[med-svn] [Git][med-team/prank][master] 3 commits: New homepage

[Charles Plessy (@plessy)]

Charles Plessy pushed to branch master at Debian Med / prank


Commits:
d1496ebc by Charles Plessy at 2025-09-05T11:11:23+09:00
New homepage

- - - - -
0b93bee4 by Charles Plessy at 2025-09-05T11:15:21+09:00
prank (170703-1) unstable; urgency=medium

- - - - -
27af0b3d by Charles Plessy at 2025-09-05T11:16:19+09:00
Finaly, this file is added by patch.

- - - - -


3 changed files:

- − VERSION_HISTORY
- debian/changelog
- debian/control


Changes:

=====================================
VERSION_HISTORY deleted
=====================================
@@ -1,135 +0,0 @@
-v.170703
-Many changes not previously uploaded to GitHub, for example:
-- guide tree inference with FastTree 
-- ancestral states with RAxML
-- possible re-estimation of branch lengths
- 
-
-v.170427
-Changes by Nikolai Hecker
-- make the temp files thread safe
-- fix a compile issue with GCC 6.2.0
-- reduce the information written to stdout; disable with "-verbose"
-
-
-v.150803
-- force linear order of alignment anchors
-- convert multifurcating trees to bifurcating ones
-- finish despite BppAncestor failing
-
-
-v.140603
-- now avoids crashes due to weird sequence names
-- now (codon) ancestral reconstructio also for translated alignments
-- new option '-njgaps' to consider gaps as mismatches for NJ distances
-
-
-v.140110
-- a fix for the external tool paths
-
-
-v.131211
-- search order for external tools changed: use own one first
-- '-nobbpa' to run without BppAncestors (even when available)
-- a fix for rare crashes due to overly long branch lengths
-
-
-v.131119
-- ancestor inference for translated alignments of DNA sequences
-- new option '-treeonly'
-
-
-v.130820
-- disabled copmutation of alignment score for the guide tree alignment
-- more information about iteration with a user-provided tree
-- workaround for a BppAncestor bug causing incomplete last codon
-- path to other binaries no more affected by renaming of the program file
-
-
-v.130708
-- Significant bug fixes -- update *strongly* recommended:
- * option -F was mistakenly turned off by the new iterative approach
- * without option -F, ancestor reconstruction (and scoring) were incorrect
-
-
-v.130410
-- More information about optimization score and fix for last alignment
-- Minor fixes on alignment conversion and use of external models
-
-
-v.130129
-- Introduced alignment score and automatic iteration to maximise the score
-- Changed interface for the analysis input and output
-- New output: inferred evolutionary events per branch
-
-
-v.121218
-- More detailed information about unmatching names. New option "-prunedata".
-
-
-v.121212
-- Support for some NHX tags.
-
-
-v.121210
-- Fixed underflow errors affecting ancestral reconstruction of large
-  alignments.
-
-
-v.121018
-- Ancestral sequences can differently indicate insertions and deletions.
-- Can update an alignment, recomputing nodes with tag "[&&NHX:XN=realign]"
-
-
-v.121002
-- Alignment merge now accepts trees such as "(t1:#.#,t2:#.#);".
-  Provided with "-t=filename" or "-tree=tree-string".
-
-
-v.120827
-- All files now under the GPL licence.
-
-
-v.120814
-- Can now also merge "alignments" of one sequence
-- New option '-mergedist=#' to define the distance for two alignments
-
-
-v.120717
-- All input data now converted to upper-case.
-
-
-v.120716
-- Fixed the translated alignment (been broken in recent clean up)
-- Fixed the output order of ancestral sequences
-
-
-v.120712
-- For codon alignment, MAFFT guide tree now with protein sequences
-  (fixes several issues with codon alignment)
-
-
-v.120626
-- Guide tree estimation from a MAFFT alignment
-- Merge of two pre-defined alignments
-- Support for Exonerate and MAFFT on Windows
-- Clean up of some code
-
-
-v.111130
-- Exonerate anchoring now also for guidetree computation. Experimental!
-
-
-v.111129
-- Allow guide trees with no branch lengths. Default branch length is 0.1;
-  use -fixedbranches=# to change.
-- Removed the dependency to boost libraries.
-
-
-v.111013
-- First update in Google Code
-- Alignment speed ups with Exonerate anchoring.
-
-
-v.101018
-- Last version before migration to Google Code


=====================================
debian/changelog
=====================================
@@ -1,12 +1,15 @@
-prank (0.0.170427+dfsg-4) UNRELEASED; urgency=medium
+prank (170703-1) unstable; urgency=medium
 
   * Team upload.
-  * Packaging update
+  * New upstream release.
   * Standards-Version: 4.7.2 (routine-update)
   * debputy lint --auto-fix (routine-update)
   * watch file standard 4 (routine-update)
+  * Update FSF contact address in debian/copyright
+  * Refresh Makefile patches and merge them.
+  * New homepage
 
- -- Charles Plessy <plessy at debian.org>  Fri, 05 Sep 2025 09:57:21 +0900
+ -- Charles Plessy <plessy at debian.org>  Fri, 05 Sep 2025 11:14:08 +0900
 
 prank (0.0.170427+dfsg-3) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13)
 Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/prank
 Vcs-Git: https://salsa.debian.org/med-team/prank.git
-Homepage: http://wasabiapp.org/software/prank/
+Homepage: https://ariloytynoja.github.io/prank-msa/
 Rules-Requires-Root: no
 
 Package: prank



View it on GitLab: https://salsa.debian.org/med-team/prank/-/compare/49ce423639553a08a0a3275e7d558b8c9def1b11...27af0b3d8184d75760824ad4cede5f88312cb9fd

-- 
View it on GitLab: https://salsa.debian.org/med-team/prank/-/compare/49ce423639553a08a0a3275e7d558b8c9def1b11...27af0b3d8184d75760824ad4cede5f88312cb9fd
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