ipyrad: final fix

BioArchLinux/ipyrad/PKGBUILD

@@ -5,16 +5,14 @@ pkgdesc="Interactive assembly and analysis of RAD-seq data sets."
 arch=('any')
 url="https://github.com/dereneaton/ipyrad"
 license=('GPL-3.0-or-later')
-depends=('python' 'python-pandas' 'python-scipy' 'python-numpy' 'python-numba' 'python-h5py' 'python-ipyparallel' 'python-requests' 'python-mpi4py' 
-	'cutadapt' 'python-pysam'  'bedtools' 'vsearch' 'bwa' 'samtools' 'python-toyplot')
+depends=('python' 'python-pandas' 'python-scipy' 'python-numpy' 'python-numba' 'python-h5py' 
+	'python-ipyparallel' 'python-requests' 'python-mpi4py' 'python-scikit-learn'
+	'python-seaborn' 'python-matplotlib' 'python-setuptools'
+	'cutadapt' 'python-pysam'  'bedtools' 'vsearch' 'bwa' 'samtools' 'python-toyplot' 'python-toytree' 'muscle3')
 optdepends=('jupyter-notebook: for interactive')
-makedepends=('python-build' 'python-installer' 'python-wheel' 'gcc' 'make')
-source=("https://github.com/dereneaton/ipyrad/archive/${pkgver}.tar.gz"
-	"https://drive5.com/muscle/muscle_src_3.8.1551.tar.gz")
-sha256sums=('8da9e03569ee1bc0e84bafefd1204249091602a9caa732a79511f67ba81d96b1'
-            'c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e')
-provides=('muscle<5')
-conflicts=('muscle')
+makedepends=('python-build' 'python-setuptools' 'python-installer' 'python-wheel')
+source=("https://github.com/dereneaton/ipyrad/archive/${pkgver}.tar.gz")
+sha256sums=('8da9e03569ee1bc0e84bafefd1204249091602a9caa732a79511f67ba81d96b1')
 
 prepare() {
     # fix future
@@ -24,19 +22,11 @@ prepare() {
 }
 
 build() {
-    # muscle v3
-    cd $srcdir
-    make CFLAGS=" -march=x86-64 -mtune=generic -O2 -pipe" LDLIBS=" -lm"
-
     cd "${srcdir}/${pkgname}-${pkgver}"
     python -m build --wheel --no-isolation
 }
 
 package() {
-    #muscle v3
-    cd "$srcdir"
-    install -D -m755 muscle "$pkgdir/usr/bin/muscle"
-
     cd "${srcdir}/${pkgname}-${pkgver}"
     python -m installer --destdir="${pkgdir}" dist/*.whl
 }

BioArchLinux/ipyrad/lilac.yaml

@@ -15,8 +15,11 @@ repo_depends:
   - bwa
   - samtools
   - python-toyplot
+  - python-toytree
+  - muscle3
 update_on:
   - source: github
     github: dereneaton/ipyrad
     use_latest_release: true
   - alias: python
+