Andreas Tille pushed to branch master at Debian Med / terraphast
Commits:
ec5af772 by Andreas Tille at 2025-10-20T13:53:28+02:00
Fix build with CMake 4 Closes: #1113569
- - - - -
04aac0de by Andreas Tille at 2025-10-20T13:56:40+02:00
d/watch: version=5 (now based on release tag)
- - - - -
ac16efdb by Andreas Tille at 2025-10-20T13:56:51+02:00
New upstream version 0.1.0+dfsg
- - - - -
32c7ce13 by Andreas Tille at 2025-10-20T13:56:51+02:00
New upstream version
- - - - -
6bfc794f by Andreas Tille at 2025-10-20T13:56:52+02:00
Update upstream source from tag 'upstream/0.1.0+dfsg'
Update to upstream version '0.1.0+dfsg'
with Debian dir 608080874889fc9c0622a808992f9b8dba21ba6e
- - - - -
fd361d01 by Andreas Tille at 2025-10-20T13:56:52+02:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
a985874b by Andreas Tille at 2025-10-20T13:57:09+02:00
debputy lint --auto-fix (routine-update)
- - - - -
56bc7e44 by Andreas Tille at 2025-10-20T14:06:35+02:00
Provide test data as examples and do not require autopkgtest accessing internet
- - - - -
e4ac4706 by Andreas Tille at 2025-10-20T14:18:21+02:00
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/rules
- debian/terraphast.doc → debian/terraphast.docs
- − debian/tests/README.md
- debian/tests/control
- debian/tests/run-unit-test
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+terraphast (0.1.0+dfsg-1) unstable; urgency=medium
+
+ * Fix build with CMake 4
+ Closes: #1113569
+ * d/watch: version=5 (now based on release tag)
+ * New upstream version
+ * Standards-Version: 4.7.2 (routine-update)
+ * debputy lint --auto-fix (routine-update)
+ * Provide test data as examples and do not require autopkgtest
+ accessing internet
+
+ -- Andreas Tille <tille at debian.org> Mon, 20 Oct 2025 14:16:38 +0200
+
terraphast (0.0+git20200413.8af2e4c+dfsg-3) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,15 +1,17 @@
Source: terraphast
+Standards-Version: 4.7.2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 13),
- cmake,
- d-shlibs,
- dh-exec,
- catch,
- libgmp3-dev
-Standards-Version: 4.6.2
+Build-Depends:
+ debhelper-compat (= 13),
+ cmake,
+ d-shlibs,
+ dh-exec,
+ catch,
+ libgmp3-dev,
Vcs-Browser: https://salsa.debian.org/med-team/terraphast
Vcs-Git: https://salsa.debian.org/med-team/terraphast.git
Homepage: https://github.com/amkozlov/terraphast-one
@@ -18,9 +20,10 @@ Rules-Requires-Root: no
Package: terraphast
Architecture: any
Section: libs
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- libterraces0 (= ${binary:Version})
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ libterraces0 (= ${binary:Version}),
Description: enumerate terraces in phylogenetic tree space
Terraphast takes a .nkw file in Newick format and a genes/sites file,
which denotes whether (1) or not (0) gene i is present in species j.
@@ -32,8 +35,9 @@ Description: enumerate terraces in phylogenetic tree space
Package: libterraces0
Architecture: any
Section: libs
-Depends: ${shlibs:Depends},
- ${misc:Depends}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
Description: enumerate terraces in phylogenetic tree space (shared lib)
Terraphast takes a .nkw file in Newick format and a genes/sites file,
which denotes whether (1) or not (0) gene i is present in species j.
@@ -47,9 +51,10 @@ Description: enumerate terraces in phylogenetic tree space (shared lib)
Package: libterraces-dev
Architecture: any
Section: libdevel
-Depends: libterraces0 (= ${binary:Version}),
- ${shlibs:Depends},
- ${misc:Depends}
+Depends:
+ libterraces0 (= ${binary:Version}),
+ ${shlibs:Depends},
+ ${misc:Depends},
Description: enumerate terraces in phylogenetic tree space (development lib)
Terraphast takes a .nkw file in Newick format and a genes/sites file,
which denotes whether (1) or not (0) gene i is present in species j.
=====================================
debian/rules
=====================================
@@ -20,7 +20,8 @@ override_dh_auto_configure:
dh_auto_configure -- \
-DVERSION="$(VERSION)" \
-DSOVERSION="$(SOVERSION)" \
- -DTERRAPHAST_ARCH_NATIVE=OFF
+ -DTERRAPHAST_ARCH_NATIVE=OFF \
+ -DCMAKE_POLICY_VERSION_MINIMUM=3.5
override_dh_install:
mkdir -p debian/$(DEB_SOURCE)/usr/bin
=====================================
debian/terraphast.doc → debian/terraphast.docs
=====================================
=====================================
debian/tests/README.md deleted
=====================================
@@ -1,10 +0,0 @@
-## Notes on how this package can be tested.
-────────────────────────────────────────
-
-This package can be tested by running the provided test:
-
- `sh run-unit-test`
-
-in order to confirm its integrity.
-
-Data can be referenced [here](https://github.com/terraphast/terraphast/tree/master/terraphastI/data/data)
\ No newline at end of file
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: wget, terraphast
-Restrictions: needs-internet, allow-stderr
\ No newline at end of file
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -12,11 +12,10 @@ fi
cd $AUTOPKGTEST_TMP
# Get data
-wget https://raw.githubusercontent.com/terraphast/terraphast/master/terraphastI/data/data/Meusemann.nwk
-wget https://raw.githubusercontent.com/terraphast/terraphast/master/terraphastI/data/data/Meusemann.data
+cp -a /usr/share/doc/${pkg}/examples/* .
# Enumerate terraces in phylogenetic tree space
terraphast Meusemann.nwk Meusemann.data
# Remove data
-rm Meusemann.*
\ No newline at end of file
+rm Meusemann.*
=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
-opts="mode=git,pretty=0.0+git%cd.%h,repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
- https://github.com/amkozlov/terraphast-one.git HEAD
+Template: Github
+Owner: amkozlov
+Project: terraphast-one
+Repack-Suffix: +dfsg
+Dversion-Mangle: auto
View it on GitLab: https://salsa.debian.org/med-team/terraphast/-/compare/461f56ea01cddc9ea3be8494332f5b4da1d759fe...e4ac47062488f76c90341bd1749e137fbaf81047
--
View it on GitLab: https://salsa.debian.org/med-team/terraphast/-/compare/461f56ea01cddc9ea3be8494332f5b4da1d759fe...e4ac47062488f76c90341bd1749e137fbaf81047
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