Merge pull request #60 from neherlab/debug/export

fixes issue #59

Author: mmolari

.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

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).

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"]
@@ -117,31 +117,31 @@ 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"]
 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"
@@ -355,29 +361,29 @@ 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"]
 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"]
 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"]

Project.toml

@@ -1,7 +1,7 @@
 name = "PanGraph"
 uuid = "0f9f61ca-f32c-45e1-b3bc-00138f4f8814"
 authors = ["Nicholas Noll <[email protected]>"]
-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"