.travis.yml

@@ -42,13 +42,13 @@ matrix:
       env: opt=no cairo=no
     - os: osx
       compiler: gcc
-      env: default=yes
+      env: default=yes PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig"
     - os: osx
       compiler: gcc
-      env: assert=no
+      env: assert=no PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig"
     - os: osx
       compiler: gcc
-      env: amalgamation=yes
+      env: amalgamation=yes PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig"
     - os: linux
       compiler: gcc
       env: opt=no cairo=no

CHANGELOG

+changes in version 1.6.0 (2020-01-06)
+
+- improve error handling in some tools
+- C API has been extended significantly
+
+
 changes in version 1.5.10 (2017-08-04)
 
 - bugfixes and cleanups

CONTRIBUTORS

@@ -11,5 +11,5 @@ gordon@gremme.org I left someone out or missed something.
 - Brent Pedersen (python bindings, patches)
 - Christin Schaerfer (AnnotationSketch, sketch tool)
 - David Schmitz-Huebsch (mgth/ subdirectory, mgth tool)
-- Dirk Willrodt (genomediff tool, SAM/BAM, patches)
+- Dirk Willrodt (genomediff, condenseq tool, SAM/BAM, wavelet tree, patches)
 - Daniel Standage (GtSetSourceVisitor, GtFeatureInStream, python bindings, patches)

INSTALL

@@ -101,8 +101,31 @@ preferred option.
 Use the 'useshared=yes' make option to ignore the embedded code copies in the
 GenomeTools source distribution and to use the system-wide versions. The following
 libraries (and their development headers) are required to be present:
-zlib, bzlib2, liblua5.1, lua-filesystem, lua-lpeg, lua-md5, libexpat, libtre,
-libcairo + libpango (only unless 'cairo=no' is used), libsqlite3 and libbam.
+
+ - zlib (https://zlib.net/)
+   Debian/Ubuntu: zlib1g-dev
+ - bzlib2 (https://www.sourceware.org/bzip2/)
+   Debian/Ubuntu: libbz2-dev
+ - liblua5.1 (https://www.lua.org/)
+   Debian/Ubuntu: liblua5.1-0-dev
+ - lua-filesystem (https://keplerproject.github.io/luafilesystem/)
+   Debian/Ubuntu: lua-filesystem-dev
+ - lua-lpeg (http://www.inf.puc-rio.br/~roberto/lpeg/)
+   Debian/Ubuntu: lua-lpeg-dev
+ - lua-md5 (https://keplerproject.github.io/md5/)
+   Debian/Ubuntu: lua-md5-dev
+ - libexpat (https://github.com/libexpat/libexpat)
+   Debian/Ubuntu: libexpat1-dev
+ - libtre (https://github.com/laurikari/tre/)
+   Debian/Ubuntu: libtre-dev
+ - libcairo (only unless 'cairo=no' is used) (https://cairographics.org/)
+   Debian/Ubuntu: libcairo2-dev
+ - libpango (only unless 'cairo=no' is used) (https://www.pango.org/)
+   Debian/Ubuntu: libpango1.0-dev
+ - libsqlite3 (https://www.sqlite.org/)
+   Debian/Ubuntu: libsqlite3-dev
+ - libbam (http://www.htslib.org/)
+   Debian/Ubuntu: libbam-dev
 
 
 Testing GenomeTools (optional)

Makefile

@@ -400,7 +400,6 @@ LIBGENOMETOOLS_DIRS:= src/core \
                       src/extended \
                       src/gtlua \
                       src/match \
-                      src/gth \
                       src/ltr \
                       src/mgth
 
@@ -495,6 +494,7 @@ ifeq ($(amalgamation),yes)
   LIBGENOMETOOLS_PRESRC:=$(filter-out $(SQLITE3_SRC),\
                          $(LIBGENOMETOOLS_PRESRC))
   LIBGENOMETOOLS_SRC:=obj/amalgamation.c
+  GT_CFLAGS+=-Wno-strict-overflow
 else
   LIBGENOMETOOLS_SRC:=$(LIBGENOMETOOLS_PRESRC)
 endif

VERSION

-1.5.10
+1.6.0

debian/changelog

+genometools (1.6.0+ds-1) unstable; urgency=medium
+
+  * New upstream release.
+  * Use debhelper-compat.
+
+ -- Sascha Steinbiss <satta@debian.org>  Mon, 06 Jan 2020 12:39:45 +0100
+
 genometools (1.5.10+ds-5) unstable; urgency=medium
 
   * Source upload to enable transition to testing.

debian/compat

-12

debian/control

@@ -5,6 +5,7 @@ Uploaders: Sascha Steinbiss <satta@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12),
+               debhelper-compat (= 12),
                dh-python,
                liblua5.1-0-dev,
                lua-md5-dev,

doc/devguide/devguide.tex

@@ -172,8 +172,8 @@ void gt_str_delete(GtStr *s)
 Our string class implementation so far looks like this
 
 \begin{lstlisting}
-#include "core/ma.h"
-#include "core/str.h"
+#include "core/ma_api.h"
+#include "core/str_api.h"
 
 struct GtStr {
   char *cstr;           /* the actual string (always '\0' terminated) */
@@ -315,7 +315,7 @@ function pointers given in the \keyword{GtExampleClass} object:
 
 \begin{lstlisting}
 #include "example_rep.h"       /* we need access to the class struct */
-#include "core/ma.h"           /* we need to allocate memory */
+#include "core/ma_api.h"           /* we need to allocate memory */
 
 GtExample* gt_example_create(const GtExampleClass *ec)
 {
@@ -1534,7 +1534,7 @@ int  (*UnitTestFunc)(GtError *err);
 
 They must return 0 if the test was successful and -1 if the test has failed.
 The \keyword{gt_ensure} helper macro makes writing unit tests easier. To use it,
-\keyword{#include} the file \keyword{core/ensure.h}. Then write your unit test:
+\keyword{#include} the file \keyword{core/ensure_api.h}. Then write your unit test:
 
 \begin{lstlisting}
 int gt_class_unit_test(GtError *err) /* must be called 'err'! */

gtdata/obo_files/README

 Source of the files:
 
-so.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo
-so-xp.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo
-sofa.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/subsets/SOFA.obo
+so.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/releases/so-xp.owl/so-xp-simple.obo
+so-xp.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/releases/so-xp.owl/so-xp.obo
+sofa.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/releases/so-xp.owl/subsets/SOFA.obo
 
-Current HEAD is 3a1b6bd850cff63ffac60ff3452dc01d319c793c
+Current HEAD is 6f8dfd4aebd4427baad07535b6250f4622b1b075

scripts/code_templates.rb

@@ -67,7 +67,7 @@ END_HWRAPPER
 
 $gt_class_c = <<-END_GT_CLASS_C
 
-#include "core/ma.h"
+#include "core/ma_api.h"
 
 struct <%=klass%>
 {
@@ -276,7 +276,7 @@ $interface_file = <<-INTERFACE_CODE
 
 #include "core/assert_api.h"
 #include "core/class_alloc.h"
-#include "core/ma.h"
+#include "core/ma_api.h"
 #include "core/unused_api.h"
 
 <%=create_func%>

scripts/gen-esa-bottomup.rb

@@ -450,7 +450,7 @@ print <<END_OF_FILE
 */
 
 #include <limits.h>
-#include "core/ma.h"
+#include "core/ma_api.h"
 #include "esa-seqread.h"
 #{seqnumrelpos_include(options)}
 END_OF_FILE

scripts/gen-intsets.rb

@@ -57,10 +57,10 @@ IMPL = <<-IMPL
 #include <limits.h>
 
 #include "core/assert_api.h"
-#include "core/divmodmul.h"
-#include "core/ensure.h"
+#include "core/divmodmul_api.h"
+#include "core/ensure_api.h"
 #include "core/intbits.h"
-#include "core/ma.h"
+#include "core/ma_api.h"
 #include "core/mathsupport.h"
 #include "core/unused_api.h"
 #include "extended/intset_<%=bits%>.h"

scripts/travis_installdeps.sh

@@ -3,11 +3,14 @@
 echo $TRAVIS_OS_NAME
 if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
   sudo apt-get update -q
+  sudo apt-get install libpango1.0-dev libcairo2-dev
   sudo apt-get install ncbi-blast+ gcc-multilib -y
   sudo apt-get install binutils-mingw-w64-i686 gcc-mingw-w64-i686 -y
   sudo apt-get install binutils-mingw-w64-x86-64 gcc-mingw-w64-x86-64 -y
 else
   brew update
-  brew install pango cairo
-  brew install homebrew/science/blast
+  brew install pkg-config
+  brew install pango cairo libffi
+  brew unlink proj
+  brew install blast --force
 fi

src/annotationsketch/block.c

@@ -22,9 +22,9 @@
 #include "annotationsketch/element.h"
 #include "core/array.h"
 #include "core/cstr_api.h"
-#include "core/ensure.h"
+#include "core/ensure_api.h"
 #include "core/log.h"
-#include "core/ma.h"
+#include "core/ma_api.h"
 #include "core/mathsupport.h"
 #include "core/undef_api.h"
 #include "core/unused_api.h"

src/annotationsketch/block.h

@@ -22,7 +22,7 @@
 #include "annotationsketch/block_api.h"
 #include "annotationsketch/canvas.h"
 #include "annotationsketch/style.h"
-#include "core/error.h"
+#include "core/error_api.h"
 
 void        gt_block_insert_element(GtBlock*, GtFeatureNode *node);
 void        gt_block_set_range(GtBlock*, GtRange r);