[med-svn] [Git][med-team/hyphy][master] 5 commits: New upstream version 2.5.53+dfsg

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / hyphy


Commits:
5f91e593 by Étienne Mollier at 2023-08-26T10:15:19+02:00
New upstream version 2.5.53+dfsg
- - - - -
0d95fd8f by Étienne Mollier at 2023-08-26T10:15:19+02:00
routine-update: New upstream version

- - - - -
aa24e3e3 by Étienne Mollier at 2023-08-26T10:15:27+02:00
Update upstream source from tag 'upstream/2.5.53+dfsg'

Update to upstream version '2.5.53+dfsg'
with Debian dir 36668429322c244f14c659e220d4deef067eef7c
- - - - -
a203b351 by Étienne Mollier at 2023-08-26T11:00:11+02:00
d/{clean,rules}: fix building twice in a row.

This is done by cleaning temporary test data and build results on one
hand, and by fixing some national encoded files in their temporary
installation location instead of within upstream source code on the
other hand.

Closes: #1048874

- - - - -
7bd11d6a by Étienne Mollier at 2023-08-26T11:05:20+02:00
ready for upload to unstable.

- - - - -


5 changed files:

- CMakeLists.txt
- debian/changelog
- debian/clean
- debian/rules
- src/core/global_things.cpp


Changes:

=====================================
CMakeLists.txt
=====================================
@@ -16,6 +16,14 @@ option(NOSSE4 OFF)
 option(NONEON OFF)
 option(NOZLIB OFF)
 
+
+if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
+  set(NOAVX ON)
+  set(NOSSE4 ON)
+  set(NONEON ON)
+  set(NOZLIB ON)
+endif()
+
 #-------------------------------------------------------------------------------
 # SSE MACROS
 #-------------------------------------------------------------------------------


=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+hyphy (2.5.53+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 2.5.53+dfsg
+  * d/{clean,rules}: fix building twice in a row.
+    This is done by cleaning temporary test data and build results on one
+    hand, and by fixing some national encoded files in their temporary
+    installation location instead of within upstream source code on the
+    other hand. (Closes: #1048874)
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 26 Aug 2023 11:05:10 +0200
+
 hyphy (2.5.52+dfsg-1) unstable; urgency=medium
 
   * New upstream version 2.5.52+dfsg


=====================================
debian/clean
=====================================
@@ -1 +1,5 @@
 gmon.out
+HYPHYMP
+HYPHYMPI
+hyphy
+tests/hbltests/data/temp*


=====================================
debian/rules
=====================================
@@ -7,10 +7,12 @@ export LC_ALL=C.UTF-8
 
 include /usr/share/dpkg/default.mk
 
+DTMP := $(CURDIR)/debian/tmp
+
 # a few ISO-8859-1 files needing conversion to UTF-8
-ISOFILES  = res/TemplateBatchFiles/PARRIS.bf
-ISOFILES += res/TemplateBatchFiles/TemplateModels/MEC.mdl
-ISOFILES += res/TemplateBatchFiles/TemplateModels/models.lst
+ISOFILES  = $(DTMP)/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf
+ISOFILES += $(DTMP)/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl
+ISOFILES += $(DTMP)/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst
 
 %:
 	dh $@ --buildsystem=cmake
@@ -32,12 +34,6 @@ else
 endif
 
 override_dh_auto_build:
-	# convert a few ISO-8859-1 files to address national-encoding
-	set -e \
-	; for file in $(ISOFILES) \
-	; do    iconv -f ISO-8859-1 -t UTF-8 < $${file} > "$${file}.new" \
-	;	mv "$${file}.new" "$${file}" \
-	; done
 ifeq (amd64,$(DEB_HOST_ARCH))
 	dh_auto_build -- MP MPI
 	dh_auto_build --builddirectory obj-avx -- MP MPI
@@ -47,6 +43,12 @@ else
 endif
 
 override_dh_install-arch:
+	# convert a few ISO-8859-1 files to address national-encoding
+	set -e \
+	; for file in $(ISOFILES) \
+	; do    iconv -f ISO-8859-1 -t UTF-8 < "$${file}" > "$${file}.new" \
+	;       mv -v "$${file}.new" "$${file}" \
+	; done
 	dh_install -a
 	chrpath --delete obj-*/HYPHYMPI
 ifeq (amd64,$(DEB_HOST_ARCH))


=====================================
src/core/global_things.cpp
=====================================
@@ -122,7 +122,7 @@ namespace hy_global {
                      kErrorStringMatrixExportError    ("Export matrix called with a non-polynomial matrix argument"),
                      kErrorStringNullOperand          ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"),
                      kErrorNumerical                   ("To treat numerical errors as warnings, please specify \"ENV=TOLERATE_NUMERICAL_ERRORS=1;\" as the command line argument. This often resolves the issue, which is indicative of numerical instability."),
-                     kHyPhyVersion  = _String ("2.5.52"),
+                     kHyPhyVersion  = _String ("2.5.53"),
     
                     kNoneToken = "None",
                     kNullToken = "null",



View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/4c426b58fddee7b18660e9483c70c347ed4ad64b...7bd11d6a899dcebdd99a6e729db8bbeb01ee40fe

-- 
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/4c426b58fddee7b18660e9483c70c347ed4ad64b...7bd11d6a899dcebdd99a6e729db8bbeb01ee40fe
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