[med-svn] [Git][med-team/ncbi-tools6][master] 4 commits: Start ncbi-tools6 6.1.20170106+dfsg1-5, to reinstate cn3d split.

Sun Sep 8 03:45:35 BST 2019


Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6


Commits:
3075bc8a by Aaron M. Ucko at 2019-09-08T01:53:32Z
Start ncbi-tools6 6.1.20170106+dfsg1-5, to reinstate cn3d split.

- - - - -
b9b78291 by Aaron M. Ucko at 2019-09-08T01:56:07Z
Reinstate ncbi-cn3d split from 6.1.20170106-7.

* Split Cn3D(-3.0) out into a new ncbi-cn3d binary package; update
  debian/upstream/metadata accordingly.  (Originally done in
  6.1.20170106-7, but reverted in 6.1.20170106+dfsg1-1 to avoid holding
  up DFSG fixes.)

This reverts commit 4af64252c156f12c0b1bcc6b511a9fb20c6e7ca2 (except
where it comes to debian/changelog, always a special case).

- - - - -
527058fb by Aaron M. Ucko at 2019-09-08T02:06:30Z
Give ncbi-cn3d a binary-specific version, missed earlier.

- - - - -
9fbf7d8e by Aaron M. Ucko at 2019-09-08T02:08:09Z
Finalize ncbi-tools6 6.1.20170106+dfsg1-5 for experimental.

Upload to experimental to clear NEW.

- - - - -


10 changed files:

- debian/.gitignore
- debian/changelog
- debian/control
- + debian/ncbi-cn3d.install
- debian/ncbi-tools-x11.mime → debian/ncbi-cn3d.mime
- debian/ncbi-tools-x11.postinst → debian/ncbi-cn3d.postinst
- debian/ncbi-tools-x11.prerm → debian/ncbi-cn3d.prerm
- debian/ncbi-tools-x11.install
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/.gitignore
=====================================
@@ -7,6 +7,7 @@ libncbi6
 libvibrant6b
 lib*-dbg
 lib*-dev
+ncbi-cn3d
 ncbi-data
 ncbi-rrna-data
 ncbi-tools-bin


=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+ncbi-tools6 (6.1.20170106+dfsg1-5) experimental; urgency=medium
+
+  * Split Cn3D(-3.0) out into a new ncbi-cn3d binary package; update
+    debian/upstream/metadata accordingly.  (Originally done in
+    6.1.20170106-7, but reverted in 6.1.20170106+dfsg1-1 to avoid holding
+    up DFSG fixes.)
+  * Give ncbi-cn3d a binary-specific version, missed earlier.
+  * Upload to experimental to clear NEW.
+
+ -- Aaron M. Ucko <ucko at debian.org>  Sat, 07 Sep 2019 22:07:41 -0400
+
 ncbi-tools6 (6.1.20170106+dfsg1-4) unstable; urgency=medium
 
   * debian/NEWS: Rename from ncbi-data.NEWS to work around apt-listchanges


=====================================
debian/control
=====================================
@@ -82,6 +82,7 @@ Depends: libncbi6 (<< ${source:Upstream-Version}.1),
          ${shlibs:Depends}
 Suggests: libvibrant6b,
           ncbi-blast+,
+          ncbi-cn3d,
           ncbi-tools-x11
 Breaks: blast2 (<< 1:2.2.26.20160908)
 Replaces: blast2 (<< 1:2.2.26.20160908)
@@ -101,14 +102,33 @@ Depends: libncbi6 (<< ${source:Upstream-Version}.1),
          libncbi6 (>= ${source:Upstream-Version}),
          libvibrant6b (<< ${source:Upstream-Version}.1),
          libvibrant6b (>= ${source:Upstream-Version}),
+         ncbi-cn3d,
          ${misc:Depends},
          ${shlibs:Depends}
 Suggests: ncbi-tools-bin
 Description: NCBI libraries for biology applications (X-based utilities)
  This package includes some X-based utilities distributed with the
- NCBI C SDK: Cn3D, Network Entrez, Sequin, ddv, and udv.  These
- programs are not part of ncbi-tools-bin because they depend on
- several additional library packages.
+ NCBI C SDK: Network Entrez, Sequin, ddv, and udv.  These programs
+ are not part of ncbi-tools-bin because they depend on several
+ additional library packages.
+
+Package: ncbi-cn3d
+Architecture: any
+Multi-Arch: foreign
+Section: science
+Depends: libncbi6 (<< ${source:Upstream-Version}.1),
+         libncbi6 (>= ${source:Upstream-Version}),
+         libvibrant6b (<< ${source:Upstream-Version}.1),
+         libvibrant6b (>= ${source:Upstream-Version}),
+         ${misc:Depends},
+         ${shlibs:Depends}
+Suggests: ncbi-tools-bin,
+           ncbi-tools-x11
+Breaks: ncbi-tools-x11 (<< 6.1.20170106-7~)
+Replaces: ncbi-tools-x11 (<< 6.1.20170106-7~)
+Description: 3-dimensional viewer for biological molecules
+ Cn3D is a helper application for your web browser that allows you to
+ view 3-dimensional structures from NCBI's Entrez retrieval service.
 
 Package: libvibrant6b
 Architecture: any


=====================================
debian/ncbi-cn3d.install
=====================================
@@ -0,0 +1 @@
+usr/bin/Cn3D-3.0


=====================================
debian/ncbi-tools-x11.mime → debian/ncbi-cn3d.mime
=====================================


=====================================
debian/ncbi-tools-x11.postinst → debian/ncbi-cn3d.postinst
=====================================


=====================================
debian/ncbi-tools-x11.prerm → debian/ncbi-cn3d.prerm
=====================================


=====================================
debian/ncbi-tools-x11.install
=====================================
@@ -1,4 +1,3 @@
-usr/bin/Cn3D-3.0
 usr/bin/Psequin
 usr/bin/ddv
 usr/bin/entrez2


=====================================
debian/rules
=====================================
@@ -8,8 +8,14 @@ export NCBI_VERSION_DATE =$(word 3, $(subst ., ,$(NCBI_VERSION)))
 export NCBI_VERSION_DEBREL=$(word 2, $(subst -, ,$(NCBI_VERSION_FULL)))
 export NCBI_VERSION_SHLIB=$(NCBI_VERSION:%+dfsg1=%)
 
+export CN3D_VERSION=$(shell sed -ne 's/.*Version \([1-9][0-9.]*\).*/\1/p' \
+                      cn3d/cn3dwin.c | head -n1)
+export CN3D_VERSION_DATED=$(CN3D_VERSION).$(NCBI_VERSION_DATE)
+export CN3D_VERSION_FULL=$(CN3D_VERSION_DATED)-$(NCBI_VERSION_DEBREL)
+
 testversions:
 	env | fgrep NCBI_VERSION
+	env | fgrep CN3D_VERSION
 
 # Set these here, rather than using the csh hackage that passes for an
 # upstream build system.  Mostly taken from ../platform/{ppc,}linux.ncbi.mk.
@@ -187,6 +193,7 @@ override_dh_installchangelogs:
 
 override_dh_installmenu-arch:
 	chmod +x debian/makemenu
+	debian/makemenu debian/ncbi-cn3d.install
 	debian/makemenu debian/ncbi-tools-x11.install
 #	debian/makemenu -v debian/ncbi-tools-bin.install
 	dh_installmenu
@@ -206,6 +213,7 @@ override_dh_installman:
 	dh_link # otherwise runs too late to influence debian/installman
 	chmod +x debian/installman
 ifneq "" "$(filter ncbi-tools-bin, $(shell dh_listpackages))"
+	debian/installman ncbi-cn3d
 	debian/installman ncbi-tools-bin
 	debian/installman ncbi-tools-x11
 endif
@@ -217,6 +225,10 @@ endif
 override_dh_makeshlibs-arch:
 	dh_makeshlibs -V
 
+override_dh_gencontrol-arch:
+	dh_gencontrol  -pncbi-cn3d -- -v$(CN3D_VERSION_FULL)
+	dh_gencontrol  -Nncbi-cn3d
+
 override_dh_builddeb:
 	dh_builddeb -pncbi-rrna-data -- -Zxz -z7 -Sextreme
 	dh_builddeb -Nncbi-rrna-data


=====================================
debian/upstream/metadata
=====================================
@@ -13,14 +13,14 @@ Reference:
    PMID: 10838572
    URL: https://linkinghub.elsevier.com/retrieve/pii/S0968-0004(00)01561-9
    DOI: 10.1016/S0968-0004(00)01561-9
-   Debian-package: ncbi-tools-x11
+   Debian-package: ncbi-cn3d
 Registry:
  - Name: OMICtools
    Entry:  OMICS_05052
-   Debian-package: ncbi-tools-x11
+   Debian-package: ncbi-cn3d
  - Name: bio.tools
    Entry: cn3d
-   Debian-package: ncbi-tools-x11
+   Debian-package: ncbi-cn3d
  - Name: SciCrunch
    Entry: SCR_004861
-   Debian-package: ncbi-tools-x11
+   Debian-package: ncbi-cn3d



View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/compare/2e1c28eb1294c6a5d4f49fb66f25ad2d0a322262...9fbf7d8e8048a51cf11fdf35cee107715b8c812c

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View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/compare/2e1c28eb1294c6a5d4f49fb66f25ad2d0a322262...9fbf7d8e8048a51cf11fdf35cee107715b8c812c
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