Merge branch 'release/v2.0.0'

.travis.yml

@@ -4,18 +4,19 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
   - nightly
 notifications:
   email: false
 git:
   depth: 99999999
 
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-#matrix:
-#  allow_failures:
-#  - julia: nightly
+# uncomment the following lines to allow failures on nightly julia
+# (tests will run but not make your overall status red)
+matrix:
+ allow_failures:
+ - julia: nightly
 
 ## uncomment and modify the following lines to manually install system packages
 #addons:

Manifest.toml

@@ -0,0 +1,240 @@
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[Bedgraph]]
+deps = ["Test"]
+git-tree-sha1 = "815a4d7dad0145bb4560d77840d77b33e07861fe"
+uuid = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
+version = "1.0.3"
+
+[[BinaryProvider]]
+deps = ["Libdl", "Pkg", "SHA", "Test"]
+git-tree-sha1 = "055eb2690182ebc31087859c3dd8598371d3ef9e"
+uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
+version = "0.5.3"
+
+[[CategoricalArrays]]
+deps = ["Compat", "Future", "Missings", "Printf", "Reexport", "Requires"]
+git-tree-sha1 = "94d16e77dfacc59f6d6c1361866906dbb65b6f6b"
+uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
+version = "0.5.2"
+
+[[CodecZlib]]
+deps = ["BinaryProvider", "Libdl", "Test", "TranscodingStreams"]
+git-tree-sha1 = "e3df104c84dfc108f0ca203fd7f5bbdc98641ae9"
+uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
+version = "0.5.1"
+
+[[Compat]]
+deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
+git-tree-sha1 = "ec61a16eed883ad0cfa002d7489b3ce6d039bb9a"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "1.4.0"
+
+[[DataFrames]]
+deps = ["CategoricalArrays", "CodecZlib", "Compat", "DataStreams", "Dates", "InteractiveUtils", "IteratorInterfaceExtensions", "LinearAlgebra", "Missings", "Printf", "Random", "Reexport", "SortingAlgorithms", "Statistics", "StatsBase", "TableTraits", "Tables", "Test", "TranscodingStreams", "Unicode", "WeakRefStrings"]
+git-tree-sha1 = "7e032a76f3455e38660ac456791951ac2d0b1e70"
+uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+version = "0.16.0"
+
+[[DataStreams]]
+deps = ["Dates", "Missings", "Test", "WeakRefStrings"]
+git-tree-sha1 = "69c72a1beb4fc79490c361635664e13c8e4a9548"
+uuid = "9a8bc11e-79be-5b39-94d7-1ccc349a1a85"
+version = "0.4.1"
+
+[[DataStructures]]
+deps = ["InteractiveUtils", "OrderedCollections", "Random", "Serialization", "Test"]
+git-tree-sha1 = "ca971f03e146cf144a9e2f2ce59674f5bf0e8038"
+uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+version = "0.15.0"
+
+[[DataValues]]
+deps = ["Dates", "InteractiveUtils", "LinearAlgebra", "Random", "Test"]
+git-tree-sha1 = "4fedccda7e5111354c7dcc832c7da83ff7258765"
+uuid = "e7dc6d0d-1eca-5fa6-8ad6-5aecde8b7ea5"
+version = "0.4.5"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[DelimitedFiles]]
+deps = ["Mmap"]
+uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+
+[[Distributed]]
+deps = ["LinearAlgebra", "Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[FileIO]]
+deps = ["Pkg", "Random", "Test"]
+git-tree-sha1 = "1a114d08094e7267ba8d4d684f930d5a722184de"
+uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+version = "1.0.4"
+
+[[Future]]
+deps = ["Random"]
+uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
+
+[[InteractiveUtils]]
+deps = ["LinearAlgebra", "Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[IterableTables]]
+deps = ["DataValues", "IteratorInterfaceExtensions", "Requires", "TableTraits", "TableTraitsUtils", "Test"]
+git-tree-sha1 = "0eec91e8185899f3926f56db515559bfe95b9db7"
+uuid = "1c8ee90f-4401-5389-894e-7a04a3dc0f4d"
+version = "0.10.0"
+
+[[IteratorInterfaceExtensions]]
+deps = ["Test"]
+git-tree-sha1 = "5484e5ede2a4137b9643f4d646e8e7b87b794415"
+uuid = "82899510-4779-5014-852e-03e436cf321d"
+version = "0.1.1"
+
+[[JSON]]
+deps = ["Dates", "Distributed", "Mmap", "Sockets", "Test", "Unicode"]
+git-tree-sha1 = "1f7a25b53ec67f5e9422f1f551ee216503f4a0fa"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.20.0"
+
+[[LibGit2]]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Missings]]
+deps = ["Dates", "InteractiveUtils", "SparseArrays", "Test"]
+git-tree-sha1 = "adc26d2ee85a49c413464110d922cf21efc9d233"
+uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
+version = "0.3.1"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[OrderedCollections]]
+deps = ["Random", "Serialization", "Test"]
+git-tree-sha1 = "85619a3f3e17bb4761fe1b1fd47f0e979f964d5b"
+uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+version = "1.0.2"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[Reexport]]
+deps = ["Pkg"]
+git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
+uuid = "189a3867-3050-52da-a836-e630ba90ab69"
+version = "0.2.0"
+
+[[Requires]]
+deps = ["Test"]
+git-tree-sha1 = "f6fbf4ba64d295e146e49e021207993b6b48c7d1"
+uuid = "ae029012-a4dd-5104-9daa-d747884805df"
+version = "0.5.2"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[SortingAlgorithms]]
+deps = ["DataStructures", "Random", "Test"]
+git-tree-sha1 = "03f5898c9959f8115e30bc7226ada7d0df554ddd"
+uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
+version = "0.3.1"
+
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[StatsBase]]
+deps = ["DataStructures", "DelimitedFiles", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "Test"]
+git-tree-sha1 = "7b596062316c7d846b67bf625d5963a832528598"
+uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+version = "0.27.0"
+
+[[TableShowUtils]]
+deps = ["DataValues", "Dates", "JSON", "Markdown", "Test"]
+git-tree-sha1 = "6ffc18504eab3f900af2d23adc0e7bddf94bd29b"
+uuid = "5e66a065-1f0a-5976-b372-e0b8c017ca10"
+version = "0.2.1"
+
+[[TableTraits]]
+deps = ["IteratorInterfaceExtensions", "Test"]
+git-tree-sha1 = "eba4b1d0a82bdd773307d652c6e5f8c82104c676"
+uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
+version = "0.4.1"
+
+[[TableTraitsUtils]]
+deps = ["DataValues", "IteratorInterfaceExtensions", "Missings", "TableTraits", "Test"]
+git-tree-sha1 = "a355f1882d64881a11f853e64dcc353975c4df6e"
+uuid = "382cd787-c1b6-5bf2-a167-d5b971a19bda"
+version = "0.3.1"
+
+[[Tables]]
+deps = ["IteratorInterfaceExtensions", "Requires", "TableTraits", "Test"]
+git-tree-sha1 = "89f8fde6394579580fb75088e45ad95551199c7c"
+uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+version = "0.1.14"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[TranscodingStreams]]
+deps = ["Pkg", "Random", "Test"]
+git-tree-sha1 = "a34a2d588e2d2825602bf14a24216d5c8b0921ec"
+uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
+version = "0.8.1"
+
+[[UUIDs]]
+deps = ["Random"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[WeakRefStrings]]
+deps = ["Missings", "Random", "Test"]
+git-tree-sha1 = "1087e8be380f2c8b96434b02bb1150fc1c511135"
+uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
+version = "0.5.3"

Project.toml

@@ -0,0 +1,21 @@
+name = "BedgraphFiles"
+uuid = "d731aa1e-17bd-11e9-0e1c-5f48a895e48a"
+authors = ["Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
+version = "2.0.0"
+
+[deps]
+Bedgraph = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DataValues = "e7dc6d0d-1eca-5fa6-8ad6-5aecde8b7ea5"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+IterableTables = "1c8ee90f-4401-5389-894e-7a04a3dc0f4d"
+IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d"
+TableShowUtils = "5e66a065-1f0a-5976-b372-e0b8c017ca10"
+TableTraits = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
+TableTraitsUtils = "382cd787-c1b6-5bf2-a167-d5b971a19bda"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

README.md

@@ -3,7 +3,7 @@
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![Build Status](https://travis-ci.org/CiaranOMara/BedgraphFiles.jl.svg?branch=master)](https://travis-ci.org/CiaranOMara/BedgraphFiles.jl)
 [![Build status](https://ci.appveyor.com/api/projects/status/jny2ep4u3cmly8pj/branch/master?svg=true)](https://ci.appveyor.com/project/CiaranOMara/Bedgraphfiles-jl/branch/master)
-[![BedgraphFiles](http://pkg.julialang.org/badges/BedgraphFiles_0.6.svg)](http://pkg.julialang.org/?pkg=BedgraphFiles)
+[![BedgraphFiles](http://pkg.julialang.org/badges/BedgraphFiles_0.7.svg)](http://pkg.julialang.org/?pkg=BedgraphFiles)
 [![codecov.io](http://codecov.io/github/CiaranOMara/BedgraphFiles.jl/coverage.svg?branch=master)](http://codecov.io/github/CiaranOMara/BedgraphFiles.jl?branch=master)
 [![Coverage Status](https://coveralls.io/repos/github/CiaranOMara/BedgraphFiles.jl/badge.svg?branch=master)](https://coveralls.io/github/CiaranOMara/BedgraphFiles.jl?branch=master)
 
@@ -15,8 +15,12 @@ under the [FileIO.jl](https://github.com/JuliaIO/FileIO.jl) package.
 This package is largely -- if not completely -- inspired by the work of [David Anthoff](https://github.com/davidanthoff).
 
 ## Installation
-
-Use Pkg.add("BedgraphFiles") in Julia to install BedgraphFiles and its dependencies.
+Install BedgraphFiles from the Julia REPL:
+```julia
+using Pkg
+add("BedgraphFiles")
+#Pkg.add("BedgraphFiles") for julia prior to v 0.7
+```
 
 ## Usage
 
@@ -30,7 +34,7 @@ using FileIO, BedgraphFiles, DataFrames
 df = DataFrame(load("data.bedgraph"))
 ````
 
-The call to ``load`` returns a ``struct`` that is an [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl), so it can be passed to any function that can handle iterable tables, i.e. all the sinks in [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl). Here are some examples of materializing a Bedgraph file into data structures that are not a ``DataFrame``:
+The call to ``load`` returns a ``struct`` that is an [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl), so it can be passed to any function that can handle iterable tables, i.e. all the sinks in [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl). Here are some examples of materialising a Bedgraph file into data structures that are not a ``DataFrame``:
 
 ````julia
 using FileIO, BedgraphFiles, DataTables, IndexedTables, Gadfly

REQUIRE

@@ -1,6 +1 @@
-julia 0.6
-TableTraits 0.0.1
-IterableTables 0.5.0
-FileIO 0.6.0
-DataFrames 0.9.0
-Bedgraph 0.3.0
+julia 0.7

appveyor.yml

@@ -1,16 +1,18 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.6/julia-0.6-latest-win32.exe"
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
-
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-#matrix:
-#  allow_failures:
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+  - julia_version: 0.7
+  - julia_version: 1
+  - julia_version: nightly
+
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
+
+# Uncomment the following lines to allow failures on nightly julia
+# (tests will run but not make your overall status red)
+matrix:
+  allow_failures:
+  - julia_version: nightly
 
 branches:
   only:
@@ -24,24 +26,18 @@ notifications:
     on_build_status_changed: false
 
 install:
-  - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
-# If there's a newer build queued for the same PR, cancel this one
-  - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
-        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
-        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
-        throw "There are newer queued builds for this pull request, failing early." }
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $env:JULIA_URL,
-        "C:\projects\julia-binary.exe")
-# Run installer silently, output to C:\projects\julia
-  - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
 
 build_script:
-# Need to convert from shallow to complete for Pkg.clone to work
-  - IF EXIST .git\shallow (git fetch --unshallow)
-  - C:\projects\julia\bin\julia -e "versioninfo();
-      Pkg.clone(pwd(), \"BedgraphFiles\"); Pkg.build(\"BedgraphFiles\")"
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
 
 test_script:
-  - C:\projects\julia\bin\julia -e "Pkg.test(\"BedgraphFiles\")"
+  - echo "%JL_TEST_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"
+
+# # Uncomment to support code coverage upload. Should only be enabled for packages
+# # which would have coverage gaps without running on Windows
+# on_success:
+#   - echo "%JL_CODECOV_SCRIPT%"
+#   - C:\julia\bin\julia -e "%JL_CODECOV_SCRIPT%"