From 8821f864c4cefe7e7cd5f5d9d78455139ffa90a0 Mon Sep 17 00:00:00 2001 From: Marco Molari Date: Thu, 24 Aug 2023 09:28:11 +0200 Subject: [PATCH 1/3] feat: update TreeTools --- .gitignore | 4 +- Manifest.toml | 134 ++++++++++++++++++++++++++------------------------ 2 files changed, 72 insertions(+), 66 deletions(-) diff --git a/.gitignore b/.gitignore index 9c6645f5..15db53f3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,3 @@ -\.cache .dep .local data @@ -14,7 +13,7 @@ pangraph.tar.gz bin tutorial playgrounds -.vscode +/.vscode script/synthetic_data script/panx_data script/.snakemake @@ -25,6 +24,7 @@ script/panx_results script/local_scripts __pycache__ tests/data +/debug deps/minimap2/build deps/minimap2/products diff --git a/Manifest.toml b/Manifest.toml index 23770584..1a0cc8e3 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -25,36 +25,36 @@ version = "0.5.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" +git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.6" +version = "1.16.0" [[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" +deps = ["InverseFunctions", "LinearAlgebra", "Test"] +git-tree-sha1 = "2fba81a302a7be671aefe194f0525ef231104e7f" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.4" +version = "0.1.8" [[deps.Compat]] deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "3ca828fe1b75fa84b021a7860bd039eaea84d2f2" +git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.3.0" +version = "4.9.0" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" [[deps.DataAPI]] -git-tree-sha1 = "46d2680e618f8abd007bce0c3026cb0c4a8f2032" +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.12.0" +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.Dates]] deps = ["Printf"] @@ -78,9 +78,9 @@ version = "0.25.76" [[deps.DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "c36550cb29cbe373e95b3f40486b9a4148f89ffd" +git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.2" +version = "0.9.3" [[deps.Documenter]] deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] @@ -100,15 +100,15 @@ version = "0.6.8" [[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.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "802bfc139833d2ba893dd9e62ba1767c88d708ae" +git-tree-sha1 = "7072f1e3e5a8be51d525d64f63d3ec1287ff2790" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.5" +version = "0.13.11" [[deps.GZip]] deps = ["Libdl"] @@ -117,16 +117,16 @@ uuid = "92fee26a-97fe-5a0c-ad85-20a5f3185b63" version = "0.5.1" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] -git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.11" +version = "0.3.23" [[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.InteractiveUtils]] deps = ["Markdown"] @@ -134,14 +134,14 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" +git-tree-sha1 = "68772f49f54b479fa88ace904f6127f0a3bb2e46" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" +version = "0.1.12" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.JLD2]] deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] @@ -150,10 +150,10 @@ uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" version = "0.4.25" [[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"] @@ -190,18 +190,18 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "94d9c52ca447e23eac0c0f074effbcd38830deb5" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.18" +version = "0.3.26" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[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.Markdown]] deps = ["Base64"] @@ -213,9 +213,9 @@ uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -225,9 +225,9 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.1" +version = "1.0.2" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -253,9 +253,9 @@ version = "1.6.0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" +git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.16" +version = "0.11.17" [[deps.PackageCompiler]] deps = ["Artifacts", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs"] @@ -264,20 +264,26 @@ uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" version = "2.1.0" [[deps.Parsers]] -deps = ["Dates"] -git-tree-sha1 = "6c01a9b494f6d2a9fc180a08b182fcb06f0958a0" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.4.2" +version = "2.7.2" [[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.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 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.0" [[deps.Printf]] deps = ["Unicode"] @@ -291,9 +297,9 @@ version = "1.7.2" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734" +git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.6.0" +version = "2.8.2" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -328,24 +334,24 @@ version = "1.3.0" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.0" +version = "0.7.1" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" +git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.3.0+0" +version = "0.4.0+0" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" +git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.1.1" +version = "1.2.0" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -355,9 +361,9 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" +git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.0.1" +version = "1.1.1" [[deps.SparseArrays]] deps = ["LinearAlgebra", "Random"] @@ -365,9 +371,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.7" +version = "2.3.1" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -375,9 +381,9 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" +git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.5.0" +version = "1.6.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -387,9 +393,9 @@ version = "0.33.21" [[deps.StatsFuns]] deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "5783b877201a82fc0014cbf381e7e6eb130473a4" +git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.0.1" +version = "1.3.0" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -409,15 +415,15 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "8a75929dcd3c38611db2f8d08546decb514fcadf" +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.9" +version = "0.9.13" [[deps.TreeTools]] deps = ["Random"] -git-tree-sha1 = "f3ebeb47ecddbc6a0810afe77c89469cea7c6e5b" +git-tree-sha1 = "9b93f8e4c93dcefee01e086de0160e9a15b9bd2b" uuid = "62f0eae3-8c0e-4032-a621-7756092209e5" -version = "0.6.2" +version = "0.6.5" [[deps.UUIDs]] deps = ["Random", "SHA"] From 4a4d2a43b1803c6da6e54cc7a25a9de5a132e8d5 Mon Sep 17 00:00:00 2001 From: Marco Molari Date: Thu, 24 Aug 2023 10:02:33 +0200 Subject: [PATCH 2/3] chore: updated version and fixed treetools --- CHANGELOG.md | 4 ++++ Project.toml | 4 ++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 968beec7..7b77ac4f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,9 @@ # PanGraph Changelog +## v0.7.2 + +- minor fix in tree midpoint rooting during panX export, see [#59](https://github.com/neherlab/pangraph/issues/59). + ## v0.7.1 - minor fix for multi-threaded marginalize, see [#58](https://github.com/neherlab/pangraph/pull/58). diff --git a/Project.toml b/Project.toml index 8e4f73e2..b8b0c96a 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "PanGraph" uuid = "0f9f61ca-f32c-45e1-b3bc-00138f4f8814" authors = ["Nicholas Noll "] -version = "0.7.1" +version = "0.7.2" [deps] Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" @@ -24,4 +24,4 @@ TreeTools = "62f0eae3-8c0e-4032-a621-7756092209e5" minimap2_jll = "d341526d-637d-5003-8fc4-9c6812cd2b55" [compat] -TreeTools = ">= 0.6.2" +TreeTools = "0.6.5" \ No newline at end of file From 49da837a343fefd19a371d014a4d2d39d4049e10 Mon Sep 17 00:00:00 2001 From: Marco Molari Date: Thu, 24 Aug 2023 10:04:38 +0200 Subject: [PATCH 3/3] chore: add empty line in project.toml --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index b8b0c96a..ec577900 100644 --- a/Project.toml +++ b/Project.toml @@ -24,4 +24,4 @@ TreeTools = "62f0eae3-8c0e-4032-a621-7756092209e5" minimap2_jll = "d341526d-637d-5003-8fc4-9c6812cd2b55" [compat] -TreeTools = "0.6.5" \ No newline at end of file +TreeTools = "0.6.5"