[med-svn] r20749 - in trunk/packages/genometools/trunk/debian: . patches
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sat Dec 12 19:16:42 UTC 2015
Author: sascha-guest
Date: 2015-12-12 19:16:41 +0000 (Sat, 12 Dec 2015)
New Revision: 20749
Added:
trunk/packages/genometools/trunk/debian/patches/remove_png_timestamps
Modified:
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/patches/adding_soname
trunk/packages/genometools/trunk/debian/patches/fix-exports
trunk/packages/genometools/trunk/debian/patches/series
trunk/packages/genometools/trunk/debian/patches/sort-inputs
Log:
work on reproducibility of API documentation building
Modified: trunk/packages/genometools/trunk/debian/control
===================================================================
--- trunk/packages/genometools/trunk/debian/control 2015-12-12 19:15:59 UTC (rev 20748)
+++ trunk/packages/genometools/trunk/debian/control 2015-12-12 19:16:41 UTC (rev 20749)
@@ -28,7 +28,8 @@
xsltproc,
ruby,
docbook-xsl,
- faketime
+ faketime,
+ imagemagick
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/genometools/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/genometools/trunk/
Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/adding_soname 2015-12-12 19:15:59 UTC (rev 20748)
+++ trunk/packages/genometools/trunk/debian/patches/adding_soname 2015-12-12 19:16:41 UTC (rev 20749)
@@ -25,7 +25,7 @@
define PROGRAM_template
$(1): $(2)
-@@ -940,7 +942,8 @@
+@@ -944,7 +946,8 @@
$(RANLIB) $(prefix)/lib/libgenometools.a
endif
ifneq ($(sharedlib),no)
Modified: trunk/packages/genometools/trunk/debian/patches/fix-exports
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/fix-exports 2015-12-12 19:15:59 UTC (rev 20748)
+++ trunk/packages/genometools/trunk/debian/patches/fix-exports 2015-12-12 19:16:41 UTC (rev 20749)
@@ -5,7 +5,7 @@
@@ -113,6 +113,12 @@
gt_option_parser_register_hook(op, determine_outfp, ofi);
}
-
+
+/* wrapper for ABI compatibility */
+void gt_output_file_register_options(GtOutputFileInfo *ofi,
+ GtOptionParser *op, GtFile **outfp) {
Added: trunk/packages/genometools/trunk/debian/patches/remove_png_timestamps
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/remove_png_timestamps (rev 0)
+++ trunk/packages/genometools/trunk/debian/patches/remove_png_timestamps 2015-12-12 19:16:41 UTC (rev 20749)
@@ -0,0 +1,61 @@
+Description: Remove_png_timestamps
+--- a/Makefile
++++ b/Makefile
+@@ -865,6 +865,10 @@
+ bin/examples/sketch_constructed gtdata/sketch/default.style \
+ www/genometools.org/htdocs/images/constructed.png
+ endif
++ mogrify -format jpg +set date:create +set date:modify \
++ -define png:exclude-chunk=time \
++ www/genometools.org/htdocs/images/*.png && \
++ rm -rf www/genometools.org/htdocs/images/*.png
+ sed -nf scripts/incl.sed \
+ www/genometools.org/htdocs/examples_tmpl.html | \
+ sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \
+--- a/doc/manuals/annotationsketch.tex
++++ b/doc/manuals/annotationsketch.tex
+@@ -240,7 +240,7 @@
+ We will call the second part (after the ``\texttt{|}'') of these track titles \emph{track identifier strings} in the rest of this document.
+
+ \begin{figure}[ht]
+-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect.png}}
++\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect}}
+ \caption{Default AnnotationSketch output for a simple GFF3 file with simple \emph{exon}$\to$\emph{mRNA} collapsing.}
+ \label{tsexample1}
+ \end{figure}
+@@ -270,7 +270,7 @@
+ Using this track selector function would produce the desired result of separate tracks for the \emph{mRNA} features for each strand (see Fig. \ref{tsexample2}).
+
+ \begin{figure}[ht]
+-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect.png}}
++\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect}}
+ \caption{AnnotationSketch output with \texttt{strand\_track\_se\-lector()} track selector function. This image now shows separate tracks for plus and minus strand features.}
+ \label{tsexample2}
+ \end{figure}
+@@ -312,7 +312,7 @@
+ This code results in the image shown in Fig.~\ref{tsexample3} :
+
+ \begin{figure}[ht]
+-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect.png}}
++\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect}}
+ \caption{\AnnotationSketch output with \texttt{filter\_track\_selector()} track selector function. This image now shows a separate track for features with a specific caption.}
+ \label{tsexample3}
+ \end{figure}
+@@ -321,7 +321,7 @@
+ There are kinds of data which may be interesting to see together with annotation renderings, but that can not be expressed -- or only in a complicated way -- in GFF3 format. It may even be too difficult or counterintuitive to properly represent this data as typical \AnnotationSketch box graphics. For example, this may be sequence data, numerical sequence analysis results, or other kinds of data which does not fit into the simple ‘genomic feature’ scheme. For an example, see Fig. \ref{ctexample1}.
+
+ \begin{figure}[ht]
+-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct.png}}
++\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct}}
+ \caption{Example \AnnotationSketch output with a custom track at the bottom, displaying the GC content over a window size of 200 bp.}
+ \label{ctexample1}
+ \end{figure}
+@@ -414,7 +414,7 @@
+ Running layout and drawing functions on this diagram then produces the desired image (see Fig.~\ref{ctexample2}
+
+ \begin{figure}[ht]
+-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2.png}}
++\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2}}
+ \caption{The example insertion site custom track (at the bottom), displaying three sample data points.}
+ \label{ctexample2}
+ \end{figure}
Modified: trunk/packages/genometools/trunk/debian/patches/series
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/series 2015-12-12 19:15:59 UTC (rev 20748)
+++ trunk/packages/genometools/trunk/debian/patches/series 2015-12-12 19:16:41 UTC (rev 20749)
@@ -1,3 +1,4 @@
+remove_png_timestamps
adding_soname
libbam-fix
remove-gitignores
Modified: trunk/packages/genometools/trunk/debian/patches/sort-inputs
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/sort-inputs 2015-12-12 19:15:59 UTC (rev 20748)
+++ trunk/packages/genometools/trunk/debian/patches/sort-inputs 2015-12-12 19:16:41 UTC (rev 20749)
@@ -28,7 +28,7 @@
obj/public_symbols.lst: $(API_HEADERS) $(LIBGENOMETOOLS_SRC)
@echo '[gathering public API symbols to $@]'
-@@ -995,8 +995,8 @@
+@@ -999,8 +999,8 @@
ABTOOLS=${shell grep -l Blaufelder src/tools/*.c}
ALLSPLINT=${addprefix obj/,${notdir ${subst .c,.splint,\
@@ -39,3 +39,40 @@
${SKTOOLS} ${SKCORE} ${SKEXT} \
${DWTOOLS} ${DWCORE} ${DWEXT} \
${GGTOOLS} ${GGCORE} ${GGEXT} \
+--- a/gtscripts/gtdoc.lua
++++ b/gtscripts/gtdoc.lua
+@@ -104,6 +104,25 @@
+ end
+ end
+
++local function iter (a, i) -- taken from PiL, page 59
++ i = i + 1
++ local v = a[i]
++ if v then
++ return i, v
++ end
++end
++
++function sorted_dir(dir)
++ local entries = {}
++ local i = 0
++ for name in lfs.dir(dir) do
++ i = i + 1
++ entries[i] = name
++ end
++ table.sort(entries)
++ return iter, entries, 0
++end
++
+ local export = nil
+ local is_lua = nil
+
+@@ -127,7 +146,7 @@
+ for _, v in ipairs(export) do
+ local filename = gt_home .. "/" .. v
+ if is_dir(filename) then
+- for f in lfs.dir(filename) do
++ for _, f in sorted_dir(filename) do
+ local filename = filename .. "/" .. f
+ process_file(filename, be_verbose, is_lua)
+ end
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