diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml new file mode 100644 index 0000000..b525c01 --- /dev/null +++ b/.github/workflows/Documenter.yml @@ -0,0 +1,51 @@ +# Sample workflow for building and deploying a VitePress site to GitHub Pages +# +name: Documenter + +on: + # Runs on pushes targeting the `master` branch. Change this to `main` if you're + # using the `main` branch as the default branch. + push: + branches: + - master + tags: ['*'] + pull_request: + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +permissions: + contents: write + pages: write + id-token: write + statuses: write + +# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. +# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. +concurrency: + group: pages + cancel-in-progress: false + +jobs: + # Build job + build: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Setup Julia + uses: julia-actions/setup-julia@v1 + - name: Pull Julia cache + uses: julia-actions/cache@v1 + - name: Install documentation dependencies + run: julia --project=docs -e 'using Pkg; pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()' + #- name: Creating new mds from src + - name: Build and deploy docs + uses: julia-actions/julia-docdeploy@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token + DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key + GKSwstype: "100" # for Plots.jl plots (if you have them) + JULIA_DEBUG: "Documenter" + DATADEPS_ALWAYS_ACCEPT: true diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 6f7746e..5c3d089 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,7 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.7.3" +julia_version = "1.10.2" manifest_format = "2.0" +project_hash = "5df988d0623e4e038e439a2e42c99575f6f3f7ed" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -9,12 +10,13 @@ uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" [[deps.AbstractTrees]] -git-tree-sha1 = "5c0b629df8a5566a06f5fef5100b53ea56e465a0" +git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.2" +version = "0.4.5" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -22,15 +24,26 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +[[deps.CodecZlib]] +deps = ["TranscodingStreams", "Zlib_jll"] +git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.7.4" + [[deps.Compat]] -deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "9be8be1d8a6f44b96482c8af52238ea7987da3e3" +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.45.0" +version = "4.15.0" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "1.1.0+0" [[deps.Crayons]] git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" @@ -38,26 +51,26 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DBInterface]] -git-tree-sha1 = "9b0dc525a052b9269ccc5f7f04d5b3639c65bca5" +git-tree-sha1 = "a444404b3f94deaa43ca2a58e18153a82695282b" uuid = "a10d1c49-ce27-4219-8d33-6db1a4562965" -version = "2.5.0" +version = "2.6.1" [[deps.DataAPI]] -git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40" +git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.10.0" +version = "1.16.0" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "daa21eb85147f72e41f6352a57fccea377e310a9" +deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.3.4" +version = "1.6.1" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.13" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -68,60 +81,76 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -[[deps.DelimitedFiles]] -deps = ["Mmap"] -uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" - -[[deps.Distributed]] -deps = ["Random", "Serialization", "Sockets"] -uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" - [[deps.DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "5158c2b41018c5f7eb1470d558127ac274eca0c9" +git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.1" +version = "0.9.3" [[deps.Documenter]] -deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "ee945ed10767de73cf8b610951b98228cb65af80" +deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "CodecZlib", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "TOML", "Test", "Unicode"] +git-tree-sha1 = "5461b2a67beb9089980e2f8f25145186b6d34f91" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.22" +version = "1.4.1" [[deps.DocumenterTools]] deps = ["AbstractTrees", "Base64", "DocStringExtensions", "Documenter", "FileWatching", "Gumbo", "LibGit2", "OpenSSH_jll", "Sass"] -git-tree-sha1 = "6760c21f6eeee52eee7a5fa916e9e496196fd179" +git-tree-sha1 = "7605a88f75625836ce47102b8915041fae231ff5" uuid = "35a29f4d-8980-5a13-9543-d66fff28ecb8" -version = "0.1.15" +version = "0.1.19" + +[[deps.DocumenterVitepress]] +deps = ["ANSIColoredPrinters", "Base64", "DocStringExtensions", "Documenter", "IOCapture", "Markdown", "NodeJS_20_jll", "REPL"] +git-tree-sha1 = "a162b99600fb589c192a9b041cbeae3cc3fa0ccc" +uuid = "4710194d-e776-4893-9690-8d956a29c365" +version = "0.0.19" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +version = "1.6.0" + +[[deps.Expat_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" +uuid = "2e619515-83b5-522b-bb60-26c02a35a201" +version = "2.6.2+0" + +[[deps.ExprTools]] +git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" +uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" +version = "0.1.10" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -[[deps.Formatting]] -deps = ["Printf"] -git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" -uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" -version = "0.4.2" - [[deps.FunSQL]] deps = ["DBInterface", "Dates", "LRUCache", "OrderedCollections", "PrettyPrinting", "Tables"] -git-tree-sha1 = "e95a4efcbb1a133f5c6346dc73b5ee7747a33c4c" +git-tree-sha1 = "f319b0974f0ca14264ae9810dc47d25188594db5" uuid = "cf6cc811-59f4-4a10-b258-a8547a8f6407" -version = "0.10.2" +version = "0.11.2" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" +[[deps.Git]] +deps = ["Git_jll"] +git-tree-sha1 = "51764e6c2e84c37055e846c516e9015b4a291c7d" +uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2" +version = "1.3.0" + +[[deps.Git_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "d8be4aab0f4e043cc40984e9097417307cce4c03" +uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" +version = "2.36.1+2" + [[deps.Gumbo]] deps = ["AbstractTrees", "Gumbo_jll", "Libdl"] -git-tree-sha1 = "a4b03190a8d79e95b2f418df44f74cbc34289920" +git-tree-sha1 = "a1a138dfbf9df5bace489c7a9d5196d6afdfa140" uuid = "708ec375-b3d6-5a57-a7ce-8257bf98657a" -version = "0.8.1" +version = "0.8.2" [[deps.Gumbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -131,18 +160,24 @@ version = "0.10.2+0" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.2" +version = "0.2.4" + +[[deps.InlineStrings]] +deps = ["Parsers"] +git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" +uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" +version = "1.4.0" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.InvertedIndices]] -git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.1.0" +version = "1.3.0" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -150,92 +185,130 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[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"] -git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" +git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.3" +version = "0.21.4" [[deps.LRUCache]] -git-tree-sha1 = "d64a0aff6691612ab9fb0117b0995270871c5dfc" +git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59" uuid = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" -version = "1.3.0" +version = "1.6.1" +weakdeps = ["Serialization"] + + [deps.LRUCache.extensions] + SerializationExt = ["Serialization"] + +[[deps.LaTeXStrings]] +git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" +version = "1.3.1" + +[[deps.LazilyInitializedFields]] +git-tree-sha1 = "8f7f3cabab0fd1800699663533b6d5cb3fc0e612" +uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" +version = "1.2.2" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" +version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" +version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" +version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" +[[deps.Libiconv_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" +version = "1.17.0+0" + [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -[[deps.MacroTools]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" -uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.9" - [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MarkdownAST]] +deps = ["AbstractTrees", "Markdown"] +git-tree-sha1 = "465a70f0fc7d443a00dcdc3267a497397b8a3899" +uuid = "d0879d2d-cac2-40c8-9cee-1863dc0c7391" +version = "0.1.2" + [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" - -[[deps.Memoization]] -deps = ["MacroTools"] -git-tree-sha1 = "55dc27dc3d663900d1d768822528960acadc012a" -uuid = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" -version = "0.1.14" +version = "2.28.2+1" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" +[[deps.Mocking]] +deps = ["Compat", "ExprTools"] +git-tree-sha1 = "bf17d9cb4f0d2882351dfad030598f64286e5936" +uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" +version = "0.7.8" + [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +version = "2023.1.10" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" +version = "1.2.0" + +[[deps.NodeJS_20_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "0b1b4a83773cfdefa5d9dc0322e4c0624ce88b5b" +uuid = "c7aee132-11e1-519c-8219-0a43005e73c2" +version = "20.12.2+0" [[deps.OMOPCDMCohortCreator]] -deps = ["DBInterface", "DataFrames", "FunSQL", "Memoization"] -git-tree-sha1 = "f42137a3d4910b4dcbae637b1b6ed700dfdba940" +deps = ["DBInterface", "DataFrames", "Dates", "FunSQL", "TimeZones"] +git-tree-sha1 = "b13f7e2710ab79f809b2885b907c753ec8858718" uuid = "f525a15e-a73f-4eef-870f-f901257eae22" -version = "0.0.2" +version = "0.5.0" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" +version = "0.3.23+4" [[deps.OpenSSH_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] @@ -244,48 +317,60 @@ uuid = "9bd350c2-7e96-507f-8002-3f2e150b4e1b" version = "8.9.0+1" [[deps.OpenSSL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e60321e3f2616584ff98f0a4f18d98ae6f89bbb3" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "a12e56c72edee3ce6b96667745e6cbbe5498f200" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.17+0" +version = "1.1.23+0" [[deps.OrderedCollections]] -git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.1" +version = "1.6.3" + +[[deps.PCRE2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" +version = "10.42.0+1" [[deps.Parsers]] -deps = ["Dates"] -git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.3.2" +version = "2.8.1" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +version = "1.10.0" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] -git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" +git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" -version = "1.4.2" +version = "1.4.3" + +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" +git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.3" [[deps.PrettyPrinting]] -git-tree-sha1 = "4be53d093e9e37772cc89e1009e8f6ad10c4681b" +git-tree-sha1 = "142ee93724a9c5d04d78df7006670a93ed1b244e" uuid = "54e16d92-306c-5ea0-a30b-337be88ac337" -version = "0.4.0" +version = "0.4.2" [[deps.PrettyTables]] -deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] -git-tree-sha1 = "dfb54c4e414caa595a1f2ed759b160f5a3ddcba5" +deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] +git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "1.3.1" +version = "2.3.1" [[deps.Printf]] deps = ["Unicode"] @@ -296,7 +381,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Reexport]] @@ -304,8 +389,15 @@ 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.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +version = "0.7.0" [[deps.Sass]] deps = ["libsass_jll"] @@ -313,33 +405,61 @@ git-tree-sha1 = "aa841c3738cec78b5dbccd56dda332710f35f6a5" uuid = "322a6be2-4ae8-5d68-aaf1-3e960788d1d9" version = "0.2.0" +[[deps.Scratch]] +deps = ["Dates"] +git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" +uuid = "6c6a2e73-6563-6170-7368-637461726353" +version = "1.2.1" + +[[deps.SentinelArrays]] +deps = ["Dates", "Random"] +git-tree-sha1 = "363c4e82b66be7b9f7c7c7da7478fdae07de44b9" +uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" +version = "1.4.2" + [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -[[deps.SharedArrays]] -deps = ["Distributed", "Mmap", "Random", "Serialization"] -uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" - [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" +git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.0.1" +version = "1.2.1" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.10.0" + +[[deps.StringManipulation]] +deps = ["PrecompileTools"] +git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" +uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" +version = "0.3.4" + +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "7.2.1+1" [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" +version = "1.0.3" + +[[deps.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "1607ad46cf8d642aa779a1d45af1c8620dbf6915" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.2.0+2024a" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -348,19 +468,41 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.7.0" +version = "1.11.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.0" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[deps.TimeZones]] +deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "96793c9316d6c9f9be4641f2e5b1319a205e6f27" +uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" +version = "1.15.0" + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" + + [deps.TimeZones.weakdeps] + RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" + +[[deps.TranscodingStreams]] +git-tree-sha1 = "5d54d076465da49d6746c647022f3b3674e64156" +uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" +version = "0.10.8" +weakdeps = ["Random", "Test"] + + [deps.TranscodingStreams.extensions] + TestExt = ["Test", "Random"] + [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" @@ -371,10 +513,12 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+1" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.8.0+1" [[deps.libsass_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -385,7 +529,9 @@ version = "3.6.4+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" diff --git a/docs/Project.toml b/docs/Project.toml index c49adf0..2eaab43 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,4 +1,5 @@ [deps] Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8" +DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365" OMOPCDMCohortCreator = "f525a15e-a73f-4eef-870f-f901257eae22" diff --git a/docs/make.jl b/docs/make.jl index 7da8928..d8b4dde 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,17 +1,17 @@ using OMOPCDMCohortCreator using Documenter +using DocumenterVitepress makedocs(; modules = [OMOPCDMCohortCreator], + warnonly = true, + checkdocs=:all, authors = "Jacob Zelko (aka TheCedarPrince) and contributors", - repo = "https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl/blob/{commit}{path}#L{line}", sitename = "OMOPCDMCohortCreator.jl", - format = Documenter.HTML(; - prettyurls = get(ENV, "CI", "false") == "true", - canonical = "https://JuliaHealth.github.io/OMOPCDMCohortCreator.jl", - assets = String[], - edit_link = "dev", - footer = "Created by [Jacob Zelko](https://jacobzelko.com) & [Georgia Tech Research Institute](https://www.gtri.gatech.edu). [License](https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl/blob/main/LICENSE)" + format=DocumenterVitepress.MarkdownVitepress( + repo = "github.com/JuliaHealth/OMOPCDMCohortCreator.jl", # this must be the full URL! + devbranch = "main", + devurl = "dev"; ), pages = [ "Home" => "index.md", @@ -23,10 +23,15 @@ makedocs(; "API" => "api.md", "Contributing" => "contributing.md" ], + draft = false, + source = "src", + build = "build" ) deploydocs(; repo = "github.com/JuliaHealth/OMOPCDMCohortCreator.jl", push_preview = true, devbranch = "main", + target = "build", # this is where Vitepress stores its output + branch = "gh-pages", ) diff --git a/docs/src/.vitepress/config.mts b/docs/src/.vitepress/config.mts new file mode 100644 index 0000000..eff9e4f --- /dev/null +++ b/docs/src/.vitepress/config.mts @@ -0,0 +1,59 @@ +import { defineConfig } from 'vitepress' +import { tabsMarkdownPlugin } from 'vitepress-plugin-tabs' +import mathjax3 from "markdown-it-mathjax3"; +import footnote from "markdown-it-footnote"; +import { transformerMetaWordHighlight } from '@shikijs/transformers'; + +// https://vitepress.dev/reference/site-config +export default defineConfig({ + base: 'REPLACE_ME_DOCUMENTER_VITEPRESS', // TODO: replace this in makedocs! + title: 'REPLACE_ME_DOCUMENTER_VITEPRESS', + description: 'REPLACE_ME_DOCUMENTER_VITEPRESS', + lastUpdated: true, + cleanUrls: true, + outDir: 'REPLACE_ME_DOCUMENTER_VITEPRESS', // This is required for MarkdownVitepress to work correctly... + head: [['link', { rel: 'icon', href: '/DocumenterVitepress.jl/dev/favicon.ico' }]], + + markdown: { + math: true, + config(md) { + md.use(tabsMarkdownPlugin), + md.use(mathjax3), + md.use(footnote) + }, + theme: { + light: "github-light", + dark: "github-dark" + }, + codeTransformers: [ transformerMetaWordHighlight(), ], + + }, + themeConfig: { + outline: 'deep', + // https://vitepress.dev/reference/default-theme-config + logo: 'REPLACE_ME_DOCUMENTER_VITEPRESS', + search: { + provider: 'local', + options: { + detailedView: true + } + }, + nav: [ + { text: 'Home', link: '/' }, + { text: 'Getting Started', link: '/getting_started' }, + { text: 'Markdown', link: '/markdown-examples' }, + { text: 'Code', link: '/code_example' }, + { text: 'API', link: '/api' } + ], + + sidebar: 'REPLACE_ME_DOCUMENTER_VITEPRESS', + editLink: 'REPLACE_ME_DOCUMENTER_VITEPRESS', + socialLinks: [ + { icon: 'github', link: 'REPLACE_ME_DOCUMENTER_VITEPRESS' } + ], + footer: { + message: 'Made with Documenter.jl, VitePress and DocumenterVitepress.jl
', + copyright: `© Copyright ${new Date().getUTCFullYear()}.` + } + } +}) diff --git a/docs/src/.vitepress/theme/index.ts b/docs/src/.vitepress/theme/index.ts new file mode 100644 index 0000000..5ac1c91 --- /dev/null +++ b/docs/src/.vitepress/theme/index.ts @@ -0,0 +1,21 @@ +// .vitepress/theme/index.ts +import { h } from 'vue' +import type { Theme } from 'vitepress' +import DefaultTheme from 'vitepress/theme' +import AsideTrustees from '../../components/AsideTrustees.vue' + +import { enhanceAppWithTabs } from 'vitepress-plugin-tabs/client' +import './style.css' + +export default { + extends: DefaultTheme, + Layout() { + return h(DefaultTheme.Layout, null, { + // 'home-hero-info-after': () => h(HomeTrustees), + 'aside-ads-before': () => h(AsideTrustees), + }) + }, + enhanceApp({ app, router, siteData }) { + enhanceAppWithTabs(app) + } +} satisfies Theme \ No newline at end of file diff --git a/docs/src/.vitepress/theme/style.css b/docs/src/.vitepress/theme/style.css new file mode 100644 index 0000000..af3f2e4 --- /dev/null +++ b/docs/src/.vitepress/theme/style.css @@ -0,0 +1,199 @@ +/* Customize default theme styling by overriding CSS variables: +https://github.com/vuejs/vitepress/blob/main/src/client/theme-default/styles/vars.css + */ + + /* Layouts */ + +/* + :root { + --vp-layout-max-width: 1440px; +} */ + +.VPHero .clip { + white-space: pre; + max-width: 500px; +} + +/* Fonts */ + +@font-face { + font-family: JuliaMono-Regular; + src: url("https://cdn.jsdelivr.net/gh/cormullion/juliamono/webfonts/JuliaMono-Regular.woff2"); +} + + :root { + /* Typography */ + --vp-font-family-base: "Barlow", "Inter var experimental", "Inter var", + -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, + Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", sans-serif; + + /* Code Snippet font */ + --vp-font-family-mono: JuliaMono-Regular, monospace; + +} + +.mono { + /* + Disable contextual alternates (kind of like ligatures but different) in monospace, + which turns `/>` to an up arrow and `|>` (the Julia pipe symbol) to an up arrow as well. + This is pretty bad for Julia folks reading even though copy+paste retains the same text. + */ + font-feature-settings: 'calt' 0; + pre { + font-family: JuliaMono-Light; +}; +code { + font-family: JuliaMono-Light; + }; +} + +/* Colors */ + +:root { + --julia-blue: #4063D8; + --julia-purple: #9558B2; + --julia-red: #CB3C33; + --julia-green: #389826; + + --vp-c-brand: #389826; + --vp-c-brand-light: #3dd027; + --vp-c-brand-lighter: #9499ff; + --vp-c-brand-lightest: #bcc0ff; + --vp-c-brand-dark: #535bf2; + --vp-c-brand-darker: #454ce1; + --vp-c-brand-dimm: #212425; +} + + /* Component: Button */ + +:root { + --vp-button-brand-border: var(--vp-c-brand-light); + --vp-button-brand-text: var(--vp-c-white); + --vp-button-brand-bg: var(--vp-c-brand); + --vp-button-brand-hover-border: var(--vp-c-brand-light); + --vp-button-brand-hover-text: var(--vp-c-white); + --vp-button-brand-hover-bg: var(--vp-c-brand-light); + --vp-button-brand-active-border: var(--vp-c-brand-light); + --vp-button-brand-active-text: var(--vp-c-white); + --vp-button-brand-active-bg: var(--vp-button-brand-bg); +} + +/* Component: Home */ + +:root { + --vp-home-hero-name-color: transparent; + --vp-home-hero-name-background: -webkit-linear-gradient( + 120deg, + #9558B2 30%, + #CB3C33 + ); + + --vp-home-hero-image-background-image: linear-gradient( + -45deg, + #9558B2 30%, + #389826 30%, + #CB3C33 + ); + --vp-home-hero-image-filter: blur(40px); +} + +@media (min-width: 640px) { + :root { + --vp-home-hero-image-filter: blur(56px); + } +} + +@media (min-width: 960px) { + :root { + --vp-home-hero-image-filter: blur(72px); + } +} + +/* Component: Custom Block */ + +:root.dark { + --vp-custom-block-tip-border: var(--vp-c-brand); + --vp-custom-block-tip-text: var(--vp-c-brand-lightest); + --vp-custom-block-tip-bg: var(--vp-c-brand-dimm); + + /* // Tweak the color palette for blacks and dark grays */ + --vp-c-black: hsl(220 20% 9%); + --vp-c-black-pure: hsl(220, 24%, 4%); + --vp-c-black-soft: hsl(220 16% 13%); + --vp-c-black-mute: hsl(220 14% 17%); + --vp-c-gray: hsl(220 8% 56%); + --vp-c-gray-dark-1: hsl(220 10% 39%); + --vp-c-gray-dark-2: hsl(220 12% 28%); + --vp-c-gray-dark-3: hsl(220 12% 23%); + --vp-c-gray-dark-4: hsl(220 14% 17%); + --vp-c-gray-dark-5: hsl(220 16% 13%); + + /* // Backgrounds */ + /* --vp-c-bg: hsl(240, 2%, 11%); */ + --vp-custom-block-info-bg: hsl(220 14% 17%); + /* --vp-c-gutter: hsl(220 20% 9%); + + --vp-c-bg-alt: hsl(220 20% 9%); + --vp-c-bg-soft: hsl(220 14% 17%); + --vp-c-bg-mute: hsl(220 12% 23%); + */ +} + + /* Component: Algolia */ + +.DocSearch { + --docsearch-primary-color: var(--vp-c-brand) !important; +} + +/* Component: MathJax */ + +mjx-container > svg { + display: block; + margin: auto; +} + +mjx-container { + padding: 0.5rem 0; +} + +mjx-container { + display: inline-block; + margin: auto 2px -2px; +} + +mjx-container > svg { + margin: auto; + display: inline-block; +} + +/** + * Colors links + * -------------------------------------------------------------------------- */ + + :root { + --vp-c-brand-1: #CB3C33; + --vp-c-brand-2: #CB3C33; + --vp-c-brand-3: #CB3C33; + --vp-c-sponsor: #ca2971; + --vitest-c-sponsor-hover: #c13071; +} + +.dark { + --vp-c-brand-1: #91dd33; + --vp-c-brand-2: #91dd33; + --vp-c-brand-3: #91dd33; + --vp-c-sponsor: #91dd33; + --vitest-c-sponsor-hover: #e51370; +} + +/** + * Change images from light to dark theme + * -------------------------------------------------------------------------- */ + + :root:not(.dark) .dark-only { + display: none; +} + +:root:is(.dark) .light-only { + display: none; +}