Commit 877ab635 authored by Vincent Danjean's avatar Vincent Danjean
Browse files

Bump version, new release

parent 299a312b
Revision history for Perl extension Alphy::Utils.
Revision history for Altree Perl program
0.9.2 Tue Aug 2 19:19:05 2005
- New name : ALTree instead of ALPhy
Version v1.3.0
==============
0.01 Sun Jun 5 19:04:07 2005
- original version; created by h2xs 1.23 with options
-AX -n Alphy::Utils
Vincent Danjean (37):
Merge RepeatAssociationQuali and RepeatAssociationQuanti
Merge CleanCaseControl, CleanChi2 and CleanQuanti into CleanStats
Add gitignore for build files
Compute tree representation for efficient stat computation
Fix depth computation
Refactor code
Cleanup C headers
Cleanup headers
Cleanup name in XS functions
ClassicalChi2 as a C function with validation checks
Remove perl version of ClassicalChi2
Cleanup and comments in CUtils, add debugging facilities
move ALTree/Chi2.pm function into CUtils
Rewrite CalculChi2 in C
Rewrite Chi2 resampling in C
Use Chi2 resampling accelerator...
Run altree in tree for an example
cleanup Manifest
Fix "Use Chi2 resampling accelerator..."
memory managed outside inner functions
Parallel execution of Chi2 resampling
Fix some compilation warnings and protect debugging code
Do not compile with debug code by default
Fix link so that all functions are found, even if TamuAnova is not loaded
Get the R code source of the hypergeometric distribution
Add missing MT-aware random functions
Use internal mt19937ar_t per thread structure
Use the hypergeometric distribution
If ALTREE_PARALLEL is set to -1, all available CPU are used
Increase compiler warning level
Optimize rhyper.c for our use case
Remove dependencies on PDL and PDL::GSL::CDF
Cleanup version handling
Update make-release for git
Fix typo in function name
Fix linkage for CUtils
Bump version, new release
Version v1.2.1
==============
Vincent Danjean (5):
Update external perl modules
Bump version
Move to_rewrite.pm into ALTree namespace
Update MANIFEST
Ignore generated files in SVN
Version v1.2
==============
Vincent Danjean (2):
pour release 1.2
Pour release avec fix bug
Version v1.1.1
==============
Vincent Danjean (3):
changement adresse e-mail
MacOSX does not handle files with different case For example, altree and ALTree can not be both existing Now, altree is moved into progs/
Version v1.1.0
==============
Claire Bardel (6):
ajout de la fonctionalité: éliminer les haplotypes présents en moins de xxx examplaires
commit avant la release de la 1.1.0
re-commit pré-release
la dernière?
la vraie dernière?
correction meta-données (email, license)
Vincent Danjean (32):
check for .tar.gz before trying to create it
Stop with an error when input file contains no tree
prolongation -> no-prologation, à vérifier...
ajout de FillQuanti (pas finie) et modif de ReadCorrespondQuanti
doc
verification que j'ai bien commité tout
debuggage avec Vince
bug tableaux
fin de FillQuanti, ça marche
modif de la doc pour rapporteurs
parcoursQuanti et CalculAnova modifiées mais pas finies (non testées)
pb avec l'appel de tamuanova
bash completion
correction bash_completion
modif dans la lecture de l'arbre
suite adaptation en quanti: affichage marche, pas la permutation
Youhou! Ca tourne en quanto anova 1 facteur
Qualitatif: correction bugs, déplacement de code et suite du développement
ajout du quantitatif pour phase/paup dans altree-convert
ajout quanti dans altree-add-S
récupération de la distrib de pmin
un reste de cvs
Ajout de la possibilité de traiter plusieurs fichiers conjointement
ajout de nanova.pm
Correction de FillHeight Calcul de la matrice d'un arbre
correction de bug de la localisation du fait de la modif 9 fichiers
correction bug sur all_file foret, calcul des Vi pour tous fichiers
Version v1.0.1
==============
Vincent Danjean (9):
make-release to create a release
Correct make-release for META.yml
Check for already existing version earlier
modification du numero de version dans le MAKEFILE.PL
Version v1.0.0
==============
Vincent Danjean (77):
résolution du pb des _ dans les noms, plus de flexibilité dans les noms
On garde root
selection des arbres
selection des arbres (correction bugs)
paup exemples
phylip/paml exemples
bug mineur
debut reorg
run_altree
lecture refaite
restructuration Input
no CI
altree un peu mieux
option output-file
options
correction version
paup ignore le root supplémentaire inutile (comme phylip)
Deletetion of old Documentation/example_files/ Version 1.0.0
Release 1.0.0
Version v0.9.2
==============
Vincent Danjean (34):
Amélioration README Alphy tourne en localisation
Renommage chi2.pm en Alphy::Chi2.pm
change warn for warning
orrection du chemin e la bib cutils lgne 1880
modification in alphy-add-S
Addition of example files for case control data
prog avec pb ligne 570
plein de modifs partout pour adapter à phylip
modifs dans alphy-add-S: il prend les nb cas/controle dans correspond.txt maintenant
modifs dans alphy-add-S: opt-s est devenu opt-e
doc
version
fix tests
version
man alphy-add-S
début de man pour alphy-add-S et alphy-convert
file to ignore
modif du manuel
version 0d
Switching Alphy to ALTree
Version v0.01
==============
Vincent Danjean (8):
original version; created by h2xs 1.23 with options -AX -n Alphy::Utils
initial import
ajout du .bib
cvs2svn (1):
New repository initialized by cvs2svn.
.gitignore
ALTree/Base.pm
ALTree/Chi2.pm
ALTree/Foret.pm
......@@ -20,11 +21,23 @@ bash_completion
Changes
CUtils/c_sources/chisq.c
CUtils/c_sources/chisq.h
CUtils/c_sources/datatype.h
CUtils/c_sources/debug.h
CUtils/c_sources/double_permutation.c
CUtils/c_sources/double_permutation.h
CUtils/c_sources/fisher.c
CUtils/c_sources/fisher.h
CUtils/c_sources/Makefile.PL
CUtils/c_sources/mt19937ar.c
CUtils/c_sources/mt19937ar.h
CUtils/c_sources/myrand.c
CUtils/c_sources/myrand.h
CUtils/c_sources/resampling.c
CUtils/c_sources/resampling.h
CUtils/c_sources/rhyper.c
CUtils/c_sources/rhyper.h
CUtils/c_sources/stats.c
CUtils/c_sources/stats.h
CUtils/c_sources/z.c
CUtils/c_sources/z.h
CUtils/const-c.inc
......@@ -54,7 +67,6 @@ Documentation/manual.tex
Documentation/stage.bib
Makefile.PL
MANIFEST This list of files
META.yml
progs/altree
progs/altree-add-S
progs/altree-convert
......
......@@ -10,7 +10,7 @@ use Data::Dumper;
srand(654321);
use version; our $VERSION = qv(1.2.1);
use version; our $VERSION = qv(1.3.0);
# Positionner la variable PERL5LIB si besoin
......
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