From 49f71fa457480fc60cf005f753fdcb81bddda56e Mon Sep 17 00:00:00 2001 From: David Little Date: Tue, 12 Jul 2022 11:14:16 -0400 Subject: [PATCH] Use Released Intervals.jl (#9) * Delete manifest files * Depends on released Intervals.jl * Fix Julia 1.6 compatibility Co-authored-by: Phillip Alday Co-authored-by: Phillip Alday --- .gitignore | 1 + Manifest.toml | 307 -------------------------------------- Project.toml | 2 +- README.md | 9 +- docs/Manifest.toml | 240 ----------------------------- src/DataFrameIntervals.jl | 4 +- 6 files changed, 5 insertions(+), 558 deletions(-) create mode 100644 .gitignore delete mode 100644 Manifest.toml delete mode 100644 docs/Manifest.toml diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..ba39cc5 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +Manifest.toml diff --git a/Manifest.toml b/Manifest.toml deleted file mode 100644 index 8c60f2c..0000000 --- a/Manifest.toml +++ /dev/null @@ -1,307 +0,0 @@ -# This file is machine-generated - 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-[[Statistics]] -deps = ["LinearAlgebra", "SparseArrays"] -uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" - -[[TOML]] -deps = ["Dates"] -uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" - -[[TableTraits]] -deps = ["IteratorInterfaceExtensions"] -git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" -uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" -version = "1.0.1" - -[[Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" -uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.7.0" - -[[Tar]] -deps = ["ArgTools", "SHA"] -uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" - -[[Test]] -deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] -uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[[TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Serialization", "Unicode"] -git-tree-sha1 = "0a4d8838dc28b4bcfaa3a20efb8d63975ad6781d" -uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.8.0" - -[[UUIDs]] -deps = ["Random", "SHA"] -uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" - -[[Unicode]] -uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" - -[[Zlib_jll]] -deps = ["Libdl"] -uuid = "83775a58-1f1d-513f-b197-d71354ab007a" - -[[libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" - -[[nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" - -[[p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/Project.toml b/Project.toml index 20b9bf4..165b534 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "DataFrameIntervals" uuid = "33b79e07-adbe-4034-b8be-6bacde625d75" authors = ["Beacon Biosignals, Inc."] -version = "0.0.2" +version = "0.1.0" [deps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" diff --git a/README.md b/README.md index 418ab4e..3824b95 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![Docs: Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://beacon-biosignals.github.io/DataFrameIntervals.jl/dev) DataFrameIntervals provides two functions that are handy for computing joins over intervals -of time: `interval_join` and `groupby_interval_join`, and a helper function called `quantile_windows`. +of time: `interval_join` and `groupby_interval_join`, and a helper function called `quantile_windows`. See their doc strings for details. Rows match in this join if their time spans overlap. The time spans can be represented as @@ -15,13 +15,6 @@ Rows match in this join if their time spans overlap. The time spans can be repre - [`Interval`](https://juliapackages.com/p/intervals) objects. - `NamedTuples` with a `start` and `stop` field. -Currently this requires an unreleased version of `Intervals.jl` (which should be version 1.8 when released). If you don't use the manifest, make sure to add the following to your project before adding `DataFrameIntervals`. - -``` -julia> ]add https://github.com/invenia/Intervals.jl#rf/intervalset-type -``` - - ## Example ```julia diff --git a/docs/Manifest.toml b/docs/Manifest.toml deleted file mode 100644 index 2bb238c..0000000 --- a/docs/Manifest.toml +++ /dev/null @@ -1,240 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.7.3" -manifest_format = "2.0" - -[[deps.ANSIColoredPrinters]] -git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" -uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" -version = "0.0.1" - -[[deps.ArgTools]] -uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" - -[[deps.Artifacts]] -uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" - -[[deps.Base64]] -uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" - -[[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" -uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.45.0" - -[[deps.CompilerSupportLibraries_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" - -[[deps.Dates]] -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 = "b19534d1895d702889b219c382a6e18010797f0b" -uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.6" - -[[deps.Documenter]] -deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "f7809f532671564e48cd81627ddcfb1ba670f87d" -uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.19" - -[[deps.Downloads]] -deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] -uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" - -[[deps.ExprTools]] -git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" -uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.8" - -[[deps.FileWatching]] -uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" - -[[deps.IOCapture]] -deps = ["Logging", "Random"] -git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" -uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.2" - -[[deps.InlineStrings]] -deps = ["Parsers"] -git-tree-sha1 = "a8671d5c9670a62cb36b7d44c376bdb09181aa26" -uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.1.3" - -[[deps.InteractiveUtils]] -deps = ["Markdown"] -uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" - -[[deps.Intervals]] -deps = ["Dates", "Printf", "RecipesBase", "Serialization", "TimeZones"] -git-tree-sha1 = "c6a1efca1968f7f6a572510756c3df6741c6b9f0" -repo-rev = "rf/intervalset-type" -repo-url = "https://github.com/invenia/Intervals.jl.git" -uuid = "d8418881-c3e1-53bb-8760-2df7ec849ed5" -version = "1.8.0" - -[[deps.JSON]] -deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" -uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.3" - 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-[[deps.Mmap]] -uuid = "a63ad114-7e13-5084-954f-fe012c677804" - -[[deps.Mocking]] -deps = ["Compat", "ExprTools"] -git-tree-sha1 = "29714d0a7a8083bba8427a4fbfb00a540c681ce7" -uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" -version = "0.7.3" - -[[deps.MozillaCACerts_jll]] -uuid = "14a3606d-f60d-562e-9121-12d972cd8159" - -[[deps.NetworkOptions]] -uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" - -[[deps.OpenBLAS_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] -uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" - -[[deps.Parsers]] -deps = ["Dates"] -git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" -uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.3.2" - -[[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] -uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" - -[[deps.Printf]] -deps = ["Unicode"] -uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" - -[[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] -uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" - -[[deps.Random]] -deps = ["SHA", "Serialization"] -uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" - -[[deps.RecipesBase]] -git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" -uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.2.1" - -[[deps.SHA]] -uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" - -[[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.SparseArrays]] -deps = ["LinearAlgebra", "Random"] -uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" - -[[deps.Statistics]] -deps = ["LinearAlgebra", "SparseArrays"] -uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" - -[[deps.TOML]] -deps = ["Dates"] -uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" - -[[deps.Tar]] -deps = ["ArgTools", "SHA"] -uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" - -[[deps.Test]] -deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] -uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Serialization", "Unicode"] -git-tree-sha1 = "0a4d8838dc28b4bcfaa3a20efb8d63975ad6781d" -uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.8.0" - -[[deps.UUIDs]] -deps = ["Random", "SHA"] -uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" - -[[deps.Unicode]] -uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" - -[[deps.Zlib_jll]] -deps = ["Libdl"] -uuid = "83775a58-1f1d-513f-b197-d71354ab007a" - -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" - -[[deps.nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" - -[[deps.p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/src/DataFrameIntervals.jl b/src/DataFrameIntervals.jl index d7fa091..2613258 100644 --- a/src/DataFrameIntervals.jl +++ b/src/DataFrameIntervals.jl @@ -119,7 +119,7 @@ right.on))`). function interval_join(left, right; makeunique=false, kwds...) left = DataFrame(left; copycols=false) right = DataFrame(right; copycols=false) - (; left_on, right_on, joined_on) = setup_column_names!(left, right; kwds...) + (left_on, right_on, joined_on) = setup_column_names!(left, right; kwds...) regions = find_intersections_(view(right, :, right_on), view(left, :, left_on)) # perform the join @@ -240,7 +240,7 @@ function groupby_interval_join(left, right, groups; on, makeunique=false, kwds.. # setup column names left = DataFrame(left; copycols=false) right = DataFrame(right; copycols=false) - (; left_on, right_on, joined_on) = setup_column_names!(left, right; on, kwds...) + (left_on, right_on, joined_on) = setup_column_names!(left, right; on, kwds...) # compute interval intersections left_index = gensym(:__left_index__)