[med-svn] [Git][med-team/kallisto][master] 5 commits: Fix build with CMake 4 Closes: #1113067

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / kallisto


Commits:
72ff60fa by Andreas Tille at 2025-10-18T11:39:23+02:00
Fix build with CMake 4 Closes: #1113067

- - - - -
78baf707 by Andreas Tille at 2025-10-18T11:42:01+02:00
d/watch: version=5

- - - - -
ef7a91b9 by Andreas Tille at 2025-10-18T11:42:36+02:00
Standards-Version: 4.7.2 (routine-update)

- - - - -
f63744bf by Andreas Tille at 2025-10-18T11:45:19+02:00
Cleanup properly after build time test Closes: #1047324

- - - - -
096fd9a5 by Andreas Tille at 2025-10-18T11:54:34+02:00
Fix clean target

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/rules
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -2,12 +2,16 @@ kallisto (0.51.1+dfsg-1) UNRELEASED; urgency=medium
 
   [ Andreas Tille ]
   * New upstream version
-  * Standards-Version: 4.7.0 (routine-update)
-  * d/watch: Fix download name
+  * Standards-Version: 4.7.2 (routine-update)
   * Add support for loongarch64 in d/control
     Closes: #1057131
   * Remove patch Check_busOptions.seq_length_before_accessing.patch that is
     missing from debian/patches/series.
+  * Fix build with CMake 4
+    Closes: #1113067
+  * d/watch: version=5
+  * Cleanup properly after build time test + fix clean target
+    Closes: #1047324
 
   [ Michael R. Crusoe ]
   * d/control: simplify architecture specifications by using provisions


=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
                libhdf5-dev,
                libhts-dev,
                snakemake <!nocheck>,
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/kallisto
 Vcs-Git: https://salsa.debian.org/med-team/kallisto.git
 Homepage: https://pachterlab.github.io/kallisto


=====================================
debian/rules
=====================================
@@ -6,14 +6,20 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
                      -DLINK=shared \
-                     -DBUILD_FUNCTESTING=1 -DUSE_BAM=1
+                     -DBUILD_FUNCTESTING=1 -DUSE_BAM=1 \
+                     -DCMAKE_POLICY_VERSION_MINIMUM=3.5
 
 %:
 	dh $@
 
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -rf ext/bifrost/build ext/bifrost/tmp ext/bifrost/src/bifrost-build ext/bifrost/src/bifrost-stamp
+
 override_dh_auto_configure:
 	dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
 
 execute_after_dh_auto_test:
 	cd test && PATH=$$(find ../obj-* -name src):$(PATH) HOME=$$(mktemp --directory) snakemake --cores 1
-	rm -rf test/.snakemake test/bus_out test/quant_out/run_info.json test/transcripts.kidx.gz
+	rm -rf test/.snakemake test/bus_out test/quant_out/run_info.json test/transcripts.kidx.gz \
+	        test/quant_out test/transcripts.kidx


=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
 
-opts="repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
-  https://github.com/pachterlab/kallisto/tags .*/v?@ANY_VERSION@@ARCHIVE_EXT@
+Template: Github
+Owner: pachterlab
+Project: kallisto
+Repack-Suffix: +dfsg
+Dversion-Mangle: auto



View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/84c31f65218466b3a00c0bff495fc1ed5e563935...096fd9a5934b5ee5f29ac66cd8b7c633d29ef97d

-- 
View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/84c31f65218466b3a00c0bff495fc1ed5e563935...096fd9a5934b5ee5f29ac66cd8b7c633d29ef97d
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