[med-svn] [Git][med-team/milib][master] 9 commits: Removing unneeded versioned dependencies in d/control
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sun Jul 3 13:56:08 BST 2022
Pierre Gruet pushed to branch master at Debian Med / milib
Commits:
4ab401ea by Pierre Gruet at 2022-07-02T14:38:04+02:00
Removing unneeded versioned dependencies in d/control
- - - - -
31489ffb by Pierre Gruet at 2022-07-03T13:42:11+02:00
Adding the version number of the package to our build.gradle file
- - - - -
1c786e76 by Pierre Gruet at 2022-07-03T13:43:15+02:00
Using javahelper and maven-repo-helper, determining dependencies with javahelper
- - - - -
a5691f2a by Pierre Gruet at 2022-07-03T13:43:29+02:00
Defining the classpath of the built jar
- - - - -
fdd640c8 by Pierre Gruet at 2022-07-03T13:44:24+02:00
Updating changelog
- - - - -
305147bd by Pierre Gruet at 2022-07-03T13:46:31+02:00
Preparing to repack without the gradle jar
- - - - -
fe36770e by Pierre Gruet at 2022-07-03T13:47:01+02:00
New upstream version 2.0.0+dfsg
- - - - -
e748d8a2 by Pierre Gruet at 2022-07-03T13:47:03+02:00
Update upstream source from tag 'upstream/2.0.0+dfsg'
Update to upstream version '2.0.0+dfsg'
with Debian dir cee2c0dfa057030509cd49d9f976a719803ee3e5
- - - - -
00ef6c47 by Pierre Gruet at 2022-07-03T14:53:08+02:00
Upload to unstable
- - - - -
13 changed files:
- − .github/workflows/build.yaml
- debian/changelog
- debian/control
- debian/copyright
- + debian/libmilib-java.classpath
- + debian/libmilib-java.jlibs
- debian/libmilib-java.poms
- debian/rules
- debian/watch
- − gradle/wrapper/gradle-wrapper.jar
- − gradle/wrapper/gradle-wrapper.properties
- − gradlew
- − gradlew.bat
Changes:
=====================================
.github/workflows/build.yaml deleted
=====================================
@@ -1,38 +0,0 @@
-name: Build application
-
-on:
- push:
- tags: [ '*' ]
- branches: [ '*' ]
-
- workflow_dispatch: {}
-
-jobs:
- run:
- uses: milaboratory/github-ci/.github/workflows/java-gradle-lib.yaml at v1
- with:
- lib-name: MiLib
- lib-name-slug: 'milib'
- java-version: '8'
- build-project: ''
- notify-telegram: true
- publish-dev-tasks: |
- publishAllPublicationsToMipubRepository
- publish-release-tasks: |
- publishToSonatype
- closeSonatypeStagingRepository
-
- secrets:
- GRADLE_PROPERTIES: |
- miRepoAccessKeyId=${{ secrets.AWS_CI_ACCESS_KEY_ID }}
- miRepoSecretAccessKey= ${{ secrets.AWS_CI_SECRET_ACCESS_KEY }}
-
- sonatypeUsername=${{ secrets.MVN_SONATYPE_USERNAME }}
- sonatypePassword=${{ secrets.MVN_SONATYPE_PASSWORD }}
- signingKey=${{ secrets.MVN_SIGNING_KEY }}
-
- AWS_KEY_ID: ${{ secrets.AWS_CI_ACCESS_KEY_ID }}
- AWS_KEY_SECRET: ${{ secrets.AWS_CI_SECRET_ACCESS_KEY }}
-
- TELEGRAM_NOTIFICATION_TARGET: ${{ secrets.TG_CHANNEL_MIBUILDS }}
- TELEGRAM_API_TOKEN: ${{ secrets.TG_CI_BOT_TOKEN }}
=====================================
debian/changelog
=====================================
@@ -1,30 +1,30 @@
-milib (2.0.0-1) UNRELEASED; urgency=medium
+milib (2.0.0+dfsg-1) unstable; urgency=medium
* Team upload.
+ * New upstream version
[ Steffen Moeller ]
- * New upstream version
* d/u/metadata: Updates and cosmetics
[ Andreas Tille ]
* Standards-Version: 4.6.1 (routine-update)
- * See how far we move with simply adding --buildsystem=gradle
- * No need to patch pom.xml
+ * Removing a patch as Maven is not used anymore
[ Pierre Gruet ]
* Removing files from debian/ we needed for Maven previously
- * Refreshing dependencies
+ * Repacking without the gradle jar
+ * Refreshing build-dependencies
* Refreshing Maven rules
* Patching build.gradle.kts to form a gradle build file
- * Changing a call to a guava method
- * Deactivating a test relying on a build properties file we don't provide
-
- TODO:
- - repack without the jar, maybe also remove gradlew
- - add a home-made pom.xml to provide a maven-repo structure
- - installing the built jar
-
- -- Pierre Gruet <pgt at debian.org> Fri, 01 Jul 2022 23:18:33 +0200
+ * Adding the version number of the package to our build.gradle file
+ * Build-depending on javahelper and maven-repo-helper, determining
+ dependencies with javahelper
+ * Defining the classpath of the built jar in d/libmilib-java.classpath
+ * Patching code:
+ - Changing a call to some guava method
+ - Deactivating a test relying on a build properties file we don't provide
+
+ -- Pierre Gruet <pgt at debian.org> Sun, 03 Jul 2022 13:48:39 +0200
milib (1.13-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -5,10 +5,12 @@ Section: java
Priority: optional
Build-Depends: debhelper-compat (= 13),
default-jdk,
- gradle-debian-helper
+ gradle-debian-helper,
+ javahelper,
+ maven-repo-helper
Build-Depends-Indep: junit4 <!nocheck>,
- libcommons-compress-java (>= 1.13),
- libcommons-io-java (>= 2.5),
+ libcommons-compress-java,
+ libcommons-io-java,
libcommons-math3-java,
libguava-java,
libjackson2-core-java,
@@ -28,10 +30,8 @@ Rules-Requires-Root: no
Package: libmilib-java
Architecture: all
Depends: ${misc:Depends},
- ${maven:Depends},
- libjaxb-java
-Suggests: ${maven:OptionalDepends},
- ncbi-blast+
+ ${java:Depends}
+Suggests: ncbi-blast+
Description: library for Next Generation Sequencing (NGS) data processing
A helping Java package adopted by a range of Open Source tools for the
analysis of B and T cell repertoires.
=====================================
debian/copyright
=====================================
@@ -1,6 +1,11 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: MiLib
Source: https://milaboratory.com/
+Files-Excluded: gradle
+ gradlew
+ gradlew.bat
+ .github
+Comment: Removing the gradle jar, the gradle scripts we don't use, and cruft.
Files: *
Copyright: 2018, Bolotin Dmitriy <bolotin.dmitriy at gmail.com>
@@ -13,5 +18,3 @@ License: Apache-2.0
License: Apache-2.0
On Debian systems, the full text of the Apache-2.0 license
can be found in the file '/usr/share/common-licenses/Apache-2.0'
-
-
=====================================
debian/libmilib-java.classpath
=====================================
@@ -0,0 +1 @@
+usr/share/java/milib.jar /usr/share/java/commons-compress.jar /usr/share/java/commons-io.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-math3.jar /usr/share/java/guava.jar /usr/share/java/jackson-annotations.jar /usr/share/java/jackson-core.jar /usr/share/java/jackson-databind.jar /usr/share/java/jcommander.jar /usr/share/java/lz4-java.jar /usr/share/java/picocli.jar /usr/share/java/pipe.jar /usr/share/java/trove4j.jar
=====================================
debian/libmilib-java.jlibs
=====================================
@@ -0,0 +1 @@
+build/libs/milib-*.jar
=====================================
debian/libmilib-java.poms
=====================================
@@ -25,4 +25,4 @@
# --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.
# Empty by default. [mh_install]
#
-pom.xml --no-parent --has-package-version
+build/debian/milib.pom --artifact=build/libs/milib-*.jar
=====================================
debian/rules
=====================================
@@ -1,12 +1,17 @@
#!/usr/bin/make -f
+include /usr/share/dpkg/pkg-info.mk
+
%:
- dh $@ --buildsystem=gradle
+ dh $@ --with javahelper --with maven_repo_helper
override_dh_auto_clean:
dh_auto_clean
+ # Clearing the build.gradle file we provide
-rm build.gradle
override_dh_auto_configure:
- cp build.gradle.kts build.gradle
+ # Adding the upstream version number (without +dfsg) to the build.gradle file
+ # we got by patching build.gradle.kts
+ sed "s/\(^group.*\)/\1\nversion = '$(DEB_VERSION_UPSTREAM)'/ ; s/\+dfsg[[:digit:]]*//" build.gradle.kts > build.gradle
dh_auto_configure
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=4
-opts="repack,compression=xz" \
-https://github.com/milaboratory/milib/tags .*/(?:.*?)([\d\.]+)\.tar\.gz
+opts="repack, compression=xz, dversionmangle=auto, repacksuffix=+dfsg" \
+ https://github.com/milaboratory/milib/tags .*/(?:.*?)([\d\.]+)\.tar\.gz
=====================================
gradle/wrapper/gradle-wrapper.jar deleted
=====================================
Binary files a/gradle/wrapper/gradle-wrapper.jar and /dev/null differ
=====================================
gradle/wrapper/gradle-wrapper.properties deleted
=====================================
@@ -1,6 +0,0 @@
-distributionBase=GRADLE_USER_HOME
-distributionPath=wrapper/dists
-distributionSha256Sum=29e49b10984e585d8118b7d0bc452f944e386458df27371b49b4ac1dec4b7fda
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip
-zipStoreBase=GRADLE_USER_HOME
-zipStorePath=wrapper/dists
=====================================
gradlew deleted
=====================================
@@ -1,234 +0,0 @@
-#!/bin/sh
-
-#
-# Copyright © 2015-2021 the original authors.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# https://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-##############################################################################
-#
-# Gradle start up script for POSIX generated by Gradle.
-#
-# Important for running:
-#
-# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
-# noncompliant, but you have some other compliant shell such as ksh or
-# bash, then to run this script, type that shell name before the whole
-# command line, like:
-#
-# ksh Gradle
-#
-# Busybox and similar reduced shells will NOT work, because this script
-# requires all of these POSIX shell features:
-# * functions;
-# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
-# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
-# * compound commands having a testable exit status, especially «case»;
-# * various built-in commands including «command», «set», and «ulimit».
-#
-# Important for patching:
-#
-# (2) This script targets any POSIX shell, so it avoids extensions provided
-# by Bash, Ksh, etc; in particular arrays are avoided.
-#
-# The "traditional" practice of packing multiple parameters into a
-# space-separated string is a well documented source of bugs and security
-# problems, so this is (mostly) avoided, by progressively accumulating
-# options in "$@", and eventually passing that to Java.
-#
-# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
-# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
-# see the in-line comments for details.
-#
-# There are tweaks for specific operating systems such as AIX, CygWin,
-# Darwin, MinGW, and NonStop.
-#
-# (3) This script is generated from the Groovy template
-# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
-# within the Gradle project.
-#
-# You can find Gradle at https://github.com/gradle/gradle/.
-#
-##############################################################################
-
-# Attempt to set APP_HOME
-
-# Resolve links: $0 may be a link
-app_path=$0
-
-# Need this for daisy-chained symlinks.
-while
- APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
- [ -h "$app_path" ]
-do
- ls=$( ls -ld "$app_path" )
- link=${ls#*' -> '}
- case $link in #(
- /*) app_path=$link ;; #(
- *) app_path=$APP_HOME$link ;;
- esac
-done
-
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
-
-APP_NAME="Gradle"
-APP_BASE_NAME=${0##*/}
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
-
-# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD=maximum
-
-warn () {
- echo "$*"
-} >&2
-
-die () {
- echo
- echo "$*"
- echo
- exit 1
-} >&2
-
-# OS specific support (must be 'true' or 'false').
-cygwin=false
-msys=false
-darwin=false
-nonstop=false
-case "$( uname )" in #(
- CYGWIN* ) cygwin=true ;; #(
- Darwin* ) darwin=true ;; #(
- MSYS* | MINGW* ) msys=true ;; #(
- NONSTOP* ) nonstop=true ;;
-esac
-
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
-
-
-# Determine the Java command to use to start the JVM.
-if [ -n "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVACMD=$JAVA_HOME/jre/sh/java
- else
- JAVACMD=$JAVA_HOME/bin/java
- fi
- if [ ! -x "$JAVACMD" ] ; then
- die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
- fi
-else
- JAVACMD=java
- which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
-fi
-
-# Increase the maximum file descriptors if we can.
-if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
- case $MAX_FD in #(
- max*)
- MAX_FD=$( ulimit -H -n ) ||
- warn "Could not query maximum file descriptor limit"
- esac
- case $MAX_FD in #(
- '' | soft) :;; #(
- *)
- ulimit -n "$MAX_FD" ||
- warn "Could not set maximum file descriptor limit to $MAX_FD"
- esac
-fi
-
-# Collect all arguments for the java command, stacking in reverse order:
-# * args from the command line
-# * the main class name
-# * -classpath
-# * -D...appname settings
-# * --module-path (only if needed)
-# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables..
-
-# For Cygwin or MSYS, switch paths to Windows format before running java
-if "$cygwin" || "$msys" ; then
- APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
- CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
-
- JAVACMD=$( cygpath --unix "$JAVACMD" )
-
- # Now convert the arguments - kludge to limit ourselves to /bin/sh
- for arg do
- if
- case $arg in #(
- -*) false ;; # don't mess with options #(
- /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
- [ -e "$t" ] ;; #(
- *) false ;;
- esac
- then
- arg=$( cygpath --path --ignore --mixed "$arg" )
- fi
- # Roll the args list around exactly as many times as the number of
- # args, so each arg winds up back in the position where it started, but
- # possibly modified.
- #
- # NB: a `for` loop captures its iteration list before it begins, so
- # changing the positional parameters here affects neither the number of
- # iterations, nor the values presented in `arg`.
- shift # remove old arg
- set -- "$@" "$arg" # push replacement arg
- done
-fi
-
-# Collect all arguments for the java command;
-# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-# shell script including quotes and variable substitutions, so put them in
-# double quotes to make sure that they get re-expanded; and
-# * put everything else in single quotes, so that it's not re-expanded..
-
-set -- \
- "-Dorg.gradle.appname=$APP_BASE_NAME" \
- -classpath "$CLASSPATH" \
- org.gradle.wrapper.GradleWrapperMain \
- "$@"
-
-# Use "xargs" to parse quoted args.
-#
-# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
-#
-# In Bash we could simply go:
-#
-# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
-# set -- "${ARGS[@]}" "$@"
-#
-# but POSIX shell has neither arrays nor command substitution, so instead we
-# post-process each arg (as a line of input to sed) to backslash-escape any
-# character that might be a shell metacharacter, then use eval to reverse
-# that process (while maintaining the separation between arguments), and wrap
-# the whole thing up as a single "set" statement.
-#
-# This will of course break if any of these variables contains a newline or
-# an unmatched quote.
-#
-
-eval "set -- $(
- printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
- xargs -n1 |
- sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
- tr '\n' ' '
- )" '"$@"'
-
-exec "$JAVACMD" "$@"
=====================================
gradlew.bat deleted
=====================================
@@ -1,89 +0,0 @@
- at rem
- at rem Copyright 2015 the original author or authors.
- at rem
- at rem Licensed under the Apache License, Version 2.0 (the "License");
- at rem you may not use this file except in compliance with the License.
- at rem You may obtain a copy of the License at
- at rem
- at rem https://www.apache.org/licenses/LICENSE-2.0
- at rem
- at rem Unless required by applicable law or agreed to in writing, software
- at rem distributed under the License is distributed on an "AS IS" BASIS,
- at rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- at rem See the License for the specific language governing permissions and
- at rem limitations under the License.
- at rem
-
- at if "%DEBUG%" == "" @echo off
- at rem ##########################################################################
- at rem
- at rem Gradle startup script for Windows
- at rem
- at rem ##########################################################################
-
- at rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
- at rem Resolve any "." and ".." in APP_HOME to make it shorter.
-for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
-
- at rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
-
- at rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto execute
-
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto execute
-
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:execute
- at rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-
- at rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
-
-:end
- at rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
View it on GitLab: https://salsa.debian.org/med-team/milib/-/compare/8f0c1ba50a3dc057704eed6985606c810234dc61...00ef6c4706144fea7f6c08d3f1a58c84d6075b35
--
View it on GitLab: https://salsa.debian.org/med-team/milib/-/compare/8f0c1ba50a3dc057704eed6985606c810234dc61...00ef6c4706144fea7f6c08d3f1a58c84d6075b35
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