From 2618d4f84636d23165829419bf195307ef7d6142 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 5 Mar 2024 13:00:14 +0200
Subject: [PATCH] r-nebulosa: fix depends, use metadata checks

---
 BioArchLinux/r-nebulosa/PKGBUILD   | 31 +++++++++++++++---------------
 BioArchLinux/r-nebulosa/lilac.py   | 11 ++++++-----
 BioArchLinux/r-nebulosa/lilac.yaml | 10 ++++++----
 3 files changed, 28 insertions(+), 24 deletions(-)

diff --git a/BioArchLinux/r-nebulosa/PKGBUILD b/BioArchLinux/r-nebulosa/PKGBUILD
index 3080f55c05..5014f3bca0 100644
--- a/BioArchLinux/r-nebulosa/PKGBUILD
+++ b/BioArchLinux/r-nebulosa/PKGBUILD
@@ -1,20 +1,20 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=Nebulosa
-_pkgver=1.12.0
+_pkgver=1.12.1
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
-pkgrel=1
-pkgdesc='Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-ggplot2
+  r-ggrastr
   r-ks
   r-patchwork
-  r-seurat
+  r-seuratobject
   r-singlecellexperiment
   r-summarizedexperiment
 )
@@ -28,18 +28,19 @@ optdepends=(
   r-rmarkdown
   r-scater
   r-scran
-  r-seuratobject
+  r-seurat
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('cc08da2bf124e836890656c51090e87041d8947da864bcd8a2f750983b6ff34f')
+md5sums=('daedaeb79ec239323487565bce3f7ca2')
+b2sums=('b3472b0f74b6aefc9aa5953758cb5d8cc6d92071c2d77f17e54a3a983b4ca72365c370c2e2bd57978785ab0632b3b5c3f79d91f9b3607c7aab381ed44b648155')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:
diff --git a/BioArchLinux/r-nebulosa/lilac.py b/BioArchLinux/r-nebulosa/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-nebulosa/lilac.py
+++ b/BioArchLinux/r-nebulosa/lilac.py
@@ -1,12 +1,13 @@
 #!/usr/bin/env python3
 from lilaclib import *
 
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
 def pre_build():
-    for line in edit_file('PKGBUILD'):
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-nebulosa/lilac.yaml b/BioArchLinux/r-nebulosa/lilac.yaml
index 4333e09bb0..3d5457f048 100644
--- a/BioArchLinux/r-nebulosa/lilac.yaml
+++ b/BioArchLinux/r-nebulosa/lilac.yaml
@@ -4,13 +4,15 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-ggplot2
+- r-ggrastr
 - r-ks
 - r-patchwork
-- r-seurat
+- r-seuratobject
 - r-singlecellexperiment
 - r-summarizedexperiment
 update_on:
-- regex: Nebulosa_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/Nebulosa
+- source: rpkgs
+  pkgname: Nebulosa
+  repo: bioc
+  md5: true
 - alias: r