[med-svn] [Git][med-team/varna][master] 9 commits: * debian/README.Debian: document jar location.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Aug 24 10:00:42 BST 2022
Michael R. Crusoe pushed to branch master at Debian Med / varna
Commits:
f44ec968 by Michael R. Crusoe at 2022-08-24T10:50:50+02:00
* debian/README.Debian: document jar location.
- - - - -
d13c116a by Michael R. Crusoe at 2022-08-24T10:52:32+02:00
make and install a manpage
- - - - -
32d24355 by Michael R. Crusoe at 2022-08-24T10:53:32+02:00
add basic test & autopkgtest
- - - - -
3fc1ce9d by Michael R. Crusoe at 2022-08-24T10:54:19+02:00
debian/watch: switch to HTTPS
- - - - -
ee3e5f95 by Michael R. Crusoe at 2022-08-24T10:59:23+02:00
debian/upstream/metadata: add upstream contact for bug reporting
- - - - -
6130c273 by Michael R. Crusoe at 2022-08-24T10:59:26+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
2e24310f by Michael R. Crusoe at 2022-08-24T10:59:27+02:00
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
f18692c9 by Michael R. Crusoe at 2022-08-24T10:59:27+02:00
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
9032c03f by Michael R. Crusoe at 2022-08-24T10:59:28+02:00
routine-update: Ready to upload to unstable
- - - - -
12 changed files:
- + debian/README.Debian
- + debian/bin/varna
- debian/changelog
- debian/control
- + debian/install
- + debian/man_helper/varna
- + debian/manpages
- debian/rules
- + debian/tests/control
- + debian/tests/run-simple-test
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,7 @@
+The VARNA jar file is located at /usr/share/java/varna.jar
+
+You can launch VARNA by running the command `varna`, which also accepts the command
+line options documented at http://varna.lri.fr/index.php?lang=en&page=command&css=varna
+
+a subset of the documentation for these options are available from the manual
+page for VARNA: `man varna`
=====================================
debian/bin/varna
=====================================
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+java -cp /usr/share/java/varna.jar fr.orsay.lri.varna.applications.VARNAcmd $@
=====================================
debian/changelog
=====================================
@@ -1,7 +1,24 @@
+varna (3-93+ds-4) unstable; urgency=medium
+
+ * Update my email address.
+ * debian/README.Debian: document jar location.
+ * debian/{install,bin/varna}: install a shortcut for launching VARNA
+ ("varna")
+ * debian/{rules,manpages,control}: generate a manual page for the "varna"
+ command
+ * debian/{rules,tests/*}: add a simple build time test and autopkgtest
+ * debian/watch: switch to HTTPS
+ * debian/upstream/metadata: add upstream contact for bug reporting
+ * Standards-Version: 4.6.1 (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Use secure URI in Homepage field.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 24 Aug 2022 10:58:06 +0200
+
varna (3-93+ds-3) unstable; urgency=medium
* Team Upload.
-
+
[ Michael R. Crusoe ]
* Update my email address.
* Secure URI in copyright format
=====================================
debian/control
=====================================
@@ -1,15 +1,16 @@
Source: varna
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
+Uploaders: Michael R. Crusoe <crusoe at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
javahelper,
- default-jdk
-Standards-Version: 4.5.0
+ default-jdk,
+ help2man
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/varna
Vcs-Git: https://salsa.debian.org/med-team/varna.git
-Homepage: http://varna.lri.fr/
+Homepage: https://varna.lri.fr/
Rules-Requires-Root: no
Package: varna
=====================================
debian/install
=====================================
@@ -0,0 +1 @@
+debian/bin/varna /usr/bin/
=====================================
debian/man_helper/varna
=====================================
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+java fr.orsay.lri.varna.applications.VARNAcmd $@
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/varna.1
=====================================
debian/rules
=====================================
@@ -3,6 +3,25 @@
DH_VERBOSE := 1
JAVA_HOME=/usr/lib/jvm/default-java
export JAVA_TOOL_OPTIONS=-Dfile.encoding=ISO-8859-1
+include /usr/share/dpkg/default.mk
%:
dh $@ --with javahelper
+
+override_dh_installman:
+ CLASSPATH=$(CURDIR)/varna.jar \
+ PATH=$$PATH:debian/man_helper help2man \
+ --version-string "$(DEB_VERSION_UPSTREAM)" \
+ --no-info \
+ --name "Assisted drawing of RNA secondary structure" \
+ --output debian/varna.1 \
+ --help-option=-x \
+ varna
+ dh_installman
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ java -cp $(CURDIR)/varna.jar \
+ fr.orsay.lri.varna.applications.VARNAcmd -structureDBN "((..))" \
+ -sequenceDBN "AACCUU" -o "./out.png"
+endif
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-simple-test
+Depends: varna
+Restrictions: allow-stderr
=====================================
debian/tests/run-simple-test
=====================================
@@ -0,0 +1,4 @@
+#!/bin/sh -e
+
+varna -structureDBN "((..))" -sequenceDBN "AACCUU" -o "./out.png"
+md5sum < ./out.png | grep 781823a49c30e45deb05bc40408ebe3f
=====================================
debian/upstream/metadata
=====================================
@@ -20,3 +20,4 @@ Registry:
Entry: NA
- Name: conda:lb_arrakistx
Entry: varna
+Bug-Submit: mailto:ponty at lri.fr
=====================================
debian/watch
=====================================
@@ -1,5 +1,5 @@
version=4
opts="repacksuffix=+ds,dversionmangle=s/\+ds//g,compression=xz" \
-http://varna.lri.fr/index.php?page=downloads .*/VARNAv(.*)-src.jar
+https://varna.lri.fr/index.php?page=downloads .*/VARNAv(.*)-src.jar
View it on GitLab: https://salsa.debian.org/med-team/varna/-/compare/3150e272290555e1f2b826c838c59ef2e1a34384...9032c03f4c12a9d77aa242f6b1a1777257630f47
--
View it on GitLab: https://salsa.debian.org/med-team/varna/-/compare/3150e272290555e1f2b826c838c59ef2e1a34384...9032c03f4c12a9d77aa242f6b1a1777257630f47
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