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doc: fix typos on doc found by Debian's lintian
2019-02-08
Carn
ë
D
raug
doc: fix
t
ypos on doc found by Debian's lintian
commit
|
commitdiff
|
tree
2019-02-07
Carnë Draug
Bio::R
o
ot::RootI->dep
r
ec
a
ted: fix when no
v
ersio
n
argume
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-02-07
Carnë Draug
Bio:
:
Root:
:
R
o
otI: deprecate deprecated() method (issue
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Carnë Draug
v1
.
7
.
4
commit
|
commitdiff
|
tree
2019-02-05
C
arnë Draug
maint
:
do not
i
nc
l
u
d
e
travis configuration
on r
e
lease
commit
|
commitdiff
|
tree
2019-02-05
Carnë
Draug
maint: update C
h
ang
e
s for upcomi
n
g
r
elease
commit
|
commitdiff
|
tree
2019-02-05
Ca
r
në Draug
t/SeqFeature/Gene
r
ic
.
t: f
i
x typo
o
n
requir
e
d modu
l
e
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Carnë
D
raug
Bio::
R
oot::Test: fix
test_network
use of Tes
t
::RequiresInternet
commit
|
commitdiff
|
tree
2019-02-05
Carnë
Draug
maint: fix re
p
ository li
n
ks on
m
et
a
d
ata (issue #306)
commit
|
commitdiff
|
tree
2019-01-30
Ca
r
në
D
raug
v1
.
7
.
3
commit
|
commitdiff
|
tree
2019-01-29
Carnë
Draug
bin/
b
p
_
genbank2gff3: fix sortin
g
by f
e
at
u
re typ
e
(issue
.
.
.
commit
|
commitdiff
|
tree
2019-01-29
Ca
r
n
ë Draug
Bio::SeqIO:
:
lasergene: move to its
o
wn di
s
tribution
commit
|
commitdiff
|
tree
2018-10-03
C
a
rnë Draug
Changes: m
o
r
e details and philoso
p
hy are o
n
HACKING
.
.
.
commit
|
commitdiff
|
tree
2018-10-03
Carnë Draug
Changes: more d
e
t
a
i
l
e
d
co
m
ple
t
e
list of modules/dependenci
e
s
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
l
i
b
/BioPerl
.
pm: start co
n
versi
o
n of P
O
D
t
o make use
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
bin/b
p
_b
i
o
f
et
c
h_g
e
nb
a
n
k_proxy: move
to Bio-DB-NCBI
H
e
lp
e
r
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
B
io::D
B
::Sw
i
ssProt:
m
ove
t
o its own distribution
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
Bi
o
::DB::BioFet
c
h: move t
o
i
t
s own dist
r
ibutio
n
commit
|
commitdiff
|
tree
2018-09-30
Carnë
Drau
g
Automatic ha
n
dling of VERSION i
n
all modules (iss
u
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
t/SeqFeatur
e
/Generic
.
t: fix failing tests (fixup fd
e
60
3
f
22aa)
commit
|
commitdiff
|
tree
2018-09-30
Ca
r
në Draug
bin/bp_fetch: move require of optional modules wher
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
a
rnë Draug
Bio::Map::* a
n
d Bio::
M
apIO::* : move i
n
to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
a
rnë Dr
a
ug
Remove manipul
a
tion of @INC and use
o
f lib - require
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Dr
a
ug
dist
.
ini: make Win
3
2 a dep
e
nd
e
ncy for Windows onl
y
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
a
rnë Draug
Bio::SeqIO
:
:agave: m
o
ve to its own
d
istribution
commit
|
commitdiff
|
tree
2018-09-29
Car
n
ë Draug
Bio::S
e
qIO::cha
d
oxml
(
and flybas
e
_
chadoxml):
m
ove to
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Carnë Drau
g
maint: l
i
st D
a
ta::Sta
g
::XMLWriter as droppe
d
depend
e
n
c
y
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
B
io
:
:SeqIO::ch
a
osxml (and chaos): move to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë
Draug
B
i
o::SeqIO::str
i
der
:
m
ove
into its own
d
i
stribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Tool
s
:
:Pr
o
t
param: move to its own distribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
maint:
u
pdate and clean r
e
moved modules a
n
d dependencie
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::DB::SeqVersion: move into it
s
own distri
b
ution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Tools::SiRNA and rela
t
e
d
moved t
o
separate
d
istrib
u
tion
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Tools::Analysis::Protein:
m
o
v
e
modules in
t
o their
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::
T
ools::A
n
alysis::P
r
ot
e
in::
S
can
s
i
te: move to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Dra
u
g
Bio::Tools::Analysis::Protei
n
:
E
L
M: mo
v
e
t
o sep
a
rate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë D
r
aug
Bio::Tools::Ana
l
ysis::D
N
A
::ESEfin
d
e
r: move to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Draug
Bi
o
::DB::RefSeq
,
Bio::DB::EMBL, and subclasses of B
i
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë
Dr
a
ug
Bio::Ta
x
onomy: mov
e
deprec
a
ted namespa
c
e to its
o
wn
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
n
ë Draug
l
ib/BioPerl
.
pm
:
convert line-
e
nding dos2unix
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë Draug
d
oc: update HACKING
instructions with dzil instr
u
ctions
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dra
u
g
t/*
:
remove "use
l
ib '
.
'" a
n
d
t/
l
ib/Erro
r
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
ra
u
g
Bio::DB::CUTG: m
o
ve into its own distribut
i
on
commit
|
commitdiff
|
tree
2018-09-25
Carnë
Draug
B
i
o::DB:
:
Taxonomy:
:
sqlite: move into
its o
w
n di
s
tribution
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
raug
B
io::DB::GFF move into its own
namespac
e
(
except
B
io
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
C
arn
ë
Draug
Bio::DB::SeqFeature::* mov
e
nam
e
space into its
ow
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dra
u
g
maint: updat
e
changes fro
m
1f7b
5
4a281a8
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bi
o
:
:
Variation::* m
o
ve
n
amespace into it
s
own
distribu
t
ion
.
commit
|
commitdiff
|
tree
2018-09-24
Ca
r
në Draug
R
e
mov
e
Bio::S
e
q
I
O sup
p
ort for
a
bi, a
l
f, ctf,
exp
,
pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë Dra
u
g
Bio::Cluster and Bio
:
:
ClusterIO
moved to their
o
wn
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
C
a
rnë
D
raug
Bio::P
h
enotype::* move what's lef
t
of the namespace
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
maint: remo
v
e no longer
used test data fi
l
e
s
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë
D
r
aug
Bio::LiveSeq::*
m
ove whole namespace to i
t
s own distribution
.
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë Draug
mai
n
t: upd
a
te gitignore rules
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
maint:
restructure to u
s
e Dis
t
::Zilla
commit
|
commitdiff
|
tree
2018-09-17
C
ar
n
ë D
r
au
g
t/Align
I
O/Alig
n
IO
.
t
:
fix number of
tests in plan (fixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Dra
u
g
t
/Annotation/Annota
t
ion
.
t: remove t
e
st for Bio
:
:SeqFeature
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
Bio/Tools/Run/Ph
y
lo/PhyloBase
.
pm: bring base class
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio/To
o
ls/Phylo/
G
umby
.
pm: move to
its
o
wn distribu
t
ion
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
DB/
S
eqFeat
u
re
/
Store/berkeleydb3
.
pm
:
fix errors
s
o
it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Ca
r
në Draug
A
djust tests ind
i
r
ectly mak
i
ng use
o
f Bio::
A
lig
n
IO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
a
r
në D
r
aug
bp_process_wormbase: move progra
m
to n
e
w Bi
o
-DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
b
p_
n
etinstall:
r
emo
v
e out of date program
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Mov
e
m
o
dules dependent
o
n Bio::Ext::Align into
d
ef
u
nct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
B
io::DB:
:
E
x
p
ressi
o
n: mov
e
to
d
efunct
b
iop
e
rl-micr
o
array
commit
|
commitdiff
|
tree
2018-09-16
Car
n
ë
D
r
aug
maint: 644 permissi
o
ns fo
r
almost all fi
l
es
commit
|
commitdiff
|
tree
2018-09-16
Car
n
ë
Dr
a
u
g
ma
i
nt
:
se
t
all s
o
urce code
with utf-
8
encoding
commit
|
commitdiff
|
tree
2018-09-16
Carnë
D
ra
u
g
m
ai
n
t: rem
o
ve maintainer out of
date files
commit
|
commitdiff
|
tree
2018-09-16
Carnë
Draug
ide: remov
e
modul
e
t
e
mpla
t
e
s
-
no longer n
e
eded after
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
C
arnë Dra
u
g
ide/
b
io
p
erl-mo
d
e: in
t
o
i
t
s own
rep
o
sito
r
y to be develo
p
ed
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë D
r
aug
maint: remove bioper
l
-mode rele
a
se tarballs fro
m
version
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
Bio
:
:In
d
e
x::Abstract-
>
_type
_
and_version: check type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t
/LocalDB/Index/Bl
a
stTable
.
t: use tempdir to avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë D
r
aug
t
/
LocalDB/Ind
e
x/B
l
a
s
t
.
t: cr
e
ate test tem
p
fil
e
s wi
t
h
in
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Drau
g
mai
n
t: remove
u
nused
t
est d
a
ta
files
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
Re
m
ove AlignIO and Index stockholm m
o
dules to n
e
w Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
C
a
rnë Dra
u
g
Bio::DB::
U
n
i
versal: move into its own distributio
n
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
ma
i
n
t
: simplify RE
A
DME to cover simple instal
l
in
s
tructions
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
Draug
Br
i
ng base c
l
a
s
ses fr
o
m
B
i
o
Perl-run
b
ack to Bi
o
P
e
r
l
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë D
r
aug
Remove use of Bio::Perl which has been mov
e
d
t
o
Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dr
a
ug
B
i
o::DB::MeSH mov
e
to its own distribut
i
on
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
Dra
u
g
Move HMMER relat
e
d
modules,
te
s
ts, and programs t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carn
ë
Draug
Bio::D
B
:
:
T
FBS namespace has be
e
n moved to its own distribu
t
i
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
C
arn
ë
D
raug
Bio::DB::H
I
V and rela
t
ed mod
u
les and script
s
moved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
arn
ë
Draug
B
i
o::Align::Gr
a
p
hics:
m
o
ve into its
o
wn dis
t
rib
u
tion
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
a
rnë Draug
Bio::
T
o
o
ls::Run::R
e
moteBla
s
t
:
move into a ne
w
distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Car
n
ë Draug
Bio::P
e
rl: move its
o
w
n di
s
tribution nam
e
d
B
io-Procedura
l
commit
|
commitdiff
|
tree
2018-09-12
Carnë D
r
a
ug
Bi
o
::MolEvol::C
o
don
M
odel:
m
ove into
it se
p
ar
a
te repo
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bi
o
::SeqIO::entre
z
gene: mo
v
e
t
o
existing Bio
-
ASN
1
-entrezgene
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
rnë Draug
B
i
o/Restriction/*: move to a
n
other
r
epo with same name
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
r
n
ë
D
r
aug
B
i
o/To
o
l
s
/Gel
.
pm: move t
o
another repo with same name
.
commit
|
commitdiff
|
tree
2018-09-11
Car
n
ë Draug
B
io/
S
eqEvolution/*: move
to anothe
r
repo w
i
th sam
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Dra
u
g
Bi
o
/
S
t
ructure/*:
m
ove to an
o
ther repo
w
ith same
n
ame
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në Draug
t/data: remove more
te
s
t data file
s
which moved to
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Draug
Bio/
A
ss
e
mbly*: move
t
o
a
no
t
her repo wi
t
h same name
.
commit
|
commitdiff
|
tree
2018-09-11
Car
n
ë D
r
aug
Bio/PhyloNetwork
*
: move
to anoth
e
r rep
o
with same name
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë D
r
a
u
g
Bio/SeqIO/excel
.
pm:
move to another r
e
po
w
ith
s
am
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/TreeIO/svggraph
.
p
m
: mov
e
to another repo
with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Drau
g
Bio/Tree/Draw/Cla
d
ogram
.
pm: move to
another repo wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Ca
r
n
ë Dr
a
u
g
Bio/Draw/Pictogram
.
pm: mo
v
e
t
o anothe
r
r
epo with same
.
.
.
commit
|
commitdiff
|
tree
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