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Changes: more details and philosophy are on HACKING and README
2018-10-03
Carnë Draug
Ch
a
nges:
m
ore d
e
tails and philos
o
p
hy are on HACKING
.
.
.
commit
|
commitdiff
|
tree
2018-10-03
C
arnë Drau
g
Change
s
: more detaile
d
c
o
mp
l
ete li
s
t o
f
modules/de
p
e
n
den
c
ies
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
C
a
r
në Draug
lib/BioPerl
.
pm: start c
o
nversion o
f
POD t
o
m
a
ke us
e
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
b
i
n/bp_
b
iofetc
h
_g
e
nbank_proxy: move to Bio-DB-NC
B
IH
e
lpe
r
commit
|
commitdiff
|
tree
2018-10-01
C
a
rnë
Draug
Bi
o
::DB::Swi
s
sProt:
m
o
v
e to its ow
n
distributio
n
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
Bio::DB:
:
BioFetch: move to i
t
s
o
w
n
d
i
s
t
ribution
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
A
utomatic handling
of VERSION in all m
o
dules (issue
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
t/S
e
qFeature/Generic
.
t:
fix failing tests (f
i
x
u
p
f
d
e603f22aa)
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
bi
n
/
bp_
f
etch: move require of optio
n
al
m
odules
w
h
ere
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
Bio::Map
:
:*
and
B
io::M
a
pIO::
*
: move
into thei
r
o
w
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
Remove
m
a
nipulat
i
on of @INC and use
of lib -
requ
i
re
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
arnë Dr
a
ug
dist
.
i
ni:
mak
e
Win
3
2
a dependency for Window
s
only
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
arnë Draug
Bio::Se
q
IO::agave
:
m
o
ve to
its own
distribu
t
io
n
commit
|
commitdiff
|
tree
2018-09-29
Carnë Dr
a
ug
B
io:
:
SeqIO::chadoxml (and
f
lybase_chadoxml): move t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
maint: list Data::Stag::XMLWriter as dro
p
ped
dependency
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
Bio::Seq
I
O::chaosxml (a
n
d chaos
)
: move
to their
own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
C
arnë D
r
aug
Bio
:
:
SeqIO::strider:
move into i
t
s own distribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Dra
u
g
Bio::Tools::Protparam: move to its own distrib
u
ti
o
n
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
m
aint: u
p
date
and clean removed modules and
de
p
endenci
e
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
C
a
r
në
Dr
a
ug
Bio
:
:DB::SeqVersion: m
o
ve
i
nto its
o
wn di
s
tribu
t
ion
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Draug
Bio:
:
Tools::
S
iRNA and relate
d
moved to s
e
parate distribution
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Draug
B
io::Tools::Analys
i
s
:
:
Protein: move
modu
l
es i
n
to their
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Drau
g
B
io
:
:Tools::Analysis::P
r
otein::Sc
a
ns
i
te: move to separat
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë Draug
B
i
o
:
:To
o
ls::Analysis::Protein:ELM: move
t
o
s
eparate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Drau
g
Bio::Tools::Analysis
:
:DNA::ESEfinder
:
move to
s
eparate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio:
:
DB::RefS
e
q, Bi
o
::
D
B
:
:
EM
B
L, and subclasses of B
i
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
D
rau
g
Bio::Taxonomy: move d
e
precate
d
namespace to
its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dr
a
u
g
l
ib/BioPerl
.
pm: convert li
n
e-endi
n
g dos2
u
nix
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Dr
a
ug
doc
:
update HA
C
KING instruction
s
with
dzil instruction
s
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
raug
t/*: remove
"use
lib '
.
'"
and t/lib/Err
o
r
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio::DB:
:
CUTG: move in
t
o
its
o
wn
d
is
t
ribution
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
r
a
u
g
Bio::DB::Taxo
n
omy::sqli
t
e: move into its own distribution
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
B
io::DB::GFF move into its own namespac
e
(
except Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
C
a
rnë
Draug
Bio:
:
DB::Se
q
Feature::*
m
ove
namesp
a
c
e into its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
maint: upda
t
e chang
e
s fro
m
1f7b54a
2
81a8
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
raug
Bio::Vari
a
tion::* move na
m
espace in
t
o it
s
ow
n
dis
t
ribution
.
commit
|
commitdiff
|
tree
2018-09-24
Ca
r
në Dra
u
g
Remo
v
e Bio::SeqIO suppo
r
t
for abi, alf,
c
tf, exp
,
p
ln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
C
arnë Draug
Bio::Clu
s
ter and Bi
o
::Cluste
r
IO moved to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë
Draug
Bio::Phenotype::* move
w
hat's lef
t
o
f the n
a
mespac
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
maint: remove no
l
onger used test data files
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë D
r
aug
Bio:
:
Li
v
eSeq
:
:*
m
ove whole n
a
mespa
c
e to its own d
i
stribution
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
mai
n
t
: updat
e
gi
t
ignor
e
rules
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë Draug
m
aint: r
e
str
u
ctu
r
e
t
o
us
e
Dist::
Z
illa
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
t/AlignIO/AlignIO
.
t: fix number o
f
tes
t
s in plan (f
i
x
up
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë
D
rau
g
t/Ann
o
tati
o
n
/
Annota
t
i
o
n
.
t: remove tes
t
for Bio::SeqFeature
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
a
rnë Dra
u
g
Bio/Tools/R
u
n/Phylo/PhyloBa
s
e
.
pm
:
br
i
ng
b
as
e
clas
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
Bio
/
Tools/P
h
ylo/Gumby
.
pm: move
t
o its own distribution
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Dr
a
ug
DB/Seq
F
eature/Store/b
e
rkeley
d
b3
.
pm: fix errors so it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë Draug
Ad
j
ust tests
i
ndirec
t
ly
making use of Bio::Align
I
O
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
bp_
p
rocess_
w
o
r
mb
a
s
e: move program
t
o new Bio-
D
B-Ac
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
bp_n
e
ti
n
sta
l
l: r
e
move o
u
t of date program
commit
|
commitdiff
|
tree
2018-09-17
Carn
ë
Draug
Move mo
d
ules dependent on Bio:
:
Ext::Al
i
gn into
d
ef
u
nct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
aug
Bio::DB::Expressio
n
: m
o
ve t
o
de
f
unct bioperl-microar
r
ay
commit
|
commitdiff
|
tree
2018-09-16
Carnë
D
rau
g
mai
n
t: 6
4
4
permissio
n
s for
a
lmost all files
commit
|
commitdiff
|
tree
2018-09-16
Car
n
ë
Draug
main
t
:
s
et al
l
source code with utf
-
8 encoding
commit
|
commitdiff
|
tree
2018-09-16
C
a
r
në Draug
maint: remove m
a
intainer out of da
t
e fi
l
es
commit
|
commitdiff
|
tree
2018-09-16
Carnë Drau
g
i
d
e: r
e
m
ov
e
module t
e
mplates - no longer needed afte
r
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Car
n
ë Draug
ide/bioperl-mod
e
: into
it
s
own repository to b
e
developed
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
m
aint
:
r
emov
e
b
i
op
e
rl-mode r
e
l
e
a
se tarball
s
f
r
om vers
i
o
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Dr
a
ug
Bio::Index::Abstr
a
ct-
>
_type_a
n
d_version:
ch
e
ck type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t/L
o
c
a
l
D
B/I
n
d
ex/BlastTable
.
t: use temp
d
ir to avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë D
r
aug
t
/
LocalDB/Index
/
Blast
.
t: create
t
est
t
empfiles within
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
m
a
int:
r
emove unused test data files
commit
|
commitdiff
|
tree
2018-09-14
Carnë
D
raug
Remove
A
l
i
g
nIO
and Inde
x
s
t
ockh
o
lm modul
e
s to new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Carnë
Draug
B
io::DB
:
:
U
niversal:
mov
e
into it
s
own distribution
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
maint
:
si
m
pl
i
fy R
E
ADME to c
o
ver simple install instruction
s
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dr
a
u
g
Brin
g
base
clas
s
es
from
B
i
oPe
r
l-
r
u
n
bac
k
to
BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Car
n
ë Draug
R
e
mov
e
use of
B
io::Perl which
ha
s
b
een moved to
B
i
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë D
r
a
ug
Bio::DB::MeSH move to
its own distributio
n
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Move HMMER related
m
odules, t
e
sts, and prog
r
ams t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
C
a
rnë
Draug
Bio::DB:
:
TFBS namespace has be
e
n moved to its own distributi
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
C
arn
ë
Drau
g
Bio
:
:DB::HIV a
n
d related modules a
n
d scripts moved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Align::
G
raphics: move into its own distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Dr
a
ug
Bi
o
:
:
T
o
ols::Run::Remot
e
B
l
a
st: move into a
ne
w
distrib
u
tion
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Perl: mov
e
it
s
own
d
istribution
named Bio-Procedur
a
l
commit
|
commitdiff
|
tree
2018-09-12
Car
n
ë Draug
Bio::MolEvol::CodonModel: move into
it separat
e
repo
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë
D
raug
Bio::SeqIO::en
t
rezgene: move to exi
s
ting Bio-AS
N
1-entrezgene
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në
D
raug
B
i
o/Restric
t
ion/*
:
move to a
n
ot
h
er repo
w
ith s
a
me name
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në Draug
Bio/
T
ools/
G
el
.
pm: move to
a
nothe
r
repo
with
same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/SeqEvolution/*: move to another repo with s
a
me
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë
D
raug
Bio/Structur
e
/*: move to
a
nother repo
w
i
th same
n
ame
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Drau
g
t
/
da
t
a: re
m
o
v
e more test d
a
ta files which moved to
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/Assemb
l
y*: move to an
o
ther repo
w
it
h
sa
m
e
n
ame
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në Draug
Bio/PhyloNetwork*: move
to another rep
o
wi
t
h same nam
e
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
rnë Draug
B
i
o/Se
q
IO/excel
.
pm: move to another rep
o
wi
t
h same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carn
ë
Draug
Bio
/
TreeIO/svgg
r
aph
.
pm: m
o
ve
to another
r
epo w
i
th same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Ca
r
në Dr
a
ug
B
i
o/T
r
ee/Draw/C
l
ad
o
gram
.
pm: move to an
o
ther repo with
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carn
ë
Draug
Bi
o
/Draw/
P
i
c
t
o
gram
.
p
m
: move to anot
h
er
r
epo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Car
n
ë Draug
M
o
ve all modules in
t
erfacing to ACeDB
s
er
v
ers
t
o a
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Move
all
NeXML rel
a
ted m
o
dules a
n
d tests to a new
Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Dra
u
g
Remove some un
u
sed test data
f
i
l
e
s
.
commit
|
commitdiff
|
tree
2018-09-10
C
a
rnë Draug
Remove e
n
tire Bio
:
:PopGe
n
nam
e
space and related modul
e
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
C
arnë Draug
scripts/
t
r
ee/bp_blast2
t
ree
.
pl: mo
v
ed to bioperl-run
commit
|
commitdiff
|
tree
2018-09-07
C
a
r
n
ë
D
raug
deobfuscator: remove this who
l
e projec
t
commit
|
commitdiff
|
tree
2018-09-04
Carn
ë
Draug
Consistent s
h
e
b
ang
l
ine to
'+#!/u
s
r/bin/
p
erl'
commit
|
commitdiff
|
tree
2018-08-23
Carnë
D
rau
g
d
eob
f
uscator
s
cripts: use warnin
g
s pr
a
gma
instead of
.
.
.
commit
|
commitdiff
|
tree
2018-07-25
Carnë Draug
Bio::MolEvol::Cod
o
nModel: fix docum
e
ntation (issue
.
.
.
commit
|
commitdiff
|
tree
2017-09-13
Carnë D
r
aug
examples/align/clustalw
.
p
l
: remove file, now pa
r
t
of
.
.
.
commit
|
commitdiff
|
tree
2017-09-08
C
a
rnë Draug
Rem
o
val of B
i
o:
:
Tools:
:
Phylo::
P
AML
.
p
m
and relate
d
modul
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2017-08-31
Carnë Draug
Bio::
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