Drop python2 support

3 files changed, 36 insertions, 94 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 78f0fd7c0d1a..243c8b385f86 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,39 +1,20 @@
 pkgbase = python-pybedtools
-	pkgdesc = Python wrapper for the bioinformatics genomic arithmetic tool bedtools
-	pkgver = 0.7.10
-	pkgrel = 4
-	url = https://pypi.python.org/pypi/pybedtools
+	pkgdesc = Wrapper around BEDTools for bioinformatics work
+	pkgver = 0.8.2
+	pkgrel = 1
+	url = https://github.com/daler/pybedtools
 	arch = any
 	license = GPL2
-	makedepends = python
-	makedepends = python-setuptools
 	makedepends = cython
-	makedepends = python2
-	makedepends = python2-setuptools
-	makedepends = cython2
-	options = !emptydirs
-	source = python-pybedtools-0.7.10.tar.gz::https://pypi.python.org/packages/09/57/e7668e8644c60413be05b8cc9c23aaea3a0717b4025843d8c26b7c4822af/pybedtools-0.7.10.tar.gz
-	sha256sums = 518a2311bd33f29cf2ee8fc1a028dda8c8e380c9fc83fcb0fbaa206933174b50
-
-pkgname = python-pybedtools
 	depends = bedtools
-	depends = python
-	depends = python-numpy
 	depends = python-pandas
 	depends = python-pysam
-	depends = python-six
 	optdepends = htslib: for working with SAM/BAM/CRAM files
 	optdepends = python-matplotlib: for plotting genomic intervals
 	optdepends = ucsc-kent-genome-tools: for bedgraph to bigwig conversions
+	provides = python-pyvcf
+	conflicts = python-pyvcf
+	source = https://pypi.org/packages/source/p/pybedtools/pybedtools-0.8.2.tar.gz
+	sha512sums = 82af299ec90ce3c80922c82146d0fe26897c243d08d0abc452c667f7183bc89c0f806427fb6691f730c4ddfe8f93e04f59d64b4911297bc30dcbf83a6716cd6d
 
-pkgname = python2-pybedtools
-	depends = bedtools
-	depends = python2
-	depends = python2-numpy
-	depends = python2-pandas
-	depends = python2-pysam
-	depends = python2-six
-	optdepends = htslib: for working with SAM/BAM/CRAM files
-	optdepends = python2-matplotlib: for plotting genomic intervals
-	optdepends = ucsc-kent-genome-tools: for bedgraph to bigwig conversions
-
+pkgname = python-pybedtools
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 000000000000..f59ec20aabf5
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+*
\ No newline at end of file
diff --git a/PKGBUILD b/PKGBUILD
index e5e220bbffbf..a69066195bda 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,72 +1,32 @@
 # Maintainer: Clint Valentine <valentine.clint@gmail.com>
-
-_name=pybedtools
-pkgbase='python-pybedtools'
-pkgname=('python-pybedtools' 'python2-pybedtools')
-pkgver=0.7.10
-pkgrel=4
-pkgdesc="Python wrapper for the bioinformatics genomic arithmetic tool bedtools"
+_base=pybedtools
+pkgname=python-${_base}
+pkgver=0.8.2
+pkgrel=1
+pkgdesc="Wrapper around BEDTools for bioinformatics work"
 arch=('any')
-url="https://pypi.python.org/pypi/pybedtools"
-license=('GPL2')
-makedepends=(
-  'python' 'python-setuptools' 'cython'
-  'python2' 'python2-setuptools' 'cython2')
-options=(!emptydirs)
-source=("${pkgname}"-"${pkgver}".tar.gz::https://pypi.python.org/packages/09/57/e7668e8644c60413be05b8cc9c23aaea3a0717b4025843d8c26b7c4822af/pybedtools-0.7.10.tar.gz)
-sha256sums=('518a2311bd33f29cf2ee8fc1a028dda8c8e380c9fc83fcb0fbaa206933174b50')
-
-prepare() {
-  cp -a "${_name}"-"${pkgver}"{,-py2}
-}
-
-build(){
-  cd "${srcdir}"/"${_name}"-"${pkgver}"
+url="https://github.com/daler/${_base}"
+license=(GPL2)
+depends=(bedtools python-pandas python-pysam)
+makedepends=(cython)
+optdepends=(
+  'htslib: for working with SAM/BAM/CRAM files'
+  'python-matplotlib: for plotting genomic intervals'
+  'ucsc-kent-genome-tools: for bedgraph to bigwig conversions')
+provides=('python-pyvcf')
+conflicts=('python-pyvcf')
+# options=(!emptydirs)
+source=(https://pypi.org/packages/source/${_base::1}/${_base}/${_base}-${pkgver}.tar.gz)
+sha512sums=('82af299ec90ce3c80922c82146d0fe26897c243d08d0abc452c667f7183bc89c0f806427fb6691f730c4ddfe8f93e04f59d64b4911297bc30dcbf83a6716cd6d')
+
+build() {
+  cd "${_base}-${pkgver}"
   python setup.py build
-
-  cd "${srcdir}"/"${_name}"-"${pkgver}"-py2
-  python2 setup.py build
 }
 
-package_python2-pybedtools() {
-  depends=(
-    'bedtools'
-    'python2'
-    'python2-numpy'
-    'python2-pandas'
-    'python2-pysam'
-    'python2-six')
-  optdepends=(
-    'htslib: for working with SAM/BAM/CRAM files'
-    'python2-matplotlib: for plotting genomic intervals'
-    'ucsc-kent-genome-tools: for bedgraph to bigwig conversions')
-
-  cd "${_name}"-"${pkgver}"-py2
-  python2 setup.py install --root="${pkgdir}"/ --optimize=1 --skip-build
-  install -Dm644 LICENSE.txt "${pkgdir}"/usr/share/licenses/"${pkgname}"/LICENSE.txt
-
-  sed 's/python/python2/g' "${pkgdir}"/usr/bin/pybedtools
-  mv "${pkgdir}"/usr/bin/pybedtools "${pkgdir}"/usr/bin/pybedtools2
-
-  for script in "${pkgdir}"/usr/bin/*.py;do
-    mv "${script}" "${pkgdir}"/usr/bin/$(basename "${script%.*py}")2.py
-  done
-}
-
-package_python-pybedtools() {
-  depends=(
-    'bedtools'
-    'python'
-    'python-numpy'
-    'python-pandas'
-    'python-pysam'
-    'python-six')
-  optdepends=(
-    'htslib: for working with SAM/BAM/CRAM files'
-    'python-matplotlib: for plotting genomic intervals'
-    'ucsc-kent-genome-tools: for bedgraph to bigwig conversions')
-
-  cd "${_name}"-"${pkgver}"
-  python setup.py install --root="${pkgdir}"/ --optimize=1 --skip-build
-  install -Dm644 LICENSE.txt "${pkgdir}"/usr/share/licenses/"${pkgname}"/LICENSE.txt
+package() {
+  cd "${_base}-${pkgver}"
+  export PYTHONHASHSEED=0
+  PYTHONPYCACHEPREFIX="${PWD}/.cache/cpython/" python setup.py install --prefix=/usr --root="${pkgdir}" --optimize=1 --skip-build
+  install -Dm 644 LICENSE.txt -t "${pkgdir}/usr/share/licenses/${pkgname}"
 }