[med-svn] [Git][med-team/king][master] 6 commits: Adding dependencies to perform the build with newest upstream version

Pierre Gruet (@pgt) gitlab at salsa.debian.org
Wed Feb 2 21:00:07 GMT 2022 


Pierre Gruet pushed to branch master at Debian Med / king


Commits:
016db829 by Pierre Gruet at 2022-01-30T15:27:10+01:00
Adding dependencies to perform the build with newest upstream version

- - - - -
bfb5a9e5 by Pierre Gruet at 2022-01-30T15:27:18+01:00
Refreshing patches

- - - - -
0fc9d62f by Pierre Gruet at 2022-02-01T22:40:50+01:00
Changing the path of the build jar in d/king.jlibs file

- - - - -
9227a458 by Pierre Gruet at 2022-02-01T22:44:14+01:00
Building pdf docs from lyx and tex files, building reproducibly

Providing a Perl script to put the date of the changelog file into the lyx and
tex sources of the documentation, then building them.

- - - - -
5bf903df by Pierre Gruet at 2022-02-02T21:54:18+01:00
hacking-king.pdf is no more provided

- - - - -
f164a6af by Pierre Gruet at 2022-02-02T21:59:40+01:00
Currently extratools/doc/work/tools-manual.lyx cannot be turned into a pdf file

- - - - -


13 changed files:

- + debian/clean
- debian/control
- − debian/king.doc-base.extratools
- − debian/king.doc-base.hacking-king
- debian/king.docs
- debian/king.jlibs
- + debian/makePdfDoc
- debian/patches/ignore_appbundler.patch
- debian/patches/ignore_rdcvis.jar.patch
- + debian/patches/no_extratools_doc.patch
- debian/patches/series
- debian/patches/use_debian_packaged_jars.patch
- debian/rules


Changes:

=====================================
debian/clean
=====================================
@@ -0,0 +1,5 @@
+chiropraxis/doc/tools-manual.*
+king-manual.*
+new-color-palette.*
+format-kinemage.*
+rdcvis-manual.*


=====================================
debian/control
=====================================
@@ -8,10 +8,17 @@ Build-Depends: debhelper-compat (= 13),
                javahelper,
                ant,
                inkscape,
+               junit4,
+               libhamcrest-java,
                libitext-java,
                libjogl2-java,
                libpdfbox2-java,
-               libfontbox-java
+               libpdfbox-graphics2d-java,
+               libfontbox-java,
+               lyx,
+               perl,
+               texlive-fonts-recommended,
+               texlive-latex-base
 Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/king
 Vcs-Git: https://salsa.debian.org/med-team/king.git


=====================================
debian/king.doc-base.extratools deleted
=====================================
@@ -1,14 +0,0 @@
-Document: extratools
-Title: The Extratools manual
-Author: Ian W. Davis, Vincent B. Chen, and Daniel A. Keedy
-Abstract: The KiNG Tools
- This manual describes the KiNG tools available in the ’extratools’ and
- ’rdcvis’ packages. It is roughly laid out in order of the tools menu in
- KiNG, with tools in the main menu in this chapter, and a separate
- chapter for the ’Data analysis’, ’Kin editing’, ’Structural biology’,
- ’Export’ (File menu), and ’Specialty’ tools. Also see the KiNG manual
- for descriptions of other tools.
-Section: Science/Biology
-
-Format: pdf
-Files: /usr/share/doc/king/extratools-manual.pdf


=====================================
debian/king.doc-base.hacking-king deleted
=====================================
@@ -1,23 +0,0 @@
-Document: hacking-king
-Title: Hacking KiNG
-Author: Ian W. Davis
-Abstract: Hacking KiNG
- This document is intended to provide a field guide to the code for KiNG
- and its associated libraries, Driftwood and Chiropraxis. For more
- information, please see the relevant Javadocs, and ultimately, the code
- itself. In particular, most of the references for the various published
- algorithms are somewhere in the Javadocs. Some parts of the code are
- better commented than others, but it’s mostly pretty comprehensible. If
- not, you can often use the incomprehensible parts without having to
- understand how they work.
- .
- The first part of this discussion will provide an overview of all the
- code, starting with driftwood, building chiropraxis on top of that, and
- finally building king on top of them both. The second part will cover
- the organizational principles behind the layout of code and resources,
- compiling and building, maintaining documentation, and distributing
- finished applications.
-Section: Science/Biology
-
-Format: pdf
-Files: /usr/share/doc/king/hacking-king.pdf


=====================================
debian/king.docs
=====================================
@@ -1,5 +1,7 @@
+chiropraxis/doc/tools-manual.pdf
 king/dist/king-*/doc/*.html
 king/dist/king-*/doc/*.pdf
 king/dist/king-*/doc/*.txt
 king/dist/king-*/README.html
 king/doc/work/king-manual.html
+*.pdf


=====================================
debian/king.jlibs
=====================================
@@ -1 +1 @@
-king/dist/king-*/king.jar
+king/plugins/king.jar


=====================================
debian/makePdfDoc
=====================================
@@ -0,0 +1,102 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+# Getting the changelog date at format mm/dd/yyyy.
+
+chomp(my $dateChangelog = `date --utc --date="@\$(dpkg-parsechangelog -Stimestamp)" +%m/%d/%Y`);
+
+# Temporary directory to host the .lyx directory.
+chomp(my $tempDirLyx = `mktemp -d`);
+
+# Inserting date in tools-manual.tex right after the title, copying at root.
+
+open CHIRO, "<", "chiropraxis/doc/work/tools-manual.tex"
+  or die "Cannot open chiropraxis/doc/work/tools-manual.lyx for reading: $!";
+
+open OUTCHIRO, ">", "chiropraxis/doc/tools-manual.tex"
+  or die "Cannot open chiropraxis/doc/tools-manual.tex for writing: $!";
+
+my $lignes = join '', <CHIRO>;
+$lignes =~ s/(\\title.*?$)/$1\n\\date\{$dateChangelog\}\n/m;
+
+print OUTCHIRO $lignes;
+
+close CHIRO;
+close OUTCHIRO;
+
+# Inserting date in king-manual.lyx right after the title, copying at root.
+
+open KING, "<", "king/doc/work/king-manual.lyx"
+  or die "Cannot open king/doc/work/king-manual.lyx for reading: $!";
+
+open OUTKING, ">", "king-manual.lyx"
+  or die "Cannot open king-manual.lyx for writing: $!";
+
+$lignes = join '', <KING>;
+$lignes =~ s/(manual\n\\end_layout$)/$1\n\n\\begin_layout Date\n $dateChangelog\n\\end_layout/m;
+
+print OUTKING $lignes;
+
+close KING;
+close OUTKING;
+
+# Inserting date in format-kinemage.lyx right after the title, copying at root.
+
+open FORMAT, "<", "king/doc/work/format-kinemage.lyx"
+  or die "Cannot open king/doc/work/format-kinemage.lyx for reading: $!";
+
+open OUTFORMAT, ">", "format-kinemage.lyx"
+  or die "Cannot open format-kinemage.lyx for writing: $!";
+
+$lignes = join '', <FORMAT>;
+$lignes =~ s/(Kinemage File.*?\n\\end_layout$)/$1\n\n\\begin_layout Date\n $dateChangelog\n\\end_layout/m;
+
+print OUTFORMAT $lignes;
+
+close FORMAT;
+close OUTFORMAT;
+
+# Inserting date in new-color-palette.lyx right before the title, copying at root.
+
+open PALETTE, "<", "king/doc/work/new-color-palette.lyx"
+  or die "Cannot open king/doc/work/new-color-palette.lyx for reading: $!";
+
+open OUTPALETTE, ">", "new-color-palette.lyx"
+  or die "Cannot open new-color-palette.lyx for writing: $!";
+
+$lignes = join '', <PALETTE>;
+$lignes =~ s/(\\layout Title$)/\\begin_layout Date\n $dateChangelog\n\\end_layout\n\n$1/m;
+
+print OUTPALETTE $lignes;
+
+close PALETTE;
+close OUTPALETTE;
+
+
+# Inserting date in rdcvis-manual.lyx right before the title, copying at root.
+
+open RDCVIS, "<", "rdcvis/doc/work/rdcvis-manual.lyx"
+  or die "Cannot open rdcvis/doc/work/rdcvis-manual.lyx for reading: $!";
+
+open OUTRDCVIS, ">", "rdcvis-manual.lyx"
+  or die "Cannot open rdcvis-manual.lyx for writing: $!";
+
+$lignes = join '', <RDCVIS>;
+$lignes =~ s/(\\begin_layout Title.*?$)/\\begin_layout Date\n $dateChangelog\n\\end_layout\n\n$1/m;
+
+print OUTRDCVIS $lignes;
+
+close RDCVIS;
+close OUTRDCVIS;
+
+# Compile with pdflatex (twice, for the labels) and export with lyx.
+chdir "chiropraxis/doc/";
+system "pdflatex", "tools-manual.tex";
+system "pdflatex", "tools-manual.tex";
+chdir "../../";
+system "lyx", "-userdir", $tempDirLyx, "--export", "pdf2", "king-manual.lyx";
+system "lyx", "-userdir", $tempDirLyx, "--export", "pdf2", "format-kinemage.lyx";
+system "lyx", "-userdir", $tempDirLyx, "--export", "pdf2", "new-color-palette.lyx";
+system "lyx", "-userdir", $tempDirLyx, "--export", "pdf2", "rdcvis-manual.lyx";


=====================================
debian/patches/ignore_appbundler.patch
=====================================
@@ -5,7 +5,7 @@ Forwarded: not-needed
 
 --- a/king/build.xml
 +++ b/king/build.xml
-@@ -366,10 +366,6 @@ https://groups.google.com/g/jaamsim-user
+@@ -362,10 +362,6 @@
      </exec>
  </target>
  


=====================================
debian/patches/ignore_rdcvis.jar.patch
=====================================
@@ -5,7 +5,7 @@ Forwarded: not-needed
 
 --- a/king/build.xml
 +++ b/king/build.xml
-@@ -204,7 +204,6 @@
+@@ -200,7 +200,6 @@
  <target name="dist-exe" depends="init,build">
      <copy file="${javadev}/chiropraxis/chiropraxis.jar" todir="plugins/" preservelastmodified="true"/>
      <copy file="${javadev}/extratools/extratools.jar" todir="plugins/" preservelastmodified="true"/>


=====================================
debian/patches/no_extratools_doc.patch
=====================================
@@ -0,0 +1,25 @@
+Description: skipping the installation of the manual of extratools, as we
+ cannot manage to build it from source; lyx --export pdf2 tools-manual.lyx is
+ not working.
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: https://github.com/rlabduke/javadev/issues/1
+Last-Update: 2022-01-30
+
+--- a/king/build.xml
++++ b/king/build.xml
+@@ -214,7 +214,6 @@
+     </copy>
+     <!-- extra doc files from other top-level projects; some need to be renamed -->
+     <copy file="../chiropraxis/doc/tools-manual.pdf" tofile="${dist}/${ant.project.name}-${version}/doc/chiropraxis-manual.pdf"/>
+-    <copy file="../extratools/doc/tools-manual.pdf" tofile="${dist}/${ant.project.name}-${version}/doc/extratools-manual.pdf"/>
+ </target>
+ <!-- }}} -->
+ 
+@@ -240,7 +239,6 @@
+     </copy>
+     <!-- extra doc files from other top-level projects; some need to be renamed -->
+     <copy file="../chiropraxis/doc/tools-manual.pdf" tofile="${dist}/${ant.project.name}-${version}/doc/chiropraxis-manual.pdf"/>
+-    <copy file="../extratools/doc/tools-manual.pdf" tofile="${dist}/${ant.project.name}-${version}/doc/extratools-manual.pdf"/>
+ </target>
+ 
+ <target name="jpackage-win" depends="init,build,jpackage-base">


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ java7-compat.patch
 ignore_appbundler.patch
 ignore_rdcvis.jar.patch
 using_free_iconset.patch
+no_extratools_doc.patch


=====================================
debian/patches/use_debian_packaged_jars.patch
=====================================
@@ -21,10 +21,11 @@ Forwarded: not-needed
              <pathelement location="../driftwood/build"/>
 -            <pathelement location="pdfbox.jar"/>             <!-- Required for PDF export -->
 -            <pathelement location="fontbox.jar"/>
+-            <pathelement location="pdfbox-graphics2d.jar"/>
+-            <pathelement location="commons-logging-1.2.jar"/>
 +            <pathelement location="/usr/share/java/pdfbox2.jar"/>             <!-- Required for PDF export -->
 +            <pathelement location="/usr/share/java/fontbox.jar"/>
-             <pathelement location="pdfbox-graphics2d.jar"/>
--            <pathelement location="commons-logging-1.2.jar"/>
++            <pathelement location="/usr/share/java/pdfbox-graphics2d.jar"/>
 +            <pathelement location="/usr/share/java/commons-logging.jar"/>
           </classpath>
      </javac>
@@ -56,6 +57,21 @@ Forwarded: not-needed
      <copy todir="plugins/" preservelastmodified="true" flatten="true">
 --- a/chiropraxis/build.xml
 +++ b/chiropraxis/build.xml
+@@ -64,10 +64,10 @@
+          <classpath>
+             <pathelement location="../driftwood/build"/>
+             <pathelement location="../king/build"/>
+-            <pathelement location="pdfbox.jar"/>             <!-- Required for PDF export -->
+-            <pathelement location="fontbox.jar"/>
+-            <pathelement location="pdfbox-graphics2d.jar"/>
+-            <pathelement location="commons-logging-1.2.jar"/>
++            <pathelement location="/usr/share/java/pdfbox2.jar"/>             <!-- Required for PDF export -->
++            <pathelement location="/usr/share/java/fontbox.jar"/>
++            <pathelement location="/usr/share/java/pdfbox-graphics2d.jar"/>
++            <pathelement location="/usr/share/java/commons-logging-1.2.jar"/>
+             <pathelement location="../molikin/build"/>
+          </classpath>
+     </javac>
 @@ -155,7 +155,7 @@
  <!-- Deploys the executable on the local MolProbity - applies to IWD's machine only  -->
  <target name="deploy-local-mp"  description="Deploy to local MolProbity" depends="build">
@@ -65,3 +81,16 @@ Forwarded: not-needed
  </target>
  <!-- }}} -->
  </project>
+--- a/extratools/build.xml
++++ b/extratools/build.xml
+@@ -55,8 +55,8 @@
+             <pathelement location="../driftwood/build"/>
+             <pathelement location="../chiropraxis/build"/>
+             <pathelement location="../king/build"/>
+-            <pathelement location="../lib/junit/junit-4.13-beta-1.jar"/>
+-            <pathelement location="../lib/junit/hamcrest-core-1.3.jar"/>
++            <pathelement location="/usr/share/java/junit4.jar"/>
++            <pathelement location="/usr/share/java/hamcrest-core.jar"/>
+          </classpath>
+     </javac>
+ </target>


=====================================
debian/rules
=====================================
@@ -17,6 +17,8 @@ override_dh_auto_configure:
 	        mv *.png ../../king/resource/king/images/
 
 override_dh_auto_build:
+	# Build the pdf docs from lyx and tex files.
+	debian/makePdfDoc
 	# create backups of original buildnum resources to enable building twice in a row
 	for component in chiropraxis driftwood extratools king molikin ; do \
 	  if [ -e $$component/resource/$$component/buildnum.props ] ; then \



View it on GitLab: https://salsa.debian.org/med-team/king/-/compare/1670f84c2b5281d41ddb2742e1e30f0eb017f1bc...f164a6aff85875960a18697cb032882ecbf2369a

-- 
View it on GitLab: https://salsa.debian.org/med-team/king/-/compare/1670f84c2b5281d41ddb2742e1e30f0eb017f1bc...f164a6aff85875960a18697cb032882ecbf2369a
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