bio-bigwig 0.0.1 → 0.0.2

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data/README.md CHANGED
@@ -1,5 +1,9 @@
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  # bio-bigwig
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+ [![Gem Version](https://img.shields.io/gem/v/bio-bigwig?color=brightgreen)](https://rubygems.org/gems/bio-bigwig)
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+ [![test](https://github.com/kojix2/bio-bigwig/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/bio-bigwig/actions/workflows/ci.yml)
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+ [![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://rubydoc.info/gems/bio-bigwig)
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+
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  Ruby wrapper to [libBigWig](https://github.com/dpryan79/libBigWig) compatible with [pyBigWig](https://github.com/deeptools/pyBigWig).
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  * Currently, curl does not seem to work well ((Pull requests welcome)).
@@ -7,18 +11,6 @@ Ruby wrapper to [libBigWig](https://github.com/dpryan79/libBigWig) compatible wi
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  ## Installation
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- Installation from source.
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-
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- ```
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- git clone --recursive https://github.com/kojix2/bio-bigwig
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- cd bio-bigwig
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- bundle install
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- bundle exec rake compile
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- bundle exec rake install
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- ```
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-
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- Not yet uploaded to the Gem server.
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-
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  ```
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  gem install bio-bigwig
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  ```
@@ -119,12 +111,17 @@ bb.sql
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  # )
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  ```
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+ ## Contributing
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+
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+ Bug reports and pull requests are welcome on GitHub at <https://github.com/kojix2/bio-bigwig>.
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+
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  ## Development
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  Pull requests are welcome!
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- ## Contributing
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- Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/bio-bigwig.
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+ Do you need commit rights to my repository?
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+ Do you want to get admin rights and take over the project?
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+ If so, please feel free to contact us @kojix2.
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  ## License
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@@ -32,7 +32,7 @@
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  #define NUM2INT64 NUM2LONG
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  #define UINT64_2NUM ULONG2NUM
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  #define INT64_2NUM LONG2NUM
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- #elif SIZEOF_LONGLONG == SIZEOF_INT64
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+ #elif SIZEOF_LONG_LONG == SIZEOF_INT64
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  #define NUM2UINT64 NUM2ULL
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  #define NUM2INT64 NUM2LL
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  #define UINT64_2NUM ULL2NUM
@@ -1,30 +1,12 @@
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- # frozen_string_literal: true
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-
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  require "mkmf"
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- # https://github.com/taf2/curb/blob/master/ext/extconf.rb
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- dir_config("curl")
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- if find_executable("curl-config")
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- $CFLAGS << " #{`curl-config --cflags`.strip} -g"
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- $LIBS << if ENV["STATIC_BUILD"]
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- " #{`curl-config --static-libs`.strip}"
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- else
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- " #{`curl-config --libs`.strip}"
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- end
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- ca_bundle_path = `curl-config --ca`.strip
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- if !ca_bundle_path.nil? && (ca_bundle_path != "")
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- $defs.push(%(-D HAVE_CURL_CONFIG_CA))
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- $defs.push(%(-D CURL_CONFIG_CA='#{ca_bundle_path.inspect}'))
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- end
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- end
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+ # check curl
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+ have_library("curl", "curl_easy_init")
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+ have_header("libbigwig/bigWig.h")
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- # dir_config("libbigwig")
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- # unless find_header("bigWig.h") && have_library("bigwig")
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- $INCFLAGS << " -I$(srcdir)/libBigWig"
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- $VPATH << "$(srcdir)/libBigWig"
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- $srcs = Dir.glob(["{.,libBigWig}/*.c"], base: __dir__)
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- .map { |f| File.expand_path(f, __dir__) }
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- $objs = $srcs.map { |f| f.sub(/\.c$/, ".o") }
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- # end
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+ $srcs = Dir.glob("libBigWig/*.c", base: __dir__)
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+ .map { |src| File.expand_path(src, __dir__) }
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+ .unshift(File.expand_path("bigwigext.c", __dir__))
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+ $objs = $srcs.map { |src| src.gsub(/\.c\z/, ".o") }
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  create_makefile("bio/bigwig/bigwigext")
@@ -2,6 +2,6 @@
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  module Bio
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  class BigWig
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- VERSION = "0.0.1"
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+ VERSION = "0.0.2"
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  end
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-bigwig
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  version: !ruby/object:Gem::Version
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- version: 0.0.1
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+ version: 0.0.2
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  platform: ruby
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  authors:
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  - kojix2
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2022-01-30 00:00:00.000000000 Z
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+ date: 2024-09-20 00:00:00.000000000 Z
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  dependencies: []
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  description: This is a Ruby binding for libBigWig (https://github.com/dpryan79/libBigWig),
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  which provides high-speed access to bigWig or bigBed files.
@@ -24,26 +24,9 @@ files:
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  - ext/bio/bigwig/bigwigext.c
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  - ext/bio/bigwig/bigwigext.h
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  - ext/bio/bigwig/extconf.rb
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- - ext/bio/bigwig/libBigWig/LICENSE
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- - ext/bio/bigwig/libBigWig/bigWig.h
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- - ext/bio/bigwig/libBigWig/bigWigIO.h
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- - ext/bio/bigwig/libBigWig/bwCommon.h
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- - ext/bio/bigwig/libBigWig/bwRead.c
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- - ext/bio/bigwig/libBigWig/bwStats.c
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- - ext/bio/bigwig/libBigWig/bwValues.c
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- - ext/bio/bigwig/libBigWig/bwValues.h
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- - ext/bio/bigwig/libBigWig/bwWrite.c
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- - ext/bio/bigwig/libBigWig/io.c
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- - ext/bio/bigwig/libBigWig/test/exampleWrite.c
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- - ext/bio/bigwig/libBigWig/test/testBigBed.c
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- - ext/bio/bigwig/libBigWig/test/testIterator.c
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- - ext/bio/bigwig/libBigWig/test/testLocal.c
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- - ext/bio/bigwig/libBigWig/test/testRemote.c
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- - ext/bio/bigwig/libBigWig/test/testRemoteManyContigs.c
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- - ext/bio/bigwig/libBigWig/test/testWrite.c
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  - lib/bio/bigwig.rb
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  - lib/bio/bigwig/version.rb
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- homepage: https://github.com/kojix2/bw-ruby
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+ homepage: https://github.com/kojix2/bio-bigwig
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  licenses:
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  - MIT
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  metadata: {}
@@ -62,7 +45,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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- rubygems_version: 3.3.3
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+ rubygems_version: 3.4.19
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  signing_key:
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  specification_version: 4
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  summary: A ruby library for accessing bigWig / bigBed files
@@ -1,22 +0,0 @@
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- The MIT License (MIT)
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-
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- Copyright (c) 2015 Devon Ryan
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-
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- Permission is hereby granted, free of charge, to any person obtaining a copy
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- of this software and associated documentation files (the "Software"), to deal
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- in the Software without restriction, including without limitation the rights
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- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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- copies of the Software, and to permit persons to whom the Software is
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- furnished to do so, subject to the following conditions:
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-
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- The above copyright notice and this permission notice shall be included in all
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- copies or substantial portions of the Software.
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-
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- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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- SOFTWARE.
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-