polynomials = "1"
 Shapefile = "0.6"
-StatsBase = "0.32"
+StatsBase = "0.32, 0.33"
 Tables = "0.2, 1.0"
-WeightedOnlineStats = "0.3, 0.4"
-Zarr = "0.4"
 julia = "1.3"
-DiskArrays = "0.2"
 
 [extras]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+ESDC = "78cc4143-e042-47c7-b459-414d105d7ed4"
+NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9"
 RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "CSV", "RDatasets", "StatsBase"]
+test = ["Test", "CSV", "RDatasets", "StatsBase", "NetCDF"]
diff --git a/_REQUIRE b/_REQUIRE
diff --git a/docs/src/analysis.md b/docs/src/analysis.md
@@ -117,7 +117,7 @@ ESDL.DAT.cubefittable
 
 ### Online Histograms and quantiles
 
-It is possible to estimate histograms and quantiles of larger-than-memory datasets using an adaptive-bin histogram algorithm. The `Base.quantile` method is overloaded for objects of type `AbstractCubeData`, so the following works to estimate the 10% and 90% quantiles of all datapoints for each variable:
+It is possible to estimate histograms and quantiles of larger-than-memory datasets using an adaptive-bin histogram algorithm. The `Base.quantile` method is overloaded for objects of type `YAXarray`, so the following works to estimate the 10% and 90% quantiles of all datapoints for each variable:
 
 ```julia
 using WeightedOnlineStats

diff --git a/docs/src/cube_access.md b/docs/src/cube_access.md
@@ -74,11 +74,8 @@ cubenew  = extractLonLats(cubedata,ll)
 ## Cube Types
 
 While the `subsetcube` command returns an object of type `ZarrCube`, which represents a view into the ESDC, other cube operations will return different types of data cubes.
-The returned type will depend on the size of the returned cube. If it is small enough to fit into memory, it will be a `CubeMem`, otherwise a `ZArrayCube`. All these types of data cubes share the same interface defined by [`ESDL.AbstractCubeData`](@ref), which means you can index them, do calculation using `mapCube` or plot them using the commands described in [Plotting](@ref).
+The returned type will depend on the size of the returned cube. If it is small enough to fit into memory, it will be a `CubeMem`, otherwise a `ZArrayCube`. All these types of data cubes share the same interface defined by, which means you can index them, do calculation using `mapCube` or plot them using the commands described in [Plotting](@ref).
 
-```@docs
-ESDL.Cubes.AbstractCubeData
-```
 
 ```@docs
 ESDL.Cubes.CubeMem

diff --git a/docs/src/examples/Time Mean.md b/docs/src/examples/Time Mean.md
@@ -59,7 +59,7 @@ addprocs(SlurmManager(10))
 
 inpath="zg1000_AERday_CanESM5_esm-hist_r6i1p1f1_gn_18500101-20141231.nc"
 
-c = NetCDFCube(inpath, "zg1000")
+c = Cube(inpath, "zg1000")
 
 resultcube = mapslices(mean ∘ skipmissing, c, dims="time")
 ```
diff --git a/src/CubeAPI/country_iso_numeric_iso_alpha2.jl b/src/CubeAPI/country_iso_numeric_iso_alpha2.jl