From 4da3df5606d7cc851d7a681f0d188bc1d8bc3b4f Mon Sep 17 00:00:00 2001
From: starsareintherose <starsareintherose@outlook.com>
Date: Tue, 2 Nov 2021 21:21:05 +0000
Subject: [PATCH] add spread3

---
 spread3/PKGBUILD        | 28 ++++++++++++++++++++++++++++
 spread3/lilac.py        | 10 ++++++++++
 spread3/lilac.yaml      |  8 ++++++++
 spread3/spread3.desktop | 19 +++++++++++++++++++
 4 files changed, 65 insertions(+)
 create mode 100644 spread3/PKGBUILD
 create mode 100755 spread3/lilac.py
 create mode 100644 spread3/lilac.yaml
 create mode 100644 spread3/spread3.desktop

diff --git a/spread3/PKGBUILD b/spread3/PKGBUILD
new file mode 100644
index 0000000000..9858947a9c
--- /dev/null
+++ b/spread3/PKGBUILD
@@ -0,0 +1,28 @@
+# Maintainer: Malacology <guoyizhang at malacology dot com>
+# Contributor: Malacology <guoyizhang at malacology dot com>
+
+pkgname=spread3
+pkgver=0.9.6
+_pkgver=0-9-6
+pkgrel=1
+depends=(
+	'jre-openjdk-headless'
+	'jre-openjdk'
+	'jdk-openjdk'
+	'openjdk-doc'
+	'openjdk-src'
+)
+pkgdesc="a user-friendly application to analyze and visualize pathogen phylodynamic reconstructions resulting from Bayesian inference of sequence and trait evolutionary processes"
+arch=('x86_64')
+url="https://rega.kuleuven.be/cev/ecv/software/SpreaD3"
+license=('custom')
+source=("https://rega.kuleuven.be/cev/ecv/software/${pkgname}_files/${pkgname}-v${_pkgver}.jar" "${pkgname}.desktop")
+sha256sums=('4021b6dea480bec88c17666088c47f3ec1135c8f6ea7d9bb6cc21639ffc7956f'
+            'c2d59b208dc6c334ea67ac8d557350c6e41a6d8d3b10d912ac402b7d1c2229d1')
+
+package() {
+    install -dm755 "$pkgdir"/usr/share/{applications,${pkgname}}
+    install -m 755 ${srcdir}/*.desktop ${pkgdir}/usr/share/applications
+    install -m 755 ${srcdir}/gui/icons/spread.png ${pkgdir}/usr/share/${pkgname}
+    install -m 755 ${srcdir}/${pkgname}-v${_pkgver}.jar ${pkgdir}/usr/share/${pkgname}/${pkgname}.jar
+}
diff --git a/spread3/lilac.py b/spread3/lilac.py
new file mode 100755
index 0000000000..fcbff72939
--- /dev/null
+++ b/spread3/lilac.py
@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+def pre_build():
+    update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+    run_cmd(['updpkgsums'])
+
+def post_build():
+    git_add_files('PKGBUILD')
+    git_commit()
diff --git a/spread3/lilac.yaml b/spread3/lilac.yaml
new file mode 100644
index 0000000000..f5e0560f37
--- /dev/null
+++ b/spread3/lilac.yaml
@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: regex
+    url: https://rega.kuleuven.be/cev/ecv/software/spread3_files/
+    regex: spreaD3(\s+v\d+.\d+.\d+)
diff --git a/spread3/spread3.desktop b/spread3/spread3.desktop
new file mode 100644
index 0000000000..2eee11d1f0
--- /dev/null
+++ b/spread3/spread3.desktop
@@ -0,0 +1,19 @@
+[Desktop Entry]
+Categories=
+Encoding=UTF-8
+Exec=java -jar /usr/share/spread3/spread3.jar
+GenericName=
+GenericName[zh]=
+Icon=/usr/share/spread3/spread.png
+MimeType=
+Name=SPREAD3
+Name[zh]=SPREAD3
+ServiceTypes=
+SwallowExec=
+SwallowTitle=
+Terminal=false
+TerminalOptions=
+Type=Application
+X-KDE-SubstituteUID=false
+X-KDE-Username=root
+