Merge pull request #115 from timbitz/1.5-bugfixes

Updates for julia 1.6

Author: Tim Sterne-Weiler

.gitignore

@@ -3,7 +3,7 @@ os:
   - linux
   - osx
 julia:
-  - 1.5.3
+  - 1.6
 notifications:
   email: false
 after_success:

.travis.yml

@@ -6,11 +6,11 @@ git-tree-sha1 = "4a8f4df432fd8e8a96a142c53f9432b9022a92e6"
 uuid = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 version = "1.1.1"
 
+[[ArgTools]]
+uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+
 [[Artifacts]]
-deps = ["Pkg"]
-git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
-version = "1.3.0"
 
 [[Automa]]
 deps = ["DataStructures", "Printf", "Random", "Test", "TranscodingStreams"]
@@ -33,12 +33,6 @@ git-tree-sha1 = "f610a3a965f187890edb0b1fdef4f30d77852edd"
 uuid = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
 version = "2.0.0"
 
-[[BioCore]]
-deps = ["Automa", "BufferedStreams", "YAML"]
-git-tree-sha1 = "476edbf4ef94594fff430a84ca96f86cb2327a71"
-uuid = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
-version = "2.0.5"
-
 [[BioGenerics]]
 deps = ["TranscodingStreams"]
 git-tree-sha1 = "57deb413ca9f4c8bc7d4c6e98ebe217ff728c737"
@@ -87,10 +81,8 @@ uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
 version = "3.25.0"
 
 [[CompilerSupportLibraries_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "8e695f735fca77e9708e795eda62afdb869cbb70"
+deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "0.3.4+0"
 
 [[DataAPI]]
 git-tree-sha1 = "dfb3b7e89e395be1e25c2ad6d7690dc29cc53b1d"
@@ -117,9 +109,13 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "0fc424e725eaec6ea3e9fa8df773bee18a1ab503"
+git-tree-sha1 = "e64debe8cd174cc52d7dd617ebc5492c6f8b698c"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.24.14"
+version = "0.24.15"
+
+[[Downloads]]
+deps = ["ArgTools", "LibCURL", "NetworkOptions"]
+uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
 [[FASTX]]
 deps = ["Automa", "BioGenerics", "BioSequences", "BioSymbols", "TranscodingStreams"]
@@ -137,9 +133,9 @@ version = "1.0.0"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "4705cc4e212c3c978c60b1b18118ec49b4d731fd"
+git-tree-sha1 = "dd4ab4257c257532003eb9836eea07473fcc732e"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.11.5"
+version = "0.11.6"
 
 [[GenomicFeatures]]
 deps = ["BioGenerics", "DataStructures", "IntervalTrees"]
@@ -165,10 +161,10 @@ uuid = "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d"
 version = "1.0.0"
 
 [[Indexes]]
-deps = ["BGZFStreams", "BioCore", "BufferedStreams", "GenomicFeatures"]
-git-tree-sha1 = "c124510dd96e53f9095dbb484f4a8781cbfa0dcc"
+deps = ["BGZFStreams", "BioGenerics", "GenomicFeatures", "TranscodingStreams"]
+git-tree-sha1 = "275bce824b40fd2e70358e0a652ba1b34172f240"
 uuid = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
-version = "0.1.1"
+version = "0.1.3"
 
 [[IntArrays]]
 deps = ["Mmap", "Random", "Test"]
@@ -191,10 +187,22 @@ git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
 version = "1.2.0"
 
+[[LibCURL]]
+deps = ["LibCURL_jll", "MozillaCACerts_jll"]
+uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+
+[[LibCURL_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
+uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+
 [[LibGit2]]
-deps = ["Printf"]
+deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
+[[LibSSH2_jll]]
+deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
+uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
@@ -215,6 +223,10 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
+[[MbedTLS_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+
 [[Missings]]
 deps = ["DataAPI"]
 git-tree-sha1 = "f8c673ccc215eb50fcadb285f522420e29e69e1c"
@@ -224,6 +236,12 @@ version = "0.4.5"
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
+[[MozillaCACerts_jll]]
+uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+
+[[NetworkOptions]]
+uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+
 [[Nullables]]
 git-tree-sha1 = "8f87854cc8f3685a60689d8edecaa29d2251979b"
 uuid = "4d1e1d77-625e-5b40-9113-a560ec7a8ecd"
@@ -241,13 +259,13 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.4.0"
 
 [[PDMats]]
-deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"]
-git-tree-sha1 = "95a4038d1011dfdbde7cecd2ad0ac411e53ab1bc"
+deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
+git-tree-sha1 = "f82a0e71f222199de8e9eb9a09977bd0767d52a0"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.10.1"
+version = "0.11.0"
 
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[Printf]]
@@ -265,7 +283,7 @@ uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 version = "2.4.1"
 
 [[REPL]]
-deps = ["InteractiveUtils", "Markdown", "Sockets"]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[Random]]
@@ -344,8 +362,16 @@ version = "1.0.0"
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 
+[[TOML]]
+deps = ["Dates"]
+uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+
+[[Tar]]
+deps = ["ArgTools", "SHA"]
+uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+
 [[Test]]
-deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[TextWrap]]
@@ -385,14 +411,14 @@ git-tree-sha1 = "fc98c10e8151054353ded66914f38fbac15fc899"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 version = "0.2.6"
 
-[[YAML]]
-deps = ["Base64", "Dates", "Printf"]
-git-tree-sha1 = "78c02bd295bbd0ca330f95e07ccdfcb69f6cbcd4"
-uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
-version = "0.4.6"
-
 [[Zlib_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "320228915c8debb12cb434c59057290f0834dbf6"
+deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.11+18"
+
+[[nghttp2_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+
+[[p7zip_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"

LICENSE

@@ -1,7 +1,7 @@
 name = "Whippet"
 uuid = "0af2a87d-76f3-44e3-af6e-8f91dcdf7847"
 authors = ["Tim Sterne-Weiler <tsternew@gmail.com>"]
-version = "1.5.1"
+version = "1.6"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
@@ -28,7 +28,7 @@ WaveletMatrices = "c0580c95-5bac-53b2-8f35-dbbbc8487a1f"
 XAM = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 
 [compat]
-julia = ">= 1.5"
+julia = ">= 1.6"
 
 [extras]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

Manifest.toml

@@ -32,7 +32,7 @@ Paper: https://doi.org/10.1016/j.molcel.2018.08.018
 ### 1) Install
 
 
-Whippet v1.5 works on the current version of Julia (**v1.5.3**) which is available here (https://julialang.org).  If you are new to julia, there is a [helpful guide on how to get it up and running here](https://en.wikibooks.org/wiki/Introducing_Julia/Getting_started)
+Whippet v1.6 works on the current version of Julia (**v1.6**) which is available here (https://julialang.org).  If you are new to julia, there is a [helpful guide on how to get it up and running here](https://en.wikibooks.org/wiki/Introducing_Julia/Getting_started)
 
 
 Download and install dependencies

Project.toml

@@ -1 +1 @@
-v1.5.1
+v1.6