bio-bigwig 0.0.1 → 0.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,5 +1,9 @@
 # bio-bigwig
 
+[![Gem Version](https://img.shields.io/gem/v/bio-bigwig?color=brightgreen)](https://rubygems.org/gems/bio-bigwig)
+[![test](https://github.com/kojix2/bio-bigwig/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/bio-bigwig/actions/workflows/ci.yml)
+[![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://rubydoc.info/gems/bio-bigwig)
+
 Ruby wrapper to [libBigWig](https://github.com/dpryan79/libBigWig) compatible with [pyBigWig](https://github.com/deeptools/pyBigWig).
 
 * 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
 
 ## Installation
 
-Installation from source.
-
-```
-git clone --recursive https://github.com/kojix2/bio-bigwig
-cd bio-bigwig
-bundle install
-bundle exec rake compile
-bundle exec rake install
-```
-
-Not yet uploaded to the Gem server.
-
 ```
 gem install bio-bigwig
 ```
@@ -119,12 +111,17 @@ bb.sql
 #     )
 ```
 
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at <https://github.com/kojix2/bio-bigwig>.
+
 ## Development
 
 Pull requests are welcome!
-## Contributing
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/bio-bigwig.
+    Do you need commit rights to my repository?
+    Do you want to get admin rights and take over the project?
+    If so, please feel free to contact us @kojix2.
 
 ## License
 

data/ext/bio/bigwig/bigwigext.c

@@ -32,7 +32,7 @@
 #define NUM2INT64 NUM2LONG
 #define UINT64_2NUM ULONG2NUM
 #define INT64_2NUM LONG2NUM
-#elif SIZEOF_LONGLONG == SIZEOF_INT64
+#elif SIZEOF_LONG_LONG == SIZEOF_INT64
 #define NUM2UINT64 NUM2ULL
 #define NUM2INT64 NUM2LL
 #define UINT64_2NUM ULL2NUM

data/ext/bio/bigwig/extconf.rb

@@ -1,30 +1,12 @@
-# frozen_string_literal: true
-
 require "mkmf"
 
-# https://github.com/taf2/curb/blob/master/ext/extconf.rb
-dir_config("curl")
-if find_executable("curl-config")
-  $CFLAGS << " #{`curl-config --cflags`.strip} -g"
-  $LIBS << if ENV["STATIC_BUILD"]
-             " #{`curl-config --static-libs`.strip}"
-           else
-             " #{`curl-config --libs`.strip}"
-           end
-  ca_bundle_path = `curl-config --ca`.strip
-  if !ca_bundle_path.nil? && (ca_bundle_path != "")
-    $defs.push(%(-D HAVE_CURL_CONFIG_CA))
-    $defs.push(%(-D CURL_CONFIG_CA='#{ca_bundle_path.inspect}'))
-  end
-end
+# check curl
+have_library("curl", "curl_easy_init")
+have_header("libbigwig/bigWig.h")
 
-# dir_config("libbigwig")
-# unless find_header("bigWig.h") && have_library("bigwig")
-$INCFLAGS << " -I$(srcdir)/libBigWig"
-$VPATH    << "$(srcdir)/libBigWig"
-$srcs = Dir.glob(["{.,libBigWig}/*.c"], base: __dir__)
-           .map { |f| File.expand_path(f, __dir__) }
-$objs = $srcs.map { |f| f.sub(/\.c$/, ".o") }
-# end
+$srcs = Dir.glob("libBigWig/*.c", base: __dir__)
+           .map { |src| File.expand_path(src, __dir__) }
+           .unshift(File.expand_path("bigwigext.c", __dir__))
+$objs = $srcs.map { |src| src.gsub(/\.c\z/, ".o") }
 
 create_makefile("bio/bigwig/bigwigext")

data/lib/bio/bigwig/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class BigWig
-    VERSION = "0.0.1"
+    VERSION = "0.0.2"
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigwig
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-01-30 00:00:00.000000000 Z
+date: 2024-09-20 00:00:00.000000000 Z
 dependencies: []
 description: This is a Ruby binding for libBigWig (https://github.com/dpryan79/libBigWig),
   which provides high-speed access to bigWig or bigBed files.
@@ -24,26 +24,9 @@ files:
 - ext/bio/bigwig/bigwigext.c
 - ext/bio/bigwig/bigwigext.h
 - ext/bio/bigwig/extconf.rb
-- ext/bio/bigwig/libBigWig/LICENSE
-- ext/bio/bigwig/libBigWig/bigWig.h
-- ext/bio/bigwig/libBigWig/bigWigIO.h
-- ext/bio/bigwig/libBigWig/bwCommon.h
-- ext/bio/bigwig/libBigWig/bwRead.c
-- ext/bio/bigwig/libBigWig/bwStats.c
-- ext/bio/bigwig/libBigWig/bwValues.c
-- ext/bio/bigwig/libBigWig/bwValues.h
-- ext/bio/bigwig/libBigWig/bwWrite.c
-- ext/bio/bigwig/libBigWig/io.c
-- ext/bio/bigwig/libBigWig/test/exampleWrite.c
-- ext/bio/bigwig/libBigWig/test/testBigBed.c
-- ext/bio/bigwig/libBigWig/test/testIterator.c
-- ext/bio/bigwig/libBigWig/test/testLocal.c
-- ext/bio/bigwig/libBigWig/test/testRemote.c
-- ext/bio/bigwig/libBigWig/test/testRemoteManyContigs.c
-- ext/bio/bigwig/libBigWig/test/testWrite.c
 - lib/bio/bigwig.rb
 - lib/bio/bigwig/version.rb
-homepage: https://github.com/kojix2/bw-ruby
+homepage: https://github.com/kojix2/bio-bigwig
 licenses:
 - MIT
 metadata: {}
@@ -62,7 +45,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.3
+rubygems_version: 3.4.19
 signing_key: 
 specification_version: 4
 summary: A ruby library for accessing bigWig / bigBed files

data/ext/bio/bigwig/libBigWig/LICENSE

@@ -1,22 +0,0 @@
-The MIT License (MIT)
-
-Copyright (c) 2015 Devon Ryan
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-