Merge branch 'master' of github.com:BioJulia/BioCore.jl

BioJulia · Aug 11, 2018 · 9762d4d · 9762d4d
2 parents 8265abe + 41b2c7b
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diff --git a/.appveyor.yml b/.appveyor.yml
@@ -1,6 +1,11 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
+  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.7/julia-0.7-latest-win64.exe"
+  - Julia_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+
+matrix:
+    allow_failures:
+    - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
 
 branches:
   only:

diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,5 @@
 .DS_Store
 docs/build/
 docs/site/
+
+BioFmtSpecimens
diff --git a/.travis.yml b/.travis.yml
@@ -3,14 +3,15 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
   - nightly
 matrix:
   allow_failures:
     - julia: nightly
 notifications:
   email: false
 after_success:
-  - julia -e 'cd(Pkg.dir("BioCore")); Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())'
-  - julia -e 'cd(joinpath(Pkg.dir("BioCore"), "docs/src")); mkdir("assets"); cd("assets"); run(pipeline(`curl https://codeload.github.com/BioJulia/assets/tar.gz/master`, `tar -xz --strip=2 assets-master/doc_assets`))'
-  - julia -e 'cd(Pkg.dir("BioCore")); Pkg.add("Documenter"); include(joinpath("docs", "make.jl"))'
+  - julia -e 'using Pkg; Pkg.add("Documenter"); Pkg.add("Coverage")'
+  - julia -e 'using Coverage; import BioCore; cd(dirname(dirname(pathof(BioCore)))); Codecov.submit(process_folder())'
+  - julia -e 'import BioCore; cd(dirname(dirname(pathof(BioCore)))); include(joinpath("docs", "make.jl"))'
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -53,7 +53,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Basic project setup.
 
 [Unreleased]: https://github.com/BioJulia/BioCore.jl/compare/v2.0.0...HEAD
-[1.4.0]: https://github.com/BioJulia/BioCore.jl/compare/v1.4.0...v2.0.0
+[2.0.0]: https://github.com/BioJulia/BioCore.jl/compare/v1.4.0...v2.0.0
 [1.4.0]: https://github.com/BioJulia/BioCore.jl/compare/v1.2.1...v1.4.0
 [1.3.0]: https://github.com/BioJulia/BioCore.jl/compare/v1.2.1...v1.3.0
 [1.2.1]: https://github.com/BioJulia/BioCore.jl/compare/v1.2.0...v1.2.1

diff --git a/README.md b/README.md
@@ -1,8 +1,11 @@
 # BioCore.jl
 
-| **Release**                                                     | **Documentation**                                                               | **Maintainers**                             |
-|:---------------------------------------------------------------:|:-------------------------------------------------------------------------------:|:-------------------------------------------:|
-| [![](https://img.shields.io/github/release/BioJulia/BioCore.jl.svg)](https://github.com/BioJulia/BioCore.jl/releases/latest) [![](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/BioCore.jl/blob/master/LICENSE) | [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/BioCore.jl/stable) [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://biojulia.github.io/BioCore.jl/latest) | ![](https://img.shields.io/badge/BioJulia%20Maintainer-Ward9250-orange.svg) |
+[![](https://img.shields.io/github/release/BioJulia/BioCore.jl.svg?style=flat-square)](https://github.com/BioJulia/BioCore.jl/releases/latest) 
+[![](https://img.shields.io/badge/license-MIT-green.svg?style=flat-square)](https://github.com/BioJulia/BioCore.jl/blob/master/LICENSE) 
+[![](https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square)](https://biojulia.github.io/BioCore.jl/stable) 
+[![](https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square)](https://biojulia.github.io/BioCore.jl/latest)
+![](https://img.shields.io/badge/lifecycle-stable-green.svg?style=flat-square)
+[![](https://img.shields.io/badge/discord-chat-blue.svg?style=flat-square&logo=discord&colorB=%237289DA)](https://discord.gg/z73YNFz)
 
 
 ## Description
@@ -32,21 +35,59 @@ the master branch to try new features before release.
 
 ## Testing
 
-BioCore.jl is tested against Julia `0.6` and current `0.7-dev` on Linux, OS X, and Windows.
+BioCore.jl is tested against Julia `0.7` and `1.0.x` on Linux, OS X, and Windows.
 
-| **PackageEvaluator**                                            | **Latest Build Status**                                                                                |
-|:---------------------------------------------------------------:|:------------------------------------------------------------------------------------------------------:|
-| [![](https://pkg.julialang.org/badges/BioCore_0.6.svg)](https://pkg.julialang.org/detail/BioCore) [![](https://pkg.julialang.org/badges/BioCore_0.7.svg)](https://pkg.julialang.org/detail/BioCore) | [![](https://img.shields.io/travis/BioJulia/BioCore.jl/master.svg?label=Linux+/+macOS)](https://travis-ci.org/BioJulia/BioCore.jl) [![Build status](https://ci.appveyor.com/api/projects/status/xl19qeob3gsgm8j7?svg=true)](https://ci.appveyor.com/project/Ward9250/biocore-jl) [![](https://codecov.io/gh/BioJulia/BioCore.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/BioCore.jl) |
+| **PackageEvaluator** | **Latest Build Status** |
+|:--------------------:|:-----------------------:|
+| [![](https://pkg.julialang.org/badges/BioCore_0.7.svg)](https://pkg.julialang.org/detail/BioCore) [![](https://pkg.julialang.org/badges/BioCore_1.0.svg)](https://pkg.julialang.org/detail/BioCore)  | [![](https://img.shields.io/travis/BioJulia/BioCore.jl/master.svg?label=Linux+/+macOS)](https://travis-ci.org/BioJulia/BioCore.jl) [![Build status](https://ci.appveyor.com/api/projects/status/xl19qeob3gsgm8j7?svg=true)](https://ci.appveyor.com/project/Ward9250/biocore-jl) [![](https://codecov.io/gh/BioJulia/BioCore.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/BioCore.jl) |
 
 
-## Contributing and Questions
+## Contributing
 
-We appreciate contributions from users including reporting bugs, fixing issues,
-improving performance and adding new features.
-Please go to the [contributing section of the documentation](biojulia.net/Contributing/latest)
-for more information.
+We appreciate contributions from users including reporting bugs, fixing
+issues, improving performance and adding new features.
+
+Take a look at the [CONTRIBUTING](CONTRIBUTING.md) file provided with
+every BioJulia package package for detailed contributor and maintainer
+guidelines.
+
+
+### Financial contributions
+
+We also welcome financial contributions in full transparency on our
+[open collective](https://opencollective.com/biojulia).
+Anyone can file an expense. If the expense makes sense for the development
+of the community, it will be "merged" in the ledger of our open collective by
+the core contributors and the person who filed the expense will be reimbursed.
+
+
+## Backers & Sponsors
+
+Thank you to all our backers and sponsors!
+
+Love our work and community? [Become a backer](https://opencollective.com/biojulia#backer).
+
+[![backers](https://opencollective.com/biojulia/backers.svg?width=890)](https://opencollective.com/biojulia#backers)
+
+Does your company use BioJulia? Help keep BioJulia feature rich and healthy by
+[sponsoring the project](https://opencollective.com/biojulia#sponsor)
+Your logo will show up here with a link to your website.
+
+[![](https://opencollective.com/biojulia/sponsor/0/avatar.svg)](https://opencollective.com/biojulia/sponsor/0/website)
+[![](https://opencollective.com/biojulia/sponsor/1/avatar.svg)](https://opencollective.com/biojulia/sponsor/1/website)
+[![](https://opencollective.com/biojulia/sponsor/2/avatar.svg)](https://opencollective.com/biojulia/sponsor/2/website)
+[![](https://opencollective.com/biojulia/sponsor/3/avatar.svg)](https://opencollective.com/biojulia/sponsor/3/website)
+[![](https://opencollective.com/biojulia/sponsor/4/avatar.svg)](https://opencollective.com/biojulia/sponsor/4/website)
+[![](https://opencollective.com/biojulia/sponsor/5/avatar.svg)](https://opencollective.com/biojulia/sponsor/5/website)
+[![](https://opencollective.com/biojulia/sponsor/6/avatar.svg)](https://opencollective.com/biojulia/sponsor/6/website)
+[![](https://opencollective.com/biojulia/sponsor/7/avatar.svg)](https://opencollective.com/biojulia/sponsor/7/website)
+[![](https://opencollective.com/biojulia/sponsor/8/avatar.svg)](https://opencollective.com/biojulia/sponsor/8/website)
+[![](https://opencollective.com/biojulia/sponsor/9/avatar.svg)](https://opencollective.com/biojulia/sponsor/9/website)
+
+
+## Questions?
+
+If you have a question about contributing or using BioJulia software, come
+on over and chat to us on [Discord](https://discord.gg/z73YNFz), or you can try the
+[Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
 
-If you have a question about
-contributing or using this package, you are encouraged to use the
-[Bio category of the Julia discourse
-site](https://discourse.julialang.org/c/domain/bio).
diff --git a/REQUIRE b/REQUIRE
@@ -1,4 +1,3 @@
-julia 0.6
-Compat 0.41.0
+julia 0.7
 Automa
-BufferedStreams 0.4.0
+BufferedStreams 1.0.0
diff --git a/docs/make.jl b/docs/make.jl
@@ -12,7 +12,7 @@ makedocs(
 
 deploydocs(
     repo = "github.com/BioJulia/BioCore.jl.git",
-    julia = "0.6",
+    julia = "1.0",
     osname = "linux",
     target = "build",
     deps = nothing,

diff --git a/docs/src/index.md b/docs/src/index.md
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -0,0 +1,93 @@
+# BioCore.jl
+
+[![](https://img.shields.io/github/release/BioJulia/BioCore.jl.svg?style=flat-square)](https://github.com/BioJulia/BioCore.jl/releases/latest) 
+[![](https://img.shields.io/badge/license-MIT-green.svg?style=flat-square)](https://github.com/BioJulia/BioCore.jl/blob/master/LICENSE) 
+[![](https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square)](https://biojulia.github.io/BioCore.jl/stable) 
+[![](https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square)](https://biojulia.github.io/BioCore.jl/latest)
+![](https://img.shields.io/badge/lifecycle-stable-green.svg?style=flat-square)
+[![](https://img.shields.io/badge/discord-chat-blue.svg?style=flat-square&logo=discord&colorB=%237289DA)](https://discord.gg/z73YNFz)
+
+
+## Description
+
+BioCore.jl provides core definitions that are common to all or many packages
+in the BioJulia ecosystem.
+
+It also includes a definition of a common IO interface for IO of Bioinformatics
+formats in BioJulia packages, and includes some helper functions for generating
+file parsers from state machine automata with Automa.jl
+
+
+## Installation
+
+BioCore is a dependency for other BioJulia packages, but you can install it
+yourself with:
+
+```julia
+using Pkg
+add("BioCore")
+#Pkg.add("BioCore") for julia prior to v0.7
+```
+
+If you are interested in the cutting edge of the development, please check out
+the master branch to try new features before release.
+
+
+## Testing
+
+BioCore.jl is tested against Julia `0.7` and `1.0.x` on Linux, OS X, and Windows.
+
+| **PackageEvaluator** | **Latest Build Status** |
+|:--------------------:|:-----------------------:|
+| [![](https://pkg.julialang.org/badges/BioCore_0.7.svg)](https://pkg.julialang.org/detail/BioCore) [![](https://pkg.julialang.org/badges/BioCore_1.0.svg)](https://pkg.julialang.org/detail/BioCore)  | [![](https://img.shields.io/travis/BioJulia/BioCore.jl/master.svg?label=Linux+/+macOS)](https://travis-ci.org/BioJulia/BioCore.jl) [![Build status](https://ci.appveyor.com/api/projects/status/xl19qeob3gsgm8j7?svg=true)](https://ci.appveyor.com/project/Ward9250/biocore-jl) [![](https://codecov.io/gh/BioJulia/BioCore.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/BioCore.jl) |
+
+
+## Contributing
+
+We appreciate contributions from users including reporting bugs, fixing
+issues, improving performance and adding new features.
+
+Take a look at the [CONTRIBUTING](https://github.com/BioJulia/BioCore.jl/blob/master/CONTRIBUTING.md) file provided with
+every BioJulia package package for detailed contributor and maintainer
+guidelines.
+
+
+### Financial contributions
+
+We also welcome financial contributions in full transparency on our
+[open collective](https://opencollective.com/biojulia).
+Anyone can file an expense. If the expense makes sense for the development
+of the community, it will be "merged" in the ledger of our open collective by
+the core contributors and the person who filed the expense will be reimbursed.
+
+
+## Backers & Sponsors
+
+Thank you to all our backers and sponsors!
+
+Love our work and community? [Become a backer](https://opencollective.com/biojulia#backer).
+
+[![backers](https://opencollective.com/biojulia/backers.svg?width=890)](https://opencollective.com/biojulia#backers)
+
+Does your company use BioJulia? Help keep BioJulia feature rich and healthy by
+[sponsoring the project](https://opencollective.com/biojulia#sponsor)
+Your logo will show up here with a link to your website.
+
+[![](https://opencollective.com/biojulia/sponsor/0/avatar.svg)](https://opencollective.com/biojulia/sponsor/0/website)
+[![](https://opencollective.com/biojulia/sponsor/1/avatar.svg)](https://opencollective.com/biojulia/sponsor/1/website)
+[![](https://opencollective.com/biojulia/sponsor/2/avatar.svg)](https://opencollective.com/biojulia/sponsor/2/website)
+[![](https://opencollective.com/biojulia/sponsor/3/avatar.svg)](https://opencollective.com/biojulia/sponsor/3/website)
+[![](https://opencollective.com/biojulia/sponsor/4/avatar.svg)](https://opencollective.com/biojulia/sponsor/4/website)
+[![](https://opencollective.com/biojulia/sponsor/5/avatar.svg)](https://opencollective.com/biojulia/sponsor/5/website)
+[![](https://opencollective.com/biojulia/sponsor/6/avatar.svg)](https://opencollective.com/biojulia/sponsor/6/website)
+[![](https://opencollective.com/biojulia/sponsor/7/avatar.svg)](https://opencollective.com/biojulia/sponsor/7/website)
+[![](https://opencollective.com/biojulia/sponsor/8/avatar.svg)](https://opencollective.com/biojulia/sponsor/8/website)
+[![](https://opencollective.com/biojulia/sponsor/9/avatar.svg)](https://opencollective.com/biojulia/sponsor/9/website)
+
+
+## Questions?
+
+If you have a question about contributing or using BioJulia software, come
+on over and chat to us on [Discord](https://discord.gg/z73YNFz), or you can try the
+[Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
+
diff --git a/src/BioCore.jl b/src/BioCore.jl
@@ -6,8 +6,6 @@
 # This file is a part of BioJulia.
 # License is MIT: https://github.com/BioJulia/BioCore.jl/blob/master/LICENSE.md
 
-__precompile__()
-
 module BioCore
 
 include("declare.jl")
@@ -17,7 +15,6 @@ include("Mem.jl")
 include("Ragel.jl")
 include("ReaderHelper.jl")
 include("RecordHelper.jl")
-include("StringFields.jl")
 include("Testing.jl")
 
 end # module BioCore
diff --git a/src/IO.jl b/src/IO.jl
@@ -52,7 +52,7 @@ See `subtypes(AbstractReader)` for all available data readers.
 """
 abstract type AbstractReader <: AbstractFormattedIO end
 
-Base.iteratorsize(::Type{T}) where T <: AbstractReader = Base.SizeUnknown()
+Base.IteratorSize(::Type{T}) where T <: AbstractReader = Base.SizeUnknown()
 
 function Base.open(::Type{T}, filepath::AbstractString, args...; kwargs...) where T <: AbstractReader
     return T(open(filepath), args...; kwargs...)

diff --git a/src/Mem.jl b/src/Mem.jl
@@ -8,7 +8,7 @@ function copy(dst, src, n::Integer)
 end
 
 function copy(dst::Ptr, src::Ptr, n::Integer)
-    return ccall(:memcpy, Ptr{Void}, (Ptr{Void}, Ptr{Void}, Csize_t), dst, src, n)
+    return ccall(:memcpy, Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t), dst, src, n)
 end
 
 end
diff --git a/src/Ragel.jl b/src/Ragel.jl
@@ -252,6 +252,15 @@ end
 # Iterator
 # --------
 
+function Base.iterate(reader::AbstractReader, nextone = eltype(reader)())
+    if isnull(tryread!(reader, nextone))
+        return nothing
+    else
+        return copy(get(nextone)), nextone
+    end
+end
+
+#=
 function Base.start(reader::AbstractReader)
     T = eltype(reader)
     nextone = T()
@@ -273,5 +282,6 @@ function Base.next(reader::AbstractReader, nextone)
         return ret, Nullable(item)
     end
 end
+=#
 
 end # module Ragel
diff --git a/src/RecordHelper.jl b/src/RecordHelper.jl
@@ -8,8 +8,6 @@
 
 module RecordHelper
 
-using Compat: Cvoid
-
 function compare_memory(p1::Ptr, p2::Ptr, len::Integer)
     return ccall(:memcmp, Cint, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t), p1, p2, len) % Int
 end