[med-svn] [Git][med-team/phast][master] 7 commits: New upstream version 1.8+dfsg

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / phast


Commits:
5f831c3b by Étienne Mollier at 2025-11-15T10:25:24+01:00
New upstream version 1.8+dfsg
- - - - -
d3625b4f by Étienne Mollier at 2025-11-15T10:25:28+01:00
Update upstream source from tag 'upstream/1.8+dfsg'

Update to upstream version '1.8+dfsg'
with Debian dir 2a7066a02d3d8cd88c551627ebac2f9b911aef6d
- - - - -
bd043b1d by Étienne Mollier at 2025-11-15T10:28:38+01:00
d/control: declare compliance to standards version 4.7.2.

- - - - -
1dc6f698 by Étienne Mollier at 2025-11-15T10:28:57+01:00
d/control: drop redundant Rules-Requires-Root: no.

- - - - -
f3d45f9b by Étienne Mollier at 2025-11-15T10:30:36+01:00
d/rules: slight readability improvements.

- - - - -
16cf0a64 by Étienne Mollier at 2025-11-15T10:32:16+01:00
d/watch convert to v5 Github template.

- - - - -
079e575f by Étienne Mollier at 2025-11-15T10:32:44+01:00
d/changelog: ready for upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/rules
- debian/watch
- src/lib/phylo/phast_trees.c


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+phast (1.8+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 1.8+dfsg
+  * d/control: declare compliance to standards version 4.7.2.
+  * d/control: drop redundant Rules-Requires-Root: no.
+  * d/rules: slight readability improvements.
+  * d/watch convert to v5 Github template.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 15 Nov 2025 10:32:38 +0100
+
 phast (1.7+dfsg-3) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -11,11 +11,10 @@ Build-Depends: debhelper-compat (= 13),
                libtmglib-dev,
                libpcre2-dev,
                help2man
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/phast
 Vcs-Git: https://salsa.debian.org/med-team/phast.git
 Homepage: http://compgen.cshl.edu/phast/
-Rules-Requires-Root: no
 
 Package: phast
 Architecture: any


=====================================
debian/rules
=====================================
@@ -7,13 +7,19 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 override_dh_auto_clean:
 	dh_auto_clean
-	cd src && $(MAKE) clean
+	cd src \
+	&& $(MAKE) clean
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	cd test && PATH=$(CURDIR)/bin:$(PATH) $(MAKE) msa_view
+	cd test \
+	&& PATH=$(CURDIR)/bin:$(PATH) \
+		$(MAKE) msa_view
 endif
 
 override_dh_installexamples:
 	dh_installexamples
-	find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \;
+	find debian/*/usr/share/doc/*/examples \
+		-type f \
+		-size +1k \
+		-exec xz \{\} \;


=====================================
debian/watch
=====================================
@@ -1,4 +1,9 @@
-version=4
+Version: 5
 
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-   https://github.com/CshlSiepelLab/phast/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+Template: Github
+Owner: CshlSiepelLab
+Project: phast
+Repack: yes
+Repacksuffix: +dfsg
+Dversionmangle: auto
+Compression: xz


=====================================
src/lib/phylo/phast_trees.c
=====================================
@@ -36,6 +36,7 @@ static int idcounter = 0;
 /* bottom-right y */
 #define BR_Y 700
 
+#define THRESHOLD_BRANCH_LENGTH 1e-8
 
 /** Parse a tree from a file in Newick (New Hampshire) format */
 TreeNode *tr_new_from_file(FILE *f) {
@@ -82,6 +83,9 @@ TreeNode *tr_new_from_string(const char *treestr) {
           die("ERROR: Can't parse distance in tree (\"%s\").\n",
               diststr->chars);
 	in_distance = FALSE;
+        if(node->dparent < THRESHOLD_BRANCH_LENGTH){
+          node->dparent = 0;
+        }      
       }
     }
 



View it on GitLab: https://salsa.debian.org/med-team/phast/-/compare/051b6abb8f2eb6c36d7a8c9379161f96b7b24244...079e575f928f8af7221007770535e1ad62a2fcab

-- 
View it on GitLab: https://salsa.debian.org/med-team/phast/-/compare/051b6abb8f2eb6c36d7a8c9379161f96b7b24244...079e575f928f8af7221007770535e1ad62a2fcab
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