[med-svn] [Git][med-team/raster3d][master] 10 commits: routine-update: New upstream version
Andreas Tille
gitlab at salsa.debian.org
Tue Sep 29 15:33:39 BST 2020
Andreas Tille pushed to branch master at Debian Med / raster3d
Commits:
3543c3d7 by Andreas Tille at 2020-09-29T12:44:22+02:00
routine-update: New upstream version
- - - - -
afa329d2 by Andreas Tille at 2020-09-29T12:44:23+02:00
New upstream version 3.0-6
- - - - -
2a05aa85 by Andreas Tille at 2020-09-29T12:44:33+02:00
Update upstream source from tag 'upstream/3.0-6'
Update to upstream version '3.0-6'
with Debian dir 6b1a029ece4deca8dad8d10b492f0ff2b98166bf
- - - - -
f148f239 by Andreas Tille at 2020-09-29T12:44:33+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
ddd12d2b by Andreas Tille at 2020-09-29T12:44:33+02:00
routine-update: debhelper-compat 13
- - - - -
6e8b04ad by Andreas Tille at 2020-09-29T15:50:10+02:00
Refresh patches
- - - - -
3f03c7ab by Andreas Tille at 2020-09-29T15:50:40+02:00
routine-update: Add salsa-ci file
- - - - -
971a1099 by Andreas Tille at 2020-09-29T15:50:40+02:00
routine-update: Rules-Requires-Root: no
- - - - -
1f42f0b7 by Andreas Tille at 2020-09-29T15:50:41+02:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
53c7aad2 by Andreas Tille at 2020-09-29T15:50:48+02:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
- - - - -
18 changed files:
- CHANGELOG
- Makefile
- Makefile.package
- README
- VERSION
- VERSION.incl
- debian/changelog
- − debian/compat
- debian/control
- debian/patches/Makefile.diff
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
- parameters.incl
- parse.f
- qinp.f
- render.f
- rods.f
Changes:
=====================================
CHANGELOG
=====================================
@@ -1,3 +1,5 @@
+12-Nov-2019 rods.f: gfortran 8.3 requires decimal point after floating 0
+12-Nov-2019 import into git
21-Jan-2019 Package 3.0-4
21-Jan-2019 suppress compiler warnings for unused variables
29-Mar-2014 Package (somewhat belatedly) 3.0-3
=====================================
Makefile
=====================================
@@ -53,13 +53,13 @@ linux:
@echo CC = gcc >> Makefile.incl
@echo CFLAGS = -g -Wall -Dgfortran >> Makefile.incl
@echo FC = gfortran >> Makefile.incl
- @echo FFLAGS = -g -w -O3 -Wtabs -ffixed-line-length-132 >> Makefile.incl
+ @echo FFLAGS = -g -w -O3 -Wno-tabs -ffixed-line-length-132 >> Makefile.incl
@echo RM = /bin/rm -f >> Makefile.incl
@echo OSDEFS = -DLINUX -DNETWORKBYTEORDER >> Makefile.incl
@echo include Makefile.package >> Makefile.incl
@echo >> Makefile.incl
@echo qinp.o: qinp.f >> Makefile.incl
- @echo " \$$(FC) -g -O0 -Wall -Wtabs -c -o qinp.o qinp.f" >> Makefile.incl
+ @echo " \$$(FC) -g -O0 -Wall -Wno-tabs -c -o qinp.o qinp.f" >> Makefile.incl
@echo >> Makefile.incl
linux-ifort:
=====================================
Makefile.package
=====================================
@@ -28,7 +28,7 @@ tar: ../$(TARFILE)
touch Makefile.incl
@echo making ../$(TARFILE)
cd `pwd`
- (cd ..; gtar -czvf $(TARFILE) Raster3D_$(VERSION)/.)
+ (cd ..; gtar --exclude-vcs --exclude-vcs-ignores -czvf $(TARFILE) Raster3D_$(VERSION)/.)
#
# Build an RPM package
=====================================
README
=====================================
@@ -1,15 +1,14 @@
-Most recent change: 21-Jan-2019
+Most recent change: 06-May-2020
-The file Raster3D_3.0-4.tar.gz contains the full source distribution for
+The file Raster3D_3.0-6.tar.gz contains the full source distribution for
version 3.0 of Raster3D.
See CHANGELOG for a history of changes to the package.
- Basically nothing has changed since verison 3.0-3 (2014) except that I
- tried to suppress some harmless compiler warnings.
+ Basically nothing has changed since verison 3.0-3 (2014) except for
+ minor tweaks to accommodate newer Fortran versions.
- Note: The programs from Raster3D version 3.0-3 are included in the
- CCP4 crystallography suite. You might find it easier to use that
- pre-built version.
+ Note: The programs from Raster3D are included in the CCP4 crystallography
+ suite. You might find it easier to use that pre-built version.
- In a nutshell, the installation procedure is:
@@ -24,9 +23,10 @@ version 3.0 of Raster3D.
7) (optional)
modify ImageMagick delegates file so that ImageMagick recognizes
*.r3d files by default. On my systems this file is in
- /usr/lib/ImageMagick-6.3.2/config/delegates.xml
+ /etc/ImageMagick-6/config/delegates.xml
Add the following line
- <delegate decode="r3d" command='"render" < "%i" > "%o"' />
+ <delegate decode="r3d" command=""render" < "%i" > "%o""/>
+
- Changes in Version 3.0
+ new code in rastep to support Skittles validation (introduced in 2.9)
=====================================
VERSION
=====================================
@@ -1 +1 @@
-VERSION = "3.0-4"
+VERSION = "3.0-6"
=====================================
VERSION.incl
=====================================
@@ -1,2 +1,2 @@
CHARACTER*8 VERSION
- PARAMETER (VERSION='V3.0.4 ')
+ PARAMETER (VERSION='V3.0.5 ')
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+raster3d (3.0-6-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Trim trailing whitespace.
+ * Remove obsolete field Name from debian/upstream/metadata (already present in
+ machine-readable debian/copyright).
+
+ -- Andreas Tille <tille at debian.org> Tue, 29 Sep 2020 12:44:22 +0200
+
raster3d (3.0-4-1) unstable; urgency=medium
* New upstream version
@@ -239,4 +252,3 @@ raster3d (2.7c-1) unstable; urgency=low
* Initial Release (Closes: #303941).
-- Nelson A. de Oliveira <naoliv at gmail.com> Fri, 25 Mar 2005 17:06:13 -0300
-
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -3,16 +3,17 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 13),
gfortran,
libgd-dev,
libjpeg-dev,
libpng-dev,
libtiff-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/raster3d
Vcs-Git: https://salsa.debian.org/med-team/raster3d.git
Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html
+Rules-Requires-Root: no
Package: raster3d
Architecture: any
=====================================
debian/patches/Makefile.diff
=====================================
@@ -12,8 +12,8 @@ Description: Several fixed in Makefile
- @echo CFLAGS = -g -Wall -Dgfortran >> Makefile.incl
+ @echo CFLAGS = -g -O2 -Wall -Dgfortran >> Makefile.incl
@echo FC = gfortran >> Makefile.incl
-- @echo FFLAGS = -g -w -O3 -Wtabs -ffixed-line-length-132 >> Makefile.incl
-+ @echo FFLAGS = -g -w -O2 -Wtabs -ffixed-line-length-132 >> Makefile.incl
+- @echo FFLAGS = -g -w -O3 -Wno-tabs -ffixed-line-length-132 >> Makefile.incl
++ @echo FFLAGS = -g -w -O2 -Wno-tabs -ffixed-line-length-132 >> Makefile.incl
@echo RM = /bin/rm -f >> Makefile.incl
@echo OSDEFS = -DLINUX -DNETWORKBYTEORDER >> Makefile.incl
@echo include Makefile.package >> Makefile.incl
=====================================
debian/rules
=====================================
@@ -34,4 +34,3 @@ override_dh_compress:
--exclude=.r3d \
--exclude=.mol \
--exclude=.pdf
-
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,3 @@
-Name: Raster3D
Reference:
- Article: MerrittBacon1997
Author: Merritt, E.A. and Bacon, D.J.
=====================================
parameters.incl
=====================================
@@ -60,7 +60,7 @@
* $$$$$$$$$$$$$$$$$ END OF LIMITS $$$$$$$$$$$$$$$$$$$$$$$
*
* Other possibly platform-dependent stuff
- REAL HUGE
+ REAL HUGE
PARAMETER (HUGE = 1.0e37)
* Slop is related to the accuracy (in pixels) to which we must predict
* shadow edges. Too low a value causes whole triangles to be spuriously
@@ -74,5 +74,5 @@
PARAMETER (EDGESLOP = 0.25)
* Ribbonslop is a kludge so that distortion due to perspective doesn't
* prevent us from identifying ribbon triangles
- REAL RIBBONSLOP
+ REAL RIBBONSLOP
PARAMETER (RIBBONSLOP = 0.001)
=====================================
parse.f
=====================================
@@ -115,8 +115,8 @@ c
else if (option(1:3).eq.'-bg') then
iarg = iarg + 1
call getarg( iarg, option )
- if (option(1:5).eq.'white') xbg = X'FFFFFF'
- if (option(1:5).eq.'black') xbg = X'000000'
+ if (option(1:5).eq.'white') xbg = Z'FFFFFF'
+ if (option(1:5).eq.'black') xbg = Z'000000'
if (option(1:1).eq.'#') then
read (option(2:7),'(1Z6)') xbg
if (verbose) then
=====================================
qinp.f
=====================================
@@ -49,7 +49,7 @@ CC
C
function qinp( buf, detail, shadow, sdtail )
* Use MODULE LISTS not COMMON /LISTS/ for dynamic allocation
- USE LISTS
+ USE LISTS
*
IMPLICIT NONE
logical qinp
@@ -58,10 +58,10 @@ C
logical shadow
*
real QQ(4,4), QP(4,4), QT(4,4)
- real xq, yq, zq, radlim, red, grn, blu
+ real xq, yq, zq, radlim, red, grn, blu
real xc, yc, zc, rc
real xr, yr, zr, xs, ys, zs, rs
- real pfac
+ real pfac
*
integer ix,iy,ixlo,ixhi,iylo,iyhi
c VOLATILE ix,iy,ixlo,ixhi,iylo,iyhi
@@ -284,4 +284,3 @@ CD write (noise,191) 'QP ',((QP(i,j),j=1,4),i=1,4)
*
return
end
-
=====================================
render.f
=====================================
@@ -968,9 +968,9 @@ C Header records and picture title
* Get background colour
READ (INPUT,*,ERR=104) BKGND
if (XBG.NE.0) then
- BKGND(3) = iand(XBG,X'00FF')
- BKGND(2) = iand(XBG,X'FF00')/256
- BKGND(1) = iand(XBG,X'FF0000')/65536
+ BKGND(3) = iand(XBG,Z'00FF')
+ BKGND(2) = iand(XBG,Z'FF00')/256
+ BKGND(1) = iand(XBG,Z'FF0000')/65536
BKGND(3) = BKGND(3) / 255.
BKGND(2) = BKGND(2) / 255.
BKGND(1) = BKGND(1) / 255.
=====================================
rods.f
=====================================
@@ -17,6 +17,8 @@
* -brad XX to set ball radius as fraction of Van der Waals radius
* EAM Jul 1999
* don't draw bonds across alternate chain locations
+* EAM Nov 2019
+* new gfortran requires a decimal point in floating constants
*
*------------------------------------------------------------------------------
INCLUDE 'VERSION.incl'
@@ -343,7 +345,7 @@ c
write(output,141)
1 RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL),
2 RGB(1,JCOL),RGB(2,JCOL),RGB(3,JCOL),
- 3 0, 0, 0
+ 3 0.0, 0.0, 0.0
ELSE
DO 136 K=1,3
136 CEN(K) = (SPAM(K,IATM)+SPAM(K,JATM))/2
View it on GitLab: https://salsa.debian.org/med-team/raster3d/-/compare/8600417a156b1f04adc7b45ad2653da371cef39b...53c7aad2987181429ffcb438a5b26fa20906c39e
--
View it on GitLab: https://salsa.debian.org/med-team/raster3d/-/compare/8600417a156b1f04adc7b45ad2653da371cef39b...53c7aad2987181429ffcb438a5b26fa20906c39e
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