diff --git a/Dockerfile b/Dockerfile index 0dc67a03..0858c700 100644 --- a/Dockerfile +++ b/Dockerfile @@ -31,7 +31,7 @@ RUN apt-get update \ ## install julia RUN mkdir /opt/julia \ - && curl -L https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.0-rc2-linux-x86_64.tar.gz | tar zxf - -C /opt/julia --strip=1 \ + && curl -L https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.3-linux-x86_64.tar.gz | tar zxf - -C /opt/julia --strip=1 \ && chown -R 1000 /opt/julia \ && ln -s /opt/julia/bin/julia /usr/local/bin diff --git a/README.md b/README.md index 958dac91..85174ee1 100644 --- a/README.md +++ b/README.md @@ -30,14 +30,14 @@ The best place to get started is to read the [documentation](https://cosmicmar.c Most of the pages in the documentation are Jupyter notebooks, and you can click the "launch binder" link at the top of each page to launch a Jupyterlab server running the notebook in your browser (courtesy of [binder](https://mybinder.org/)). -You can also clone the repository and open the notebooks in [docs/src](https://github.com/marius311/CMBLensing.jl/tree/master/docs/src) if you want to run them locally (which will usually lead to higher performance). The notebooks are stored as `.md` files rather than `.ipynb` format. Its recommended to install [Jupytext](jupytext) (`pip install jupytext`) and then you can run these `.md` directly from Jupyterlab by right-clicking on them and selecting `Open With -> Notebook`. Otherwise, run the script `docs/make_notebooks.sh` to convert the `.md` files to `.ipynb` which you can then open as desired. +You can also clone the repository and open the notebooks in [docs/src](https://github.com/marius311/CMBLensing.jl/tree/master/docs/src) if you want to run them locally (which will usually lead to higher performance). The notebooks are stored as `.md` files rather than `.ipynb` format. Its recommended to install [Jupytext](https://jupytext.readthedocs.io/en/latest/) (`pip install jupytext`) and then you can run these `.md` directly from Jupyterlab by right-clicking on them and selecting `Open With -> Notebook`. Otherwise, run the script `docs/make_notebooks.sh` to convert the `.md` files to `.ipynb` which you can then open as desired. ## Installation ### Requirements -* Julia 1.7+ +* Julia 1.8+ * _(recommended)_ An Nvidia GPU and [CUDA.jl](https://github.com/JuliaGPU/CUDA.jl) for GPU support * _(recommended)_ Python 3 + matplotlib (used for plotting) * _(recommended)_ [pycamb](https://github.com/cmbant/CAMB) to generate $C_\ell$'s (run `pip install --user camb`) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index b085de4c..1eb4930d 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.9.0-rc2" manifest_format = "2.0" -project_hash = "53a01a8de8979f0ec072c0b1870fe9277bd9e164" +project_hash = "9a8d52cd59caf3b638ae9ba64facec4effaba6f8" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -11,13 +11,14 @@ version = "0.0.1" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] -git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.3.1" -weakdeps = ["ChainRulesCore"] +version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] [deps.AbstractFFTs.extensions] AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" [[deps.AbstractNFFTs]] deps = ["LinearAlgebra", "Printf"] @@ -25,11 +26,16 @@ git-tree-sha1 = "292e21e99dedb8621c15f185b8fdb4260bb3c429" uuid = "7f219486-4aa7-41d6-80a7-e08ef20ceed7" version = "0.8.2" +[[deps.AbstractTrees]] +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.4.4" + [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.6.1" +version = "3.6.2" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -45,10 +51,10 @@ uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "38911c7737e123b28182d89027f4216cfc8a9da7" +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "f83ec24f76d4c8f525099b2ac475fc098138ec31" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.4.3" +version = "7.4.11" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -77,9 +83,9 @@ version = "1.0.1" [[deps.AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] -git-tree-sha1 = "1dd4d9f5beebac0c03446918741b1a03dc5e5788" +git-tree-sha1 = "16351be62963a67ac4083f748fdb3cca58bfd52f" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -version = "0.4.6" +version = "0.4.7" [[deps.BFloat16s]] deps = ["LinearAlgebra", "Printf", "Random", "Test"] @@ -88,10 +94,24 @@ uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" version = "0.2.0" [[deps.BangBang]] -deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca" +deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] +git-tree-sha1 = "e28912ce94077686443433c2800104b061a827ed" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.37" +version = "0.3.39" + + [deps.BangBang.extensions] + BangBangChainRulesCoreExt = "ChainRulesCore" + BangBangDataFramesExt = "DataFrames" + BangBangStaticArraysExt = "StaticArrays" + BangBangStructArraysExt = "StructArrays" + BangBangTypedTablesExt = "TypedTables" + + [deps.BangBang.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -114,9 +134,9 @@ uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" version = "1.3.2" [[deps.Bijections]] -git-tree-sha1 = "fe4f8c5ee7f76f2198d5c2a06d3961c249cce7bd" +git-tree-sha1 = "71281c0c28f97e0adeed24fdaa6bf7d37177f297" uuid = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" -version = "0.1.4" +version = "0.1.5" [[deps.CEnum]] git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" @@ -136,10 +156,10 @@ uuid = "b3e40c51-02ae-5482-8a39-3ace5868dcf4" version = "4.0.0+0" [[deps.CMBLensing]] -deps = ["AbstractFFTs", "Adapt", "Bijections", "ChainRules", "CodecZlib", "Combinatorics", "ComponentArrays", "CompositeStructs", "CoordinateTransformations", "DataStructures", "DelimitedFiles", "Distributed", "Distributions", "EllipsisNotation", "FFTW", "FileIO", "Formatting", "ForwardDiff", "Healpix", "ImageFiltering", "ImageMorphology", "Images", "InteractiveUtils", "Interpolations", "IterTools", "JLD2", "KahanSummation", "Lazy", "Libdl", "LinearAlgebra", "Loess", "MCMCDiagnosticTools", "MacroTools", "Markdown", "Match", "Measurements", "Memoization", "NFFT", "NamedTupleTools", "Optim", "PDMats", "Pkg", "PlotUtils", "Preferences", "Printf", "ProgressMeter", "QuadGK", "Random", "RecipesBase", "Requires", "Roots", "Rotations", "Serialization", "Setfield", "SnoopPrecompile", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "TimerOutputs", "Tullio", "UnPack", "Zygote"] +deps = ["AbstractFFTs", "Adapt", "Bijections", "ChainRules", "CodecZlib", "Combinatorics", "ComponentArrays", "CompositeStructs", "CoordinateTransformations", "DataStructures", "DelimitedFiles", "Distributed", "Distributions", "EllipsisNotation", "FFTW", "FileIO", "Formatting", "ForwardDiff", "Healpix", "ImageFiltering", "ImageMorphology", "Images", "InteractiveUtils", "Interpolations", "IterTools", "JLD2", "KahanSummation", "Lazy", "Libdl", "LinearAlgebra", "Loess", "MCMCDiagnosticTools", "MacroTools", "Markdown", "Match", "Measurements", "Memoization", "NFFT", "NamedTupleTools", "Optim", "PDMats", "Pkg", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "ProgressMeter", "QuadGK", "Random", "RecipesBase", "Requires", "Roots", "Rotations", "Serialization", "Setfield", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "TimerOutputs", "Tullio", "UnPack", "Zygote"] path = ".." uuid = "b60c06c0-7e54-11e8-3788-4bd722d65317" -version = "0.10.0" +version = "0.10.1" [deps.CMBLensing.extensions] CMBLensingCUDAExt = "CUDA" @@ -174,34 +194,34 @@ uuid = "aafaddc9-749c-510e-ac4f-586e18779b91" version = "0.2.2" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "7d20c2fb8ab838e41069398685e7b6b5f89ed85b" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "01b0594d8907485ed894bc59adfc0a24a9cde7a3" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.48.0" +version = "1.55.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" +git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.7" +version = "1.16.0" [[deps.CodeTracking]] deps = ["InteractiveUtils", "UUIDs"] -git-tree-sha1 = "d730914ef30a06732bdd9f763f6cc32e92ffbff1" +git-tree-sha1 = "a1296f0fe01a4c3f9bf0dc2934efbf4416f5db31" uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" -version = "1.3.1" +version = "1.3.4" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" +git-tree-sha1 = "02aa26a4cf76381be7f66e020a3eddeb27b0a092" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.1" +version = "0.7.2" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] -git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.20.0" +version = "3.24.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -227,9 +247,9 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" version = "1.0.2" [[deps.CommonSolve]] -git-tree-sha1 = "9441451ee712d1aec22edad62db1a9af3dc8d852" +git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" -version = "0.2.3" +version = "0.2.4" [[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] @@ -239,9 +259,9 @@ version = "0.3.0" [[deps.Compat]] deps = ["UUIDs"] -git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" +git-tree-sha1 = "8a62af3e248a8c4bad6b32cbbe663ae02275e32c" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.6.1" +version = "4.10.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -253,18 +273,18 @@ uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" version = "1.0.2+0" [[deps.ComponentArrays]] -deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "Requires", "StaticArrayInterface"] -git-tree-sha1 = "bbc7dd1b536d2950c2a91801283c609ef74e72fe" +deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "Functors", "LinearAlgebra", "Requires", "StaticArrayInterface"] +git-tree-sha1 = "00380a5de40736c634b867069347b721ca311673" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.13.9" +version = "0.13.15" [deps.ComponentArrays.extensions] - ConstructionBaseExt = "ConstructionBase" - GPUArraysExt = "GPUArrays" - RecursiveArrayToolsExt = "RecursiveArrayTools" - ReverseDiffExt = "ReverseDiff" - SciMLBaseExt = "SciMLBase" - StaticArraysExt = "StaticArrays" + ComponentArraysConstructionBaseExt = "ConstructionBase" + ComponentArraysGPUArraysExt = "GPUArrays" + ComponentArraysRecursiveArrayToolsExt = "RecursiveArrayTools" + ComponentArraysReverseDiffExt = "ReverseDiff" + ComponentArraysSciMLBaseExt = "SciMLBase" + ComponentArraysStaticArraysExt = "StaticArrays" [deps.ComponentArrays.weakdeps] ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" @@ -276,14 +296,20 @@ version = "0.13.9" [[deps.CompositeStructs]] deps = ["MacroTools"] -git-tree-sha1 = "79daafc7716e9c6975c94ec9e1aead9e4ccc1808" +git-tree-sha1 = "cc3eee93641dfc72dab4dd1830014eae644dcb96" uuid = "534720e6-2374-40c5-8712-bf9a2f1643c6" -version = "0.1.3" +version = "0.1.4" [[deps.CompositionsBase]] -git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" -version = "0.1.1" +version = "0.1.2" + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + + [deps.CompositionsBase.weakdeps] + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.ComputationalResources]] git-tree-sha1 = "52cb3ec90e8a8bea0e62e275ba577ad0f74821f7" @@ -292,26 +318,26 @@ version = "0.3.2" [[deps.Conda]] deps = ["Downloads", "JSON", "VersionParsing"] -git-tree-sha1 = "e32a90da027ca45d84678b826fffd3110bb3fc90" +git-tree-sha1 = "8c86e48c0db1564a1d49548d3515ced5d604c408" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.8.0" +version = "1.9.1" [[deps.CondaPkg]] -deps = ["JSON3", "Markdown", "MicroMamba", "Pidfile", "Pkg", "TOML"] -git-tree-sha1 = "741146cf2ced5859faae76a84b541aa9af1a78bb" +deps = ["JSON3", "Markdown", "MicroMamba", "Pidfile", "Pkg", "Preferences", "TOML"] +git-tree-sha1 = "bbd0c518cb11acc6707190199025dbc34b6c7ca7" uuid = "992eb4ea-22a4-4c89-a5bb-47a3300528ab" -version = "0.2.18" +version = "0.2.21" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.1" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] - IntervalSetsExt = "IntervalSets" - StaticArraysExt = "StaticArrays" + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.ContextVariablesX]] deps = ["Compat", "Logging", "UUIDs"] @@ -321,9 +347,9 @@ version = "0.1.3" [[deps.CoordinateTransformations]] deps = ["LinearAlgebra", "StaticArrays"] -git-tree-sha1 = "681ea870b918e7cff7111da58791d7f718067a19" +git-tree-sha1 = "f9d7112bfff8a19a3a4ea4e03a8e6a91fe8456bf" uuid = "150eb455-5306-5404-9cee-2592286d6298" -version = "0.6.2" +version = "0.6.3" [[deps.CustomUnitRanges]] git-tree-sha1 = "1a3f97f907e6dd8983b744d2642651bb162a3f7a" @@ -331,15 +357,15 @@ uuid = "dc8bdbbb-1ca9-579f-8c36-e416f6a65cce" version = "1.0.2" [[deps.DataAPI]] -git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.14.0" +version = "1.15.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" +git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.13" +version = "0.18.15" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -369,25 +395,29 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.13.0" +version = "1.15.1" [[deps.Distances]] -deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" +deps = ["LinearAlgebra", "Statistics", "StatsAPI"] +git-tree-sha1 = "b6def76ffad15143924a2199f72a5cd883a2e8a9" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.8" +version = "0.10.9" +weakdeps = ["SparseArrays"] + + [deps.Distances.extensions] + DistancesSparseArraysExt = "SparseArrays" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "13027f188d26206b9e7b863036f87d2f2e7d013a" +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "3d5873f811f582873bb9871fc9c451784d5dc8c7" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.87" +version = "0.25.102" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -404,10 +434,10 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.Documenter]] -deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "58fea7c536acd71f3eef6be3b21c0df5f3df88fd" +deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "Dates", "DocStringExtensions", "Downloads", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "Test", "Unicode"] +git-tree-sha1 = "f667b805e90d643aeb1ca70189827f991a7cc115" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.24" +version = "1.1.0" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -427,9 +457,9 @@ uuid = "da5c29d0-fa7d-589e-88eb-ea29b0a81949" version = "1.7.0" [[deps.ExprTools]] -git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00" +git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.9" +version = "0.1.10" [[deps.FFTViews]] deps = ["CustomUnitRanges", "FFTW"] @@ -439,9 +469,9 @@ version = "0.3.2" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "f9818144ce7c8c41edf5c4c179c684d92aa4d9fe" +git-tree-sha1 = "b4fbdd20c889804969571cc589900803edda16b7" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.6.0" +version = "1.7.1" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -463,24 +493,39 @@ version = "0.1.1" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" +git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.0" +version = "1.16.1" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "fc86b4fd3eff76c3ce4f5e96e2fdfa6282722885" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.0.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "03fcb1c42ec905d15b305359603888ec3e65f886" +deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "c6e4a1fbe73b31a3dea94b1da449503b8830c306" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.19.0" +version = "2.21.1" + + [deps.FiniteDiff.extensions] + FiniteDiffBandedMatricesExt = "BandedMatrices" + FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffStaticArraysExt = "StaticArrays" + + [deps.FiniteDiff.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -496,29 +541,35 @@ version = "0.4.2" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" +git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.35" +version = "0.10.36" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] ForwardDiffStaticArraysExt = "StaticArrays" +[[deps.Functors]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "9a68d75d466ccc1218d0552a8e1631151c569545" +uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" +version = "0.4.5" + [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "9ade6983c3dbbd492cf5729f865fe030d1541463" +git-tree-sha1 = "2e57b4a4f9cc15e85a24d603256fe08e527f48d1" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.6.6" +version = "8.8.1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "1cd7f0af1aa58abc02ea1d872953a97359cb87fa" +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.4" +version = "0.1.5" [[deps.GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] @@ -526,11 +577,10 @@ git-tree-sha1 = "19d693666a304e8c371798f4900f7435558c7cde" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" version = "0.17.3" -[[deps.Ghostscript_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "43ba3d3c82c18d88471cfd2924931658838c9d8f" -uuid = "61579ee1-b43e-5ca0-a5da-69d92c66a64b" -version = "9.55.0+4" +[[deps.Glob]] +git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" +uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" +version = "1.3.1" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] @@ -540,33 +590,33 @@ version = "1.1.2" [[deps.Healpix]] deps = ["CFITSIO", "LazyArtifacts", "Libsharp", "LinearAlgebra", "Pkg", "Printf", "Random", "RecipesBase", "StaticArrays", "Test"] -git-tree-sha1 = "b17154aa7b6c69c5484a1523872fb09a08632d2b" +git-tree-sha1 = "1445c1811919802385337d0a88b5ca67b8c2ef29" uuid = "9f4e344d-96bc-545a-84a3-ae6b9e1b672b" -version = "4.2.0" +version = "4.2.1" [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "432b5b03176f8182bd6841fbfc42c718506a2d5f" +git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.15" +version = "0.3.23" [[deps.IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] -git-tree-sha1 = "59e19713542dd9dd02f31d59edbada69530d6a14" +git-tree-sha1 = "47ac8cc196b81001a711f4b2c12c97372338f00c" uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a" -version = "1.24.0" +version = "1.24.2" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.2" +version = "0.2.3" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "0ade27f0c49cebd8db2523c4eeccf779407cf12c" +git-tree-sha1 = "eac00994ce3229a464c2847e956d77a2c64ad3a5" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.9" +version = "0.4.10" [[deps.IdentityRanges]] deps = ["OffsetArrays"] @@ -616,16 +666,16 @@ uuid = "82e4d734-157c-48bb-816b-45c225c6df19" version = "0.4.1" [[deps.ImageMagick]] -deps = ["FileIO", "ImageCore", "ImageMagick_jll", "InteractiveUtils", "Libdl", "Pkg", "Random"] -git-tree-sha1 = "5bc1cb62e0c5f1005868358db0692c994c3a13c6" +deps = ["FileIO", "ImageCore", "ImageMagick_jll", "InteractiveUtils"] +git-tree-sha1 = "b0b765ff0b4c3ee20ce6740d843be8dfce48487c" uuid = "6218d12a-5da1-5696-b52f-db25d2ecc6d1" -version = "1.2.1" +version = "1.3.0" [[deps.ImageMagick_jll]] -deps = ["Artifacts", "Ghostscript_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pkg", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "124626988534986113cfd876e3093e4a03890f58" +deps = ["JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pkg", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "1c0a2295cca535fabaf2029062912591e9b61987" uuid = "c73af94c-d91f-53ed-93a7-00f77d67a9d7" -version = "6.9.12+3" +version = "6.9.10-12+3" [[deps.ImageMetadata]] deps = ["AxisArrays", "ColorVectorSpace", "ImageAxes", "ImageCore", "IndirectArrays"] @@ -675,9 +725,9 @@ version = "0.3.1" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0cb9352ef2e01574eeebdb102948a58740dcaf83" +git-tree-sha1 = "ad37c091f7d7daf900963171600d7c1c5c3ede32" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2023.1.0+0" +version = "2023.2.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -690,10 +740,14 @@ uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" version = "0.13.6" [[deps.IntervalSets]] -deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" +deps = ["Dates", "Random"] +git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.4" +version = "0.7.7" +weakdeps = ["Statistics"] + + [deps.IntervalSets.extensions] + IntervalSetsStatisticsExt = "Statistics" [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" @@ -701,9 +755,9 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" [[deps.IterTools]] -git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" +git-tree-sha1 = "4ced6667f9974fc5c5943fa5e2ef1ca43ea9e450" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.4.0" +version = "1.8.0" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -712,15 +766,15 @@ version = "1.0.0" [[deps.JLD2]] deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" +git-tree-sha1 = "c11d691a0dc8e90acfa4740d293ade57f68bfdbb" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.31" +version = "0.4.35" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -729,10 +783,10 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" [[deps.JSON3]] -deps = ["Dates", "Mmap", "Parsers", "SnoopPrecompile", "StructTypes", "UUIDs"] -git-tree-sha1 = "84b10656a41ef564c39d2d477d7236966d2b5683" +deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] +git-tree-sha1 = "95220473901735a0f4df9d1ca5b171b568b2daa3" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.12.0" +version = "1.13.2" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -742,9 +796,9 @@ version = "2.1.91+0" [[deps.JuliaInterpreter]] deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"] -git-tree-sha1 = "6a125e6a4cb391e0b9adbd1afa9e771c2179f8ef" +git-tree-sha1 = "81dc6aefcbe7421bd62cb6ca0e700779330acff8" uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a" -version = "0.9.23" +version = "0.9.25" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -786,6 +840,11 @@ git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.0" +[[deps.LazilyInitializedFields]] +git-tree-sha1 = "410fe4739a4b092f2ffe36fcb0dcc3ab12648ce1" +uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" +version = "1.2.1" + [[deps.Lazy]] deps = ["MacroTools"] git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" @@ -848,9 +907,9 @@ version = "0.5.4" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.23" +version = "0.3.26" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -873,21 +932,21 @@ version = "2.3.0" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "889c36e76dbde08c54f5a8bb5eb5049aab1ef519" +git-tree-sha1 = "3e6db72c2ab9cadfa3278ff388473a01fc0cfb9d" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.3.1" +version = "0.3.5" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "2ce8695e1e699b68702c03402672a69f54b8aca9" +git-tree-sha1 = "eb006abbd7041c28e0d16260e50a24f8f9104913" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2022.2.0+0" +version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -896,19 +955,25 @@ version = "0.4.17" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] -git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" +git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" -version = "0.4.1" +version = "0.4.2" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MarkdownAST]] +deps = ["AbstractTrees", "Markdown"] +git-tree-sha1 = "e8513266815200c0c8f522d6d44ffb5e9b366ae4" +uuid = "d0879d2d-cac2-40c8-9cee-1863dc0c7391" +version = "0.1.1" + [[deps.Match]] git-tree-sha1 = "1d9bc5c1a6e7ee24effb93f175c9342f9154d97f" uuid = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf" @@ -926,16 +991,28 @@ uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" version = "2.28.2+0" [[deps.Measurements]] -deps = ["Calculus", "LinearAlgebra", "Printf", "RecipesBase", "Requires"] -git-tree-sha1 = "51d946d38d62709d6a2d37ea9bcc30c80c686801" +deps = ["Calculus", "LinearAlgebra", "Printf", "Requires"] +git-tree-sha1 = "bf645d369306c848b6e44e37a1e216b15468c4fc" uuid = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" -version = "2.9.0" +version = "2.10.0" + + [deps.Measurements.extensions] + MeasurementsJunoExt = "Juno" + MeasurementsRecipesBaseExt = "RecipesBase" + MeasurementsSpecialFunctionsExt = "SpecialFunctions" + MeasurementsUnitfulExt = "Unitful" + + [deps.Measurements.weakdeps] + Juno = "e5e0dc1b-0480-54bc-9374-aad01c23163d" + RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Memoization]] deps = ["MacroTools"] -git-tree-sha1 = "2f6913923a0cb8046134f5cbf8b4d7ba3c856a1d" +git-tree-sha1 = "073f080e733bc6697411901224ed4fd15fefaffa" uuid = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" -version = "0.2.0" +version = "0.2.1" [[deps.Memoize]] deps = ["MacroTools"] @@ -951,9 +1028,9 @@ version = "0.1.4" [[deps.MicroMamba]] deps = ["Pkg", "Scratch", "micromamba_jll"] -git-tree-sha1 = "a6a4771aba1dc8942bc0f44ff9f8ee0f893ef888" +git-tree-sha1 = "011cab361eae7bcd7d278f0a7a00ff9c69000c51" uuid = "0b3b1443-0f03-428d-bdfb-f27f9c1191ea" -version = "0.1.12" +version = "0.1.14" [[deps.Missings]] deps = ["DataAPI"] @@ -1015,9 +1092,9 @@ version = "1.2.0" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" +git-tree-sha1 = "2ac17d29c523ce1cd38e27785a7d23024853a4bb" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.9" +version = "1.12.10" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] @@ -1037,20 +1114,20 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "a89b11f0f354f06099e4001c151dffad7ebab015" +git-tree-sha1 = "963b004d15216f8129f6c0f7d187efa136570be0" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.5" +version = "1.7.7" [[deps.OrderedCollections]] -git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" +git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.0" +version = "1.6.2" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" +git-tree-sha1 = "35882aa39079c44ea6c1f07827f98dc78bf1ce91" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.17" +version = "0.11.22" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] @@ -1059,10 +1136,10 @@ uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" version = "0.3.17" [[deps.PackageCompiler]] -deps = ["Artifacts", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs"] -git-tree-sha1 = "7caa85906781a8fa5b1d13ad0dd858dca31b07f0" +deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs"] +git-tree-sha1 = "2d061c0088e216784587c662ec200da8bd2c8b08" uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" -version = "2.1.5" +version = "2.1.9" [[deps.PaddedViews]] deps = ["OffsetArrays"] @@ -1077,10 +1154,10 @@ uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" [[deps.Parsers]] -deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "478ac6c952fddd4399e71d4779797c538d0ff2bf" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.8" +version = "2.7.2" [[deps.Pidfile]] deps = ["FileWatching", "Test"] @@ -1094,10 +1171,10 @@ uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" version = "1.9.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "c95373e73290cf50a8a22c3375e4625ded5c5280" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "f92e1315dadf8c46561fb9396e525f7200cdc227" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.4" +version = "1.3.5" [[deps.PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -1105,11 +1182,17 @@ git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.2.0" + [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" +git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.1" [[deps.PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" @@ -1126,27 +1209,27 @@ uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "00099623ffee15972c16111bcf84c58a0051257c" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.9.0" [[deps.PythonCall]] deps = ["CondaPkg", "Dates", "Libdl", "MacroTools", "Markdown", "Pkg", "REPL", "Requires", "Serialization", "Tables", "UnsafePointers"] -git-tree-sha1 = "f27dabb05ec811675a9eefe49325a14ae7266b0b" +git-tree-sha1 = "70af6bdbde63d7d0a4ea99f3e890ebdb55e9d464" uuid = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" -version = "0.9.12" +version = "0.9.14" [[deps.PythonPlot]] deps = ["Colors", "CondaPkg", "LaTeXStrings", "PythonCall", "Sockets", "Test", "VersionParsing"] -git-tree-sha1 = "63a18f73425ce301fef12c3f1fb201b720c05015" +git-tree-sha1 = "88b305afa25e1bc4379f182152273dfc55a814b4" uuid = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9" -version = "1.0.2" +version = "1.0.3" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" +git-tree-sha1 = "9ebcd48c498668c7fa0e97a9cae873fbee7bfee1" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.8.2" +version = "2.9.1" [[deps.Quaternions]] deps = ["LinearAlgebra", "Random", "RealDot"] @@ -1164,9 +1247,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Random123]] deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "7a1a306b72cfa60634f03a911405f4e64d1b718b" +git-tree-sha1 = "552f30e847641591ba3f39fd1bed559b9deb0ef3" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.6.0" +version = "1.6.1" [[deps.RandomNumbers]] deps = ["Random", "Requires"] @@ -1181,9 +1264,13 @@ version = "0.3.2" [[deps.Ratios]] deps = ["Requires"] -git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" +git-tree-sha1 = "1342a47bf3260ee108163042310d26f2be5ec90b" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.3" +version = "0.4.5" +weakdeps = ["FixedPointNumbers"] + + [deps.Ratios.extensions] + RatiosFixedPointNumbersExt = "FixedPointNumbers" [[deps.RealDot]] deps = ["LinearAlgebra"] @@ -1192,16 +1279,22 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[deps.RecipesBase]] -deps = ["SnoopPrecompile"] -git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" +deps = ["PrecompileTools"] +git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.3.3" +version = "1.3.4" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" version = "1.2.2" +[[deps.RegistryInstances]] +deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"] +git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51" +uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3" +version = "0.1.0" + [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" @@ -1216,9 +1309,9 @@ version = "1.3.0" [[deps.Revise]] deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"] -git-tree-sha1 = "feafdc70b2e6684314e188d95fe66d116de834a7" +git-tree-sha1 = "609c26951d80551620241c3d7090c71a73da75ab" uuid = "295af30f-e4ad-537b-8983-00126c2a3abe" -version = "3.5.2" +version = "3.5.6" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1234,23 +1327,27 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "82362f2a4f756951f21ebb3ac2aed094c46a5109" +git-tree-sha1 = "06b5ac80ff1b88bd82df92c1c1875eea3954cd6e" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.12" +version = "2.0.20" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" RootsIntervalRootFindingExt = "IntervalRootFinding" + RootsSymPyExt = "SymPy" + RootsSymPyPythonCallExt = "SymPyPythonCall" [deps.Roots.weakdeps] ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807" + SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" + SymPyPythonCall = "bc8888f7-b21e-4b7c-a06a-5d9c9496438c" [[deps.Rotations]] -deps = ["LinearAlgebra", "Quaternions", "Random", "StaticArrays", "Statistics"] -git-tree-sha1 = "72a6abdcd088764878b473102df7c09bbc0548de" +deps = ["LinearAlgebra", "Quaternions", "Random", "StaticArrays"] +git-tree-sha1 = "0783924e4a332493f72490253ba4e668aeba1d73" uuid = "6038ab10-8711-5258-84ad-4b1120ba62dc" -version = "1.4.0" +version = "1.6.0" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1303,19 +1400,25 @@ version = "1.1.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" +git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.1.0" +version = "1.1.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.2.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1335,15 +1438,15 @@ version = "0.1.1" [[deps.Static]] deps = ["IfElse"] -git-tree-sha1 = "08be5ee09a7632c32695d954a602df96a877bf0d" +git-tree-sha1 = "f295e0a1da4ca425659c57441bcb59abb035a4bc" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.6" +version = "0.8.8" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "59d01f440c78ad9046680688d6ad51812953a4a9" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] +git-tree-sha1 = "03fec6800a986d191f64f5c0996b59ed526eda25" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.3.1" +version = "1.4.1" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -1351,15 +1454,19 @@ weakdeps = ["OffsetArrays", "StaticArrays"] StaticArrayInterfaceStaticArraysExt = "StaticArrays" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "63e84b7fdf5021026d0f17f76af7c57772313d99" +deps = ["LinearAlgebra", "Random", "StaticArraysCore"] +git-tree-sha1 = "0adf069a2a490c47273727e029371b31d44b72b2" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.21" +version = "1.6.5" +weakdeps = ["Statistics"] + + [deps.StaticArrays.extensions] + StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" +git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.0" +version = "1.4.2" [[deps.StatisticalTraits]] deps = ["ScientificTypesBase"] @@ -1374,9 +1481,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1399,10 +1506,10 @@ version = "1.3.0" InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] @@ -1431,10 +1538,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "a1f34829d5ac0ef499f6d84428bd6b4c71f02ead" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.1" +version = "1.11.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -1459,21 +1566,35 @@ version = "0.3.1" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f2fd3f288dfc6f507b0c3a2eb3bac009251e548b" +git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.22" +version = "0.5.23" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "0b829474fed270a4b0ab07117dce9b9a2fa7581a" +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.12" +version = "0.9.13" [[deps.Transducers]] -deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5" +deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] +git-tree-sha1 = "53bd5978b182fa7c57577bdb452c35e5b4fb73a5" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.75" +version = "0.4.78" + + [deps.Transducers.extensions] + TransducersBlockArraysExt = "BlockArrays" + TransducersDataFramesExt = "DataFrames" + TransducersLazyArraysExt = "LazyArrays" + TransducersOnlineStatsBaseExt = "OnlineStatsBase" + TransducersReferenceablesExt = "Referenceables" + + [deps.Transducers.weakdeps] + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" + OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338" + Referenceables = "42d2dcc6-99eb-4e98-b66c-637b7d73030e" [[deps.Tullio]] deps = ["ChainRulesCore", "DiffRules", "LinearAlgebra", "Requires"] @@ -1533,10 +1654,10 @@ uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" version = "1.5.5+0" [[deps.Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SnoopPrecompile", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "987ae5554ca90e837594a0f30325eeb5e7303d1e" +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "16848c23e7961e099a4152ba0d10db887f412ee9" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.60" +version = "0.6.65" [deps.Zygote.extensions] ZygoteColorsExt = "Colors" @@ -1579,9 +1700,9 @@ version = "1.0.20+0" [[deps.micromamba_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] -git-tree-sha1 = "087555b0405ed6adf526cef22b6931606b5af8ac" +git-tree-sha1 = "66d07957bcf7e4930d933195aed484078dd8cbb5" uuid = "f8abcde7-e9b7-5caa-b8af-a437887ae8e4" -version = "1.4.1+0" +version = "1.4.9+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] diff --git a/docs/Project.toml b/docs/Project.toml index 7bbe6a41..216e4935 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -18,6 +18,7 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] CUDA = "3.4" +Documenter = "1.1" [preferences.FFTW] provider = "fftw" diff --git a/docs/make.jl b/docs/make.jl index 36a4795a..4d164ff3 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -37,12 +37,15 @@ rm("src-staging/index.md",force=true) symlink("../../README.md","src-staging/index.md") -# highlight output cells (i.e. anything withouout a language specified) white -# note: "output" language is added by us in documenter.tpl -@eval Documenter.Writers.HTMLWriter function mdconvert(c::Markdown.Code, parent::MDBlockContext; settings::Union{HTML,Nothing}=nothing, kwargs...) +# # highlight output cells (i.e. anything withouout a language specified) white +# # note: "output" language is added by us in documenter.tpl +@eval Documenter.Writers.HTMLWriter function domify(dctx::DCtx, node::Node, c::MarkdownAST.CodeBlock) + ctx, navnode, settings = dctx.ctx, dctx.navnode, dctx.settings + language = c.info + # function mdconvert(c::Markdown.Code, parent::MDBlockContext; settings::Union{HTML,Nothing}=nothing, kwargs...) @tags pre code - language = Utilities.codelang(c.language) - if language == "documenter-ansi" || language == "output" # From @repl blocks (through MultiCodeBlock) + language = Documenter.codelang(language) + if language == "documenter-ansi" || language == "output" return pre(domify_ansicoloredtext(c.code, "language-output hljs")) elseif settings !== nothing && settings.prerender && !(isempty(language) || language == "nohighlight") @@ -53,90 +56,92 @@ symlink("../../README.md","src-staging/index.md") return pre(code[".$(class) .hljs"](c.code)) end + # adds the MyBinder button on each page that is a notebook @eval Documenter.Writers.HTMLWriter function render_navbar(ctx, navnode, edit_page_link::Bool) @tags div header nav ul li a span img + # Hamburger on mobile + navbar_left = a[ + "#documenter-sidebar-button.docs-sidebar-button.docs-navbar-link.fa-solid.fa-bars.is-hidden-desktop", + :href => "#", + ] + # The breadcrumb (navigation links on top) - navpath = Documents.navpath(navnode) + navpath = Documenter.navpath(navnode) header_links = map(navpath) do nn - title = mdconvert(pagetitle(ctx, nn); droplinks=true) + dctx = DCtx(ctx, nn, true) + title = domify(dctx, pagetitle(dctx)) nn.page === nothing ? li(a[".is-disabled"](title)) : li(a[:href => navhref(ctx, nn, navnode)](title)) end header_links[end] = header_links[end][".is-active"] - breadcrumb = nav[".breadcrumb"]() ### modified to not show breadcrumbs + breadcrumb = nav[".breadcrumb"]( + ul[".is-hidden-mobile"](header_links), + ul[".is-hidden-tablet"](header_links[end]) # when on mobile, we only show the page title, basically + ) # The "Edit on GitHub" links and the hamburger to open the sidebar (on mobile) float right navbar_right = div[".docs-right"] - - ### custom code to add MyBinder link - if edit_page_link - pageurl = get(getpage(ctx, navnode).globals.meta, :EditURL, getpage(ctx, navnode).source) - nbpath = foldl(replace,["src-staging"=>"src",".md"=>".ipynb"], init=pageurl) - if isfile(nbpath) - url = "https://mybinder.org/v2/gh/marius311/CMBLensing.jl/gh-pages?urlpath=lab/tree/$(basename(nbpath))" - push!(navbar_right.nodes, a[".docs-right", :href => url](img[:src => "https://mybinder.org/badge_logo.svg"]())) + + ### custom code to add MyBinder link + if edit_page_link + pageurl = get(getpage(ctx, navnode).globals.meta, :EditURL, getpage(ctx, navnode).source) + nbpath = foldl(replace,["src-staging"=>"src",".md"=>".ipynb"], init=pageurl) + if isfile(nbpath) + url = "https://mybinder.org/v2/gh/marius311/CMBLensing.jl/gh-pages?urlpath=lab/tree/$(basename(nbpath))" + push!(navbar_right.nodes, a[".docs-right", :href => url](img[:src => "https://mybinder.org/badge_logo.svg"]())) + end end - end - ### + ### - # Set the logo and name for the "Edit on.." button. - if edit_page_link && (ctx.settings.edit_link !== nothing) && !ctx.settings.disable_git - host_type = Utilities.repo_host_from_url(ctx.doc.user.repo) - if host_type == Utilities.RepoGitlab - host = "GitLab" - logo = "\uf296" - elseif host_type == Utilities.RepoGithub - host = "GitHub" - logo = "\uf09b" - elseif host_type == Utilities.RepoBitbucket - host = "BitBucket" - logo = "\uf171" - else - host = "" - logo = "\uf15c" - end - hoststring = isempty(host) ? " source" : " on $(host)" - - pageurl = get(getpage(ctx, navnode).globals.meta, :EditURL, getpage(ctx, navnode).source) - - - edit_branch = isa(ctx.settings.edit_link, String) ? ctx.settings.edit_link : nothing - url = if Utilities.isabsurl(pageurl) - pageurl - else - if !(pageurl == getpage(ctx, navnode).source) - # need to set users path relative the page itself - pageurl = joinpath(first(splitdir(getpage(ctx, navnode).source)), pageurl) - end - Utilities.url(ctx.doc.user.repo, pageurl, commit=edit_branch) + + # Set up the link to the root of the remote Git repository + # + # By default, we try to determine it from the configured remote. If that fails, the link + # is not displayed. The user can also pass `repolink` to HTML to either disable it + # (repolink = nothing) or override the link URL (if set to a string). In the latter case, + # we try to figure out what icon and string we should use based on the URL. + if !isnothing(ctx.settings.repolink) && (ctx.settings.repolink isa String || ctx.doc.user.remote isa Remotes.Remote) + url, (host, logo) = if ctx.settings.repolink isa String + ctx.settings.repolink, host_logo(ctx.settings.repolink) + else # ctx.doc.user.remote isa Remotes.Remote + Remotes.repourl(ctx.doc.user.remote), host_logo(ctx.doc.user.remote) end - if url !== nothing - edit_verb = (edit_branch === nothing) ? "View" : "Edit" - title = "$(edit_verb)$hoststring" + # repourl() can sometimes return a nothing (Remotes.URL) + if !isnothing(url) + repo_title = "View the repository" * (isempty(host) ? "" : " on $host") push!(navbar_right.nodes, - a[".docs-edit-link", :href => url, :title => title]( - span[".docs-icon.fab"](logo), - span[".docs-label.is-hidden-touch"](title) + a[".docs-navbar-link", :href => url, :title => repo_title]( + span[".docs-icon.fa-brands"](logo), + span[".docs-label.is-hidden-touch"](isempty(host) ? "Repository" : host) ) ) end end + # Add an edit link, with just an icon, but only on pages where edit_page_link is true. + # Some pages, like search, are special and do not have a source file to link to. + edit_page_link && edit_link(ctx, navnode) do logo, title, url + push!(navbar_right.nodes, + a[".docs-navbar-link", :href => url, :title => title]( + span[".docs-icon.fa-solid"](logo) + ) + ) + end # Settings cog push!(navbar_right.nodes, a[ - "#documenter-settings-button.docs-settings-button.fas.fa-cog", + "#documenter-settings-button.docs-settings-button.docs-navbar-link.fa-solid.fa-gear", :href => "#", :title => "Settings", ]) - # Hamburger on mobile + # Collapse/Expand All articles toggle push!(navbar_right.nodes, a[ - "#documenter-sidebar-button.docs-sidebar-button.fa.fa-bars.is-hidden-desktop", - :href => "#" + "#documenter-article-toggle-button.docs-article-toggle-button.fa-solid.fa-chevron-up", + :href=>"javascript:;", :title=>"Collapse all docstrings", ]) # Construct the main
node that should be the first element in div.docs-main - header[".docs-navbar"](breadcrumb, navbar_right) + header[".docs-navbar"](navbar_left, breadcrumb, navbar_right) end @@ -159,6 +164,7 @@ makedocs( "precompilation.md", "api.md" ], + remotes = nothing ) if haskey(ENV, "IMAGE_NAME") diff --git a/docs/src/01_lense_a_map.md b/docs/src/01_lense_a_map.md index 5420db61..cd879f1b 100644 --- a/docs/src/01_lense_a_map.md +++ b/docs/src/01_lense_a_map.md @@ -32,7 +32,7 @@ First we load a simulated unlensed field, $f$, and lensing potential, $\phi$, θpix = 2, # size of the pixels in arcmin Nside = 256, # number of pixels per side in the map T = Float32, # Float32 or Float64 (former is ~twice as fast) - pol = :I, # :I for Intensity, :P for polarization, or :IP for both= + pol = :I, # :I for Intensity, :P for polarization, or :IP for both ); ``` @@ -69,7 +69,7 @@ If you have your own map data in an array you'd like to load into a CMBLensing ` FlatMap(mapdata, θpix=3) ``` -For more info on `Field` objects, see [Field Basics](../05_field_basics/). +For more info on `Field` objects, see [Field Basics](05_field_basics.md). ## Inverse lensing @@ -125,4 +125,4 @@ Once cached, it's faster and less memory intensive to repeatedly apply the opera @benchmark Lϕ * f setup=(Lϕ=precompute!!(LenseFlow(ϕ),f)) ``` -Note that this documentation is generated on limited-performance cloud servers. Actual benchmarks are likely much faster locally or on a cluster, and yet (much) faster on [GPU](../06_gpu/). +Note that this documentation is generated on limited-performance cloud servers. Actual benchmarks are likely much faster locally or on a cluster, and yet (much) faster on [GPU](06_gpu.md). diff --git a/docs/src/03_joint_MAP_example.md b/docs/src/03_joint_MAP_example.md index 588e75ae..b45e0914 100644 --- a/docs/src/03_joint_MAP_example.md +++ b/docs/src/03_joint_MAP_example.md @@ -123,7 +123,7 @@ fJ, ϕJ, history = MAP_joint(ds, nsteps=30, progress=true); # Examine results -The `history` variable gives some info about the run, and more info can be saved by passing `history_keys` argument to [`MAP_joint`](api/#CMBLensing.MAP_joint). By default, we get just the value of the posterior, which we can use to check the maximizer has asymptoted to a maximum value: +The `history` variable gives some info about the run, and more info can be saved by passing `history_keys` argument to `MAP_joint`. By default, we get just the value of the posterior, which we can use to check the maximizer has asymptoted to a maximum value: ```julia plot(getindex.(history, :logpdf)) diff --git a/docs/src/04_from_python.md b/docs/src/04_from_python.md index 592f845d..597aa3c6 100644 --- a/docs/src/04_from_python.md +++ b/docs/src/04_from_python.md @@ -69,7 +69,7 @@ jl.seval("1:10") ## Calling CMBLensing.jl -You can use `seval` to essentially just paste Julia code into Python session, for example, following the [Lensing a flat-sky map](../01_lense_a_map/) example: +You can use `seval` to essentially just paste Julia code into Python session, for example, following the [Lensing a flat-sky map](01_lense_a_map.md) example: ```python jl.seval(""" diff --git a/src/chains.jl b/src/chains.jl index 88c1646f..74cf4820 100644 --- a/src/chains.jl +++ b/src/chains.jl @@ -17,7 +17,7 @@ Keyword arguments: `thin == :hasmaps`, return only samples which have maps saved. If thin is a `Function`, filter the chain by this function (e.g. `thin=haskey(:g)` on Julia 1.5+) -* `unbatch` — If true, [unbatch](@ref) the chains if they are batched. +* `unbatch` — If true, run `unbatch` on the chains if they are batched. * `join` — If true, concatenate all the chains together. * `skip_missing_chunks` — Skip missing chunks in the chain instead of terminating the chain there. diff --git a/src/dataset.jl b/src/dataset.jl index c547dc90..e8b70d54 100644 --- a/src/dataset.jl +++ b/src/dataset.jl @@ -323,7 +323,7 @@ function load_sim(; ds.D = ParamDependentOp( function (;r=r₀, _...) Cfr = Cf(;r=r) - sqrt((Cfr + I*σ²len + 2*Cn̂) * pinv(Cfr)) + sqrt((Cfr + (I*σ²len + 2*Cn̂)) * pinv(Cfr)) end, ) end